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Tagami T. Structural insights into starch-metabolizing enzymes and their applications. Biosci Biotechnol Biochem 2024; 88:864-871. [PMID: 38806254 DOI: 10.1093/bbb/zbae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024]
Abstract
Starch is a polysaccharide produced exclusively through photosynthesis in plants and algae; however, is utilized as an energy source by most organisms, from microorganisms to higher organisms. In mammals and the germinating seeds of plants, starch is metabolized by simple hydrolysis pathways. Moreover, starch metabolic pathways via unique oligosaccharides have been discovered in some bacteria. Each organism has evolved enzymes responsible for starch metabolism that are diverse in their enzymatic properties. This review, focusing on eukaryotic α-glucosidases and bacterial α-glucoside-hydrolyzing enzymes, summarizes the structural aspects of starch-metabolizing enzymes belonging to glycoside hydrolase families 15, 31, and 77 and their application for oligosaccharide production.
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Affiliation(s)
- Takayoshi Tagami
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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2
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Mareček F, Terrapon N, Janeček Š. Two newly established and mutually related subfamilies GH13_48 and GH13_49 of the α-amylase family GH13. Appl Microbiol Biotechnol 2024; 108:415. [PMID: 38990377 PMCID: PMC11239784 DOI: 10.1007/s00253-024-13251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024]
Abstract
Currently, the main α-amylase family GH13 has been divided into 47 subfamilies in CAZy, with new subfamilies regularly emerging. The present in silico study was performed to highlight the groups, represented by the maltogenic amylase from Thermotoga neapolitana and the α-amylase from Haloarcula japonica, which are worth of creating their own new GH13 subfamilies. This enlarges functional annotation and thus allows more precise prediction of the function of putative proteins. Interestingly, those two share certain sequence features, e.g. the highly conserved cysteine in the second conserved sequence region (CSR-II) directly preceding the catalytic nucleophile, or the well-preserved GQ character of the end of CSR-VII. On the other hand, the two groups bear also specific and highly conserved positions that distinguish them not only from each other but also from representatives of remaining GH13 subfamilies established so far. For the T. neapolitana maltogenic amylase group, it is the stretch of residues at the end of CSR-V highly conserved as L-[DN]. The H. japonica α-amylase group can be characterized by a highly conserved [WY]-[GA] sequence at the end of CSR-II. Other specific sequence features include an almost fully conserved aspartic acid located directly preceding the general acid/base in CSR-III or well-preserved glutamic acid in CSR-IV. The assumption that these two groups represent two mutually related, but simultaneously independent GH13 subfamilies has been supported by phylogenetic analysis as well as by comparison of tertiary structures. The main α-amylase family GH13 has thus been expanded by two novel subfamilies GH13_48 and GH13_49. KEY POINTS: • In silico analysis of two groups of family GH13 members with characterized representatives • Identification of certain common, but also some specific sequence features in seven CSRs • Creation of two novel subfamilies-GH13_48 and GH13_49 within the CAZy database.
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Affiliation(s)
- Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, 84551, Bratislava, Slovakia.
| | - Nicolas Terrapon
- Architecture Et Fonction Des Macromolécules Biologiques, UMR CNRS, Aix-Marseille University, USC INRAE, 13288, Marseille, France
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, 84551, Bratislava, Slovakia.
- Department of Biology, Institute of Biology and Biotechnology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, 91701, Trnava, Slovakia.
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3
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Scholtysek L, Poetsch A, Hofmann E, Hemschemeier A. The activation of Chlamydomonas reinhardtii alpha amylase 2 by glutamine requires its N-terminal aspartate kinase-chorismate mutase-tyrA (ACT) domain. PLANT DIRECT 2024; 8:e609. [PMID: 38911017 PMCID: PMC11190351 DOI: 10.1002/pld3.609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 06/25/2024]
Abstract
The coordination of assimilation pathways for all the elements that make up cellular components is a vital task for every organism. Integrating the assimilation and use of carbon (C) and nitrogen (N) is of particular importance because of the high cellular abundance of these elements. Starch is one of the most important storage polymers of photosynthetic organisms, and a complex regulatory network ensures that biosynthesis and degradation of starch are coordinated with photosynthetic activity and growth. Here, we analyzed three starch metabolism enzymes of Chlamydomonas reinhardtii that we captured by a cyclic guanosine monophosphate (cGMP) affinity chromatography approach, namely, soluble starch synthase STA3, starch-branching enzyme SBE1, and α-amylase AMA2. While none of the recombinant enzymes was directly affected by the presence of cGMP or other nucleotides, suggesting an indirect binding to cGMP, AMA2 activity was stimulated in the presence of L-glutamine (Gln). This activating effect required the enzyme's N-terminal aspartate kinase-chorismate mutase-tyrA domain. Gln is the first N assimilation product and not only a central compound for the biosynthesis of N-containing molecules but also a recognized signaling molecule for the N status. Our observation suggests that AMA2 might be a means to coordinate N and C metabolism at the enzymatic level, increasing the liberation of C skeletons from starch when high Gln levels signal an abundance of assimilated N.
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Affiliation(s)
- Lisa Scholtysek
- Faculty of Biology and Biotechnology, PhotobiotechnologyRuhr University BochumBochumGermany
| | - Ansgar Poetsch
- Faculty of Biology and Biotechnology, Department for Plant BiochemistryRuhr University BochumBochumGermany
- School of Basic Medical SciencesNanchang UniversityNanchangChina
| | - Eckhard Hofmann
- Faculty of Biology and Biotechnology, Protein CrystallographyRuhr University BochumBochumGermany
| | - Anja Hemschemeier
- Faculty of Biology and Biotechnology, PhotobiotechnologyRuhr University BochumBