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Christensen SJ, Madsen MS, Zinck SS, Hedberg C, Sørensen OB, Svensson B, Meyer AS. Bioinformatics and functional selection of GH77 4-α-glucanotransferases for potato starch modification. N Biotechnol 2024; 79:39-49. [PMID: 38097138 DOI: 10.1016/j.nbt.2023.12.002] [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: 07/29/2023] [Revised: 11/26/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023]
Abstract
4-α-glucanotransferases (4αGTs, EC 2.4.1.25) from glycoside hydrolase family 77 (GH77) catalyze chain elongation of starch amylopectin chains and can be utilized to structurally modify starch to tailor its gelation properties. The potential relationship between the structural design of 4αGTs and functional starch modification is unknown. Here, family GH77 was mined in silico for enzyme candidates based on sub-grouping guided by Conserved Unique Peptide Patterns (CUPP) bioinformatics categorization. From + 12,000 protein sequences a representative set of 27 4αGTs, representing four different domain architectures, different bacterial origins and diverse CUPP groups, was selected for heterologous expression and further study. Most of the enzymes catalyzed starch modification, but their efficacies varied substantially. Five of the 4αGTs were characterized in detail, and their action was compared to that of the industrial benchmark enzyme, Tt4αGT (CUPP 77_1.2), from Thermus thermophilus. Reaction optima of the five 4αGTs ranged from ∼40-60 °C and pH 7.3-9.0. Several were stable for a minimum 4 h at 70 °C. Domain architecture type A proteins, consisting only of a catalytic domain, had high thermal stability and high starch modification ability. All five novel 4αGTs (and Tt4αGT) induced enhanced gelling of potato starch. One, At4αGT from Azospirillum thermophilum (CUPP 77_2.4), displayed distinct starch modifying abilities, whereas T24αGT from Thermus sp. 2.9 (CUPP 77_1.2) modified the starch similarly to Tt4αGT, but slightly more effectively. T24αGT and At4αGT are thus interesting candidates for industrial starch modification. A model is proposed to explain the link between the 4αGT induced molecular modifications and macroscopic starch gelation.
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Affiliation(s)
- Stefan Jarl Christensen
- Protein Chemistry and Enzyme Technology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark; KMC, Brande, Denmark
| | - Michael Schmidt Madsen
- Protein Chemistry and Enzyme Technology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Signe Schram Zinck
- Protein Chemistry and Enzyme Technology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark; KMC, Brande, Denmark
| | | | | | - Birte Svensson
- Protein Chemistry and Enzyme Technology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Anne S Meyer
- Protein Chemistry and Enzyme Technology, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark.
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Wang Y, Wu Y, Christensen SJ, Janeček Š, Bai Y, Møller MS, Svensson B. Impact of Starch Binding Domain Fusion on Activities and Starch Product Structure of 4-α-Glucanotransferase. Molecules 2023; 28:molecules28031320. [PMID: 36770986 PMCID: PMC9920598 DOI: 10.3390/molecules28031320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/03/2023] Open
Abstract
A broad range of enzymes are used to modify starch for various applications. Here, a thermophilic 4-α-glucanotransferase from Thermoproteus uzoniensis (TuαGT) is engineered by N-terminal fusion of the starch binding domains (SBDs) of carbohydrate binding module family 20 (CBM20) to enhance its affinity for granular starch. The SBDs are N-terminal tandem domains (SBDSt1 and SBDSt2) from Solanum tuberosum disproportionating enzyme 2 (StDPE2) and the C-terminal domain (SBDGA) of glucoamylase from Aspergillus niger (AnGA). In silico analysis of CBM20s revealed that SBDGA and copies one and two of GH77 DPE2s belong to well separated clusters in the evolutionary tree; the second copies being more closely related to non-CAZyme CBM20s. The activity of SBD-TuαGT fusions increased 1.2-2.4-fold on amylose and decreased 3-9 fold on maltotriose compared with TuαGT. The fusions showed similar disproportionation activity on gelatinised normal maize starch (NMS). Notably, hydrolytic activity was 1.3-1.7-fold elevated for the fusions leading to a reduced molecule weight and higher α-1,6/α-1,4-linkage ratio of the modified starch. Notably, SBDGA-TuαGT and-SBDSt2-TuαGT showed Kd of 0.7 and 1.5 mg/mL for waxy maize starch (WMS) granules, whereas TuαGT and SBDSt1-TuαGT had 3-5-fold lower affinity. SBDSt2 contributed more than SBDSt1 to activity, substrate binding, and the stability of TuαGT fusions.
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Affiliation(s)
- Yu Wang
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Yazhen Wu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Stefan Jarl Christensen
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
- Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
| | - Yuxiang Bai
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Marie Sofie Møller
- Applied Molecular Enzyme Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Correspondence: (M.S.M.); (B.S.)
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Correspondence: (M.S.M.); (B.S.)
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Jung JH, Hong S, Jeon EJ, Kim MK, Seo DH, Woo EJ, Holden JF, Park CS. Acceptor dependent catalytic properties of GH57 4-α-glucanotransferase from Pyrococcus sp. ST04. Front Microbiol 2022; 13:1016675. [PMID: 36274706 PMCID: PMC9582752 DOI: 10.3389/fmicb.2022.1016675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The 4-α-glucanotransferase (4-α-GTase or amylomaltase) is an essential enzyme in maltodextrin metabolism. Generally, most bacterial 4-α-GTase is classified into glycoside hydrolase (GH) family 77. However, hyperthermophiles have unique 4-α-GTases belonging to GH family 57. These enzymes are the main amylolytic protein in hyperthermophiles, but their mode of action in maltooligosaccharide utilization is poorly understood. In the present study, we investigated the catalytic properties of 4-α-GTase from the hyperthermophile Pyrococcus sp. ST04 (PSGT) in the presence of maltooligosaccharides of various lengths. Unlike 4-α-GTases in GH family 77, GH family 57 PSGT produced maltotriose in the early stage of reaction and preferred maltose and maltotriose over glucose as the acceptor. The kinetic analysis showed that maltotriose had the lowest KM value, which increased amylose degradation activity by 18.3-fold. Structural models of PSGT based on molecular dynamic simulation revealed two aromatic amino acids interacting with the substrate at the +2 and +3 binding sites, and the mutational study demonstrated they play a critical role in maltotriose binding. These results clarify the mode of action in carbohydrate utilization and explain acceptor binding mechanism of GH57 family 4-α-GTases in hyperthermophilic archaea.
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Affiliation(s)
- Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Seungpyo Hong
- Department of Molecular Biology, Jeonbuk National University, Jeonju, South Korea
| | - Eun Jung Jeon
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Min-Kyu Kim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Dong-Ho Seo
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, South Korea
| | - Eui-Jeon Woo
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - James F. Holden
- Department of Microbiology, University of Messachusetts, Amherst, MA, United States
| | - Cheon-Seok Park
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin, South Korea
- *Correspondence: Cheon-Seok Park,
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Krusong K, Ismail A, Wangpaiboon K, Pongsawasdi P. Production of Large-Ring Cyclodextrins by Amylomaltases. Molecules 2022; 27:molecules27041446. [PMID: 35209232 PMCID: PMC8875642 DOI: 10.3390/molecules27041446] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/10/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
Amylomaltase is a well-known glucan transferase that can produce large ring cyclodextrins (LR-CDs) or so-called cycloamyloses via cyclization reaction. Amylomaltases have been found in several microorganisms and their optimum temperatures are generally around 60–70 °C for thermostable amylomaltases and 30–45 °C for the enzymes from mesophilic bacteria and plants. The optimum pHs for mesophilic amylomaltases are around pH 6.0–7.0, while the thermostable amylomaltases are generally active at more acidic conditions. Size of LR-CDs depends on the source of amylomaltases and the reaction conditions including pH, temperature, incubation time, and substrate. For example, in the case of amylomaltase from Corynebacterium glutamicum, LR-CD productions at alkaline pH or at a long incubation time favored products with a low degree of polymerization. In this review, we explore the synthesis of LR-CDs by amylomaltases, structural information of amylomaltases, as well as current applications of LR-CDs and amylomaltases.
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Affiliation(s)
- Kuakarun Krusong
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phyathai Rd., Patumwan, Bangkok 10330, Thailand; (A.I.); (K.W.)
- Correspondence: ; Tel.: + 66-(0)2-218-5413
| | - Abbas Ismail
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phyathai Rd., Patumwan, Bangkok 10330, Thailand; (A.I.); (K.W.)
| | - Karan Wangpaiboon
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phyathai Rd., Patumwan, Bangkok 10330, Thailand; (A.I.); (K.W.)
| | - Piamsook Pongsawasdi
- Starch and Cyclodextrin Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phyathai Rd., Patumwan, Bangkok 10330, Thailand;
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Identification of an Amylomaltase from the Halophilic Archaeon Haloquadratum walsbyi by Functional Metagenomics: Structural and Functional Insights. Life (Basel) 2022; 12:life12010085. [PMID: 35054477 PMCID: PMC8781629 DOI: 10.3390/life12010085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 11/20/2022] Open
Abstract
Amylomaltases are prokaryotic 4-α-glucanotransferases of the GH77 family. Thanks to the ability to modify starch, they constitute a group of enzymes of great interest for biotechnological applications. In this work we report the identification, by means of a functional metagenomics screening of the crystallization waters of the saltern of Margherita di Savoia (Italy), of an amylomaltase gene from the halophilic archaeon Haloquadratum walsbyi, and its expression in Escherichia coli cells. Sequence analysis indicated that the gene has specific insertions yet unknown in homologous genes in prokaryotes, and present only in amylomaltase genes identified in the genomes of other H. walsbyi strains. The gene is not part of any operon involved in the metabolism of maltooligosaccharides or glycogen, as it has been found in bacteria, making it impossible currently to assign a precise role to the encoded enzyme. Sequence analysis of the H. walsbyi amylomaltase and 3D modelling showed a common structure with homologous enzymes characterized in mesophilic and thermophilic bacteria. The recombinant H. walsbyi enzyme showed starch transglycosylation activity over a wide range of NaCl concentrations, with maltotriose as the best acceptor substrate compared to other maltooligosaccharides. This is the first study of an amylomaltase from a halophilic microorganism.
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Leoni C, Gattulli BAR, Pesole G, Ceci LR, Volpicella M. Amylomaltases in Extremophilic Microorganisms. Biomolecules 2021; 11:biom11091335. [PMID: 34572549 PMCID: PMC8465469 DOI: 10.3390/biom11091335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Amylomaltases (4-α-glucanotransferases, E.C. 2.4.1.25) are enzymes which can perform a double-step catalytic process, resulting in a transglycosylation reaction. They hydrolyse glucosidic bonds of α-1,4'-d-glucans and transfer the glucan portion with the newly available anomeric carbon to the 4'-position of an α-1,4'-d-glucan acceptor. The intramolecular reaction produces a cyclic α-1,4'-glucan. Amylomaltases can be found only in prokaryotes, where they are involved in glycogen degradation and maltose metabolism. These enzymes are being studied for possible biotechnological applications, such as the production of (i) sugar substitutes; (ii) cycloamyloses (molecules larger than cyclodextrins), which could potentially be useful as carriers and encapsulating agents for hydrophobic molecules and also as effective protein chaperons; and (iii) thermoreversible starch gels, which could be used as non-animal gelatin substitutes. Extremophilic prokaryotes have been investigated for the identification of amylomaltases to be used in the starch modifying processes, which require high temperatures or extreme conditions. The aim of this article is to present an updated overview of studies on amylomaltases from extremophilic Bacteria and Archaea, including data about their distribution, activity, potential industrial application and structure.
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Affiliation(s)
- Claudia Leoni
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Via Amendola, 70126 Bari, Italy; (C.L.); (B.A.R.G.); (G.P.)
| | - Bruno A. R. Gattulli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Via Amendola, 70126 Bari, Italy; (C.L.); (B.A.R.G.); (G.P.)
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Via Amendola, 70126 Bari, Italy; (C.L.); (B.A.R.G.); (G.P.)
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Luigi R. Ceci
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Via Amendola, 70126 Bari, Italy; (C.L.); (B.A.R.G.); (G.P.)
- Correspondence: (L.R.C.); (M.V.); Tel.: +39-080-544-3311 (L.R.C. & M.V.)
| | - Mariateresa Volpicella
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Via Amendola, 70126 Bari, Italy; (C.L.); (B.A.R.G.); (G.P.)
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Correspondence: (L.R.C.); (M.V.); Tel.: +39-080-544-3311 (L.R.C. & M.V.)
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Xu J, Xu R, Jia M, Su Y, Zhu W. Metatranscriptomic analysis of colonic microbiota's functional response to different dietary fibers in growing pigs. Anim Microbiome 2021; 3:45. [PMID: 34217374 PMCID: PMC8254964 DOI: 10.1186/s42523-021-00108-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 06/23/2021] [Indexed: 01/30/2023] Open
Abstract
Background Dietary fibers are widely considered to be beneficial to health as they produce nutrients through gut microbial fermentation while facilitating weight management and boosting gut health. To date, the gene expression profiles of the carbohydrate active enzymes (CAZymes) that respond to different types of fibers (raw potato starch, RPS; inulin, INU; pectin, PEC) in the gut microbes of pigs are not well understood. Therefore, we investigated the functional response of colonic microbiota to different dietary fibers in pigs through metatranscriptomic analysis. Results The results showed that the microbial composition and CAZyme structure of the three experimental groups changed significantly compared with the control group (CON). Based on a comparative analysis with the control diet, RPS increased the abundance of Parabacteroides, Ruminococcus, Faecalibacterium and Alloprevotella but decreased Sutterella; INU increased the relative abundance of Fusobacterium and Rhodococcus but decreased Bacillus; and PEC increased the relative abundance of the Streptococcus and Bacteroidetes groups but decreased Clostridium, Clostridioides, Intestinibacter, Gemmiger, Muribaculum and Vibrio. The gene expression of CAZymes GH8, GH14, GH24, GH38, GT14, GT31, GT77 and GT91 downregulated but that of GH77, GH97, GT3, GT10 and GT27 upregulated in the RPS diet group; the gene expression of AA4, AA7, GH14, GH15, GH24, GH26, GH27, GH38, GH101, GT26, GT27 and GT38 downregulated in the INU group; and the gene expression of PL4, AA1, GT32, GH18, GH37, GH101 and GH112 downregulated but that of CE14, AA3, AA12, GH5, GH102 and GH103 upregulated in the PEC group. Compared with the RPS and INU groups, the composition of colonic microbiota in the PEC group exhibited more diverse changes with the variation of CAZymes and Streptococcus as the main contributor to CBM61, which greatly promoted the digestion of pectin. Conclusion The results of this exploratory study provided a comprehensive overview of the effects of different fibers on nutrient digestibility, gut microbiota and CAZymes in pig colon, which will furnish new insights into the impacts of the use of dietary fibers on animal and human health. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00108-1.
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Affiliation(s)
- Jie Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongying Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Menglan Jia
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Su
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China. .,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
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A putative novel starch-binding domain revealed by in silico analysis of the N-terminal domain in bacterial amylomaltases from the family GH77. 3 Biotech 2021; 11:229. [PMID: 33968573 DOI: 10.1007/s13205-021-02787-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/09/2021] [Indexed: 10/21/2022] Open
Abstract
The family GH77 contains 4-α-glucanotransferase acting on α-1,4-glucans, known as amylomaltase in prokaryotes and disproportionating enzyme in plants. A group of bacterial GH77 members, represented by amylomaltases from Escherichia coli and Corynebacterium glutamicum, possesses an N-terminal extension that forms a distinct immunoglobulin-like fold domain, of which no function has been identified. Here, in silico analysis of 100 selected sequences of N-terminal domain homologues disclosed several well-conserved residues, among which Tyr108 (E. coli amylomaltase numbering) may be involved in α-glucan binding. These N-terminal domains, therefore, may represent a new type of starch-binding domain and define a new CBM family. This hypothesis is supported by docking of maltooligosaccharides to the N-terminal domain in amylomaltases, representing the four clusters of the phylogenetic tree. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02787-8.
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Janeček Š, Martinovičová M. New groups of protein homologues in the α-amylase family GH57 closely related to α-glucan branching enzymes and 4-α-glucanotransferases. Genetica 2020; 148:77-86. [PMID: 32096055 DOI: 10.1007/s10709-020-00089-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 02/17/2020] [Indexed: 10/24/2022]
Abstract
The glycoside hydrolase family GH57 is known as the second α-amylase family. Its main characteristics are as follows: (i) employing the retaining reaction mechanism; (ii) adopting the (β/α)7-barrel (the incomplete TIM-barrel) with succeeding bundle of α-helices as the catalytic domain; (iii) sharing the five conserved sequence regions (CSRs) exhibiting the sequence fingerprints of the individual enzyme specificities; and (iv) using the catalytic machinery consisting of glutamic acid (the catalytic nucleophile) and aspartic acid (the proton donor) positioned at strands β4 (CSR-3) and β7 (CSR-4) of the (β/α)7-barrel domain, respectively. Several years ago, a group of hypothetical proteins closely related to the specificity of α-amylase was revealed, the so-called α-amylase-like homologues, the members of which lack either one or even both catalytic residues. The novelty of the present study lies in delivering two additional groups of the "like" proteins that are homologues of α-glucan-branching enzyme (GBE) and 4-α-glucanotransferase (4AGT) specificities. Based on a recently published in silico analysis of more than 1600 family GH57 sequences, 13 GBE-like and 18 4AGT-like proteins from unique sources were collected and analyzed in a detail with respect to their taxonomical origin, sequence and structural features as well as evolutionary relationships. This in silico study could accelerate the efforts leading to experimental revealing the real function of the enzymes-like proteins in the α-amylase family GH57.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 84551, Bratislava, Slovakia. .,Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nam. J. Herdu 2, 91701, Trnava, Slovakia.
| | - Mária Martinovičová
- Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nam. J. Herdu 2, 91701, Trnava, Slovakia
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10
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Jeong DW, Jeong HM, Shin YJ, Woo SH, Shim JH. Properties of recombinant 4-α-glucanotransferase from Bifidobacterium longum subsp. longum JCM 1217 and its application. Food Sci Biotechnol 2019; 29:667-674. [PMID: 32419965 DOI: 10.1007/s10068-019-00707-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/27/2019] [Accepted: 10/29/2019] [Indexed: 11/26/2022] Open
Abstract
To determine the physiochemical properties of the 4-α-glucanotransferase from Bifidobacterium sp., the bllj_0114 gene encoding 4-α-glucanotransferase was cloned from Bifidobacterium longum subsp. longum JCM 1217 and expressed in Escherichia coli. The amino acid sequence alignment indicated that the recombinant protein, named BL-αGTase, belongs to the glycoside hydrolase (GH) family 77. BL-αGTase was purified using nickel-nitrilotriacetic acid affinity chromatography and characterized using various substrates. The enzyme catalyzed the disproportionation activity, which transfers a glucosyl unit from oligosaccharides to acceptor molecules, and had the highest activity at 40 °C and pH 6.0. In the presence of 5 mM metal ions, in particular Cu2+, Zn2+, and Fe2+, BL-αGTase activity was reduced. To determine whether BL-αGTase can be used to generate thermoreversible gels, potato starch was treated with BL-αGTase for various reaction times. The BL-αGTase-treated starches showed sol-gel reversibility and melted at 59.6-75.7 °C.
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Affiliation(s)
- Da-Woon Jeong
- Department of Food Science and Nutrition, and The Korean Institute of Nutrition, Hallym University, Chuncheon, 24252 Republic of Korea
| | - Hyun-Mo Jeong
- Department of Food Science and Nutrition, and The Korean Institute of Nutrition, Hallym University, Chuncheon, 24252 Republic of Korea
| | - Yu-Jeong Shin
- Department of Food Science and Nutrition, and The Korean Institute of Nutrition, Hallym University, Chuncheon, 24252 Republic of Korea
| | - Seung-Hye Woo
- Department of Food Science and Nutrition, and The Korean Institute of Nutrition, Hallym University, Chuncheon, 24252 Republic of Korea
| | - Jae-Hoon Shim
- Department of Food Science and Nutrition, and The Korean Institute of Nutrition, Hallym University, Chuncheon, 24252 Republic of Korea
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Janeček Š, Mareček F, MacGregor EA, Svensson B. Starch-binding domains as CBM families-history, occurrence, structure, function and evolution. Biotechnol Adv 2019; 37:107451. [PMID: 31536775 DOI: 10.1016/j.biotechadv.2019.107451] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/01/2019] [Accepted: 09/15/2019] [Indexed: 01/05/2023]
Abstract
The term "starch-binding domain" (SBD) has been applied to a domain within an amylolytic enzyme that gave the enzyme the ability to bind onto raw, i.e. thermally untreated, granular starch. An SBD is a special case of a carbohydrate-binding domain, which in general, is a structurally and functionally independent protein module exhibiting no enzymatic activity but possessing potential to target the catalytic domain to the carbohydrate substrate to accommodate it and process it at the active site. As so-called families, SBDs together with other carbohydrate-binding modules (CBMs) have become an integral part of the CAZy database (http://www.cazy.org/). The first two well-described SBDs, i.e. the C-terminal Aspergillus-type and the N-terminal Rhizopus-type have been assigned the families CBM20 and CBM21, respectively. Currently, among the 85 established CBM families in CAZy, fifteen can be considered as families having SBD functional characteristics: CBM20, 21, 25, 26, 34, 41, 45, 48, 53, 58, 68, 69, 74, 82 and 83. All known SBDs, with the exception of the extra long CBM74, were recognized as a module consisting of approximately 100 residues, adopting a β-sandwich fold and possessing at least one carbohydrate-binding site. The present review aims to deliver and describe: (i) the SBD identification in different amylolytic and related enzymes (e.g., CAZy GH families) as well as in other relevant enzymes and proteins (e.g., laforin, the β-subunit of AMPK, and others); (ii) information on the position in the polypeptide chain and the number of SBD copies and their CBM family affiliation (if appropriate); (iii) structure/function studies of SBDs with a special focus on solved tertiary structures, in particular, as complexes with α-glucan ligands; and (iv) the evolutionary relationships of SBDs in a tree common to all SBD CBM families (except for the extra long CBM74). Finally, some special cases and novel potential SBDs are also introduced.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia.
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia
| | - E Ann MacGregor
- 2 Nicklaus Green, Livingston EH54 8RX, West Lothian, United Kingdom
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
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Transglycosylation Properties of a Novel α-1,4-Glucanotransferase from Bacteroides thetaiotaomicron and Its Application in Developing an α-Glucosidase-Specific Inhibitor. J CHEM-NY 2018. [DOI: 10.1155/2018/2981596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In this study, α-glucanotransferase from Bacteroides thetaiotaomicron was expressed in Escherichia coli and characterized. Conserved amino-acid sequence alignment showed that Bacteroides thetaiotaomicron α-glucanotransferase (BtαGTase) belongs to the glycoside hydrolase family 77. The enzyme exhibited optimal catalytic activity at 60°C and pH 3.0. BtαGTase catalyzed transglycosylation reactions that produced only glycosyl or maltosyl transfer products, which are preferable for the generation of transglycosylated products with high yield. The 1-deoxynojirimycin (DNJ) glycosylation product G1-DNJ was generated using BtαGTase, and the inhibitory effect of G1-DNJ was analyzed. A kinetic study of inhibition revealed that G1-DNJ inhibited α-glucosidase to a greater extent than did DNJ but did not show any inhibitory effects towards α-amylase, suggesting that G1-DNJ is a potential candidate for the prevention of diabetes.
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13
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Smirnova J, Fernie AR, Spahn CMT, Steup M. Photometric assay of maltose and maltose-forming enzyme activity by using 4-alpha-glucanotransferase (DPE2) from higher plants. Anal Biochem 2017; 532:72-82. [PMID: 28576440 DOI: 10.1016/j.ab.2017.05.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 05/09/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022]
Abstract
Maltose frequently occurs as intermediate of the central carbon metabolism of prokaryotic and eukaryotic cells. Various mutants possess elevated maltose levels. Maltose exists as two anomers, (α- and β-form) which are rapidly interconverted without requiring enzyme-mediated catalysis. As maltose is often abundant together with other oligoglucans, selective quantification is essential. In this communication, we present a photometric maltose assay using 4-alpha-glucanotransferase (AtDPE2) from Arabidopsis thaliana. Under in vitro conditions, AtDPE2 utilizes maltose as glucosyl donor and glycogen as acceptor releasing the other hexosyl unit as free glucose which is photometrically quantified following enzymatic phosphorylation and oxidation. Under the conditions used, DPE2 does not noticeably react with other di- or oligosaccharides. Selectivity compares favorably with that of maltase frequently used in maltose assays. Reducing end interconversion of the two maltose anomers is in rapid equilibrium and, therefore, the novel assay measures total maltose contents. Furthermore, an AtDPE2-based continuous photometric assay is presented which allows to quantify β-amylase activity and was found to be superior to a conventional test. Finally, the AtDPE2-based maltose assay was used to quantify leaf maltose contents of both Arabidopsis wild type and AtDPE2-deficient plants throughout the light-dark cycle. These data are presented together with assimilatory starch levels.
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Affiliation(s)
- Julia Smirnova
- Institute for Biochemistry and Biology, Department of Plant Physiology, University of Potsdam, Building 20, Karl-Liebknecht-Str. 20, 14461 Potsdam, Germany; Institute of Biophysics and Medical Physics of the Charité, Universitätsmedizin Berlin, Campus Berlin Mitte, 10117 Berlin, Germany; Max-Planck-Institute of Molecular Plant Physiology, Department 1 (Willmitzer), Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Department 1 (Willmitzer), Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Christian M T Spahn
- Institute of Biophysics and Medical Physics of the Charité, Universitätsmedizin Berlin, Campus Berlin Mitte, 10117 Berlin, Germany
| | - Martin Steup
- Institute for Biochemistry and Biology, Department of Plant Physiology, University of Potsdam, Building 20, Karl-Liebknecht-Str. 20, 14461 Potsdam, Germany.
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Janeček Š, Majzlová K, Svensson B, MacGregor EA. The starch-binding domain family CBM41-Anin silicoanalysis of evolutionary relationships. Proteins 2017; 85:1480-1492. [DOI: 10.1002/prot.25309] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/05/2017] [Accepted: 04/17/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Štefan Janeček
- Institute of Molecular Biology, Slovak Academy of Sciences; Bratislava Slovakia
- Department of Biology; Faculty of Natural Sciences, University of SS. Cyril and Methodius; Trnava Slovakia
| | - Katarína Majzlová
- Institute of Molecular Biology, Slovak Academy of Sciences; Bratislava Slovakia
| | - Birte Svensson
- Department of Biotechnology and Biomedicine; Technical University of Denmark; Kgs. Lyngby Denmark
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15
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Janeček Š, Gabriško M. Remarkable evolutionary relatedness among the enzymes and proteins from the α-amylase family. Cell Mol Life Sci 2016; 73:2707-25. [PMID: 27154042 PMCID: PMC11108405 DOI: 10.1007/s00018-016-2246-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/17/2022]
Abstract
The α-amylase is a ubiquitous starch hydrolase catalyzing the cleavage of the α-1,4-glucosidic bonds in an endo-fashion. Various α-amylases originating from different taxonomic sources may differ from each other significantly in their exact substrate preference and product profile. Moreover, it also seems to be clear that at least two different amino acid sequences utilizing two different catalytic machineries have evolved to execute the same α-amylolytic specificity. The two have been classified in the Cabohydrate-Active enZyme database, the CAZy, in the glycoside hydrolase (GH) families GH13 and GH57. While the former and the larger α-amylase family GH13 evidently forms the clan GH-H with the families GH70 and GH77, the latter and the smaller α-amylase family GH57 has only been predicted to maybe define a future clan with the family GH119. Sequences and several tens of enzyme specificities found throughout all three kingdoms in many taxa provide an interesting material for evolutionarily oriented studies that have demonstrated remarkable observations. This review emphasizes just the three of them: (1) a close relatedness between the plant and archaeal α-amylases from the family GH13; (2) a common ancestry in the family GH13 of animal heavy chains of heteromeric amino acid transporter rBAT and 4F2 with the microbial α-glucosidases; and (3) the unique sequence features in the primary structures of amylomaltases from the genus Borrelia from the family GH77. Although the three examples cannot represent an exhaustive list of exceptional topics worth to be interested in, they may demonstrate the importance these enzymes possess in the overall scientific context.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia.
- Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius in Trnava, Nám. J. Herdu 2, 91701, Trnava, Slovakia.
| | - Marek Gabriško
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia
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Characterization of amylomaltase from Thermus filiformis and the increase in alkaline and thermo-stability by E27R substitution. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.08.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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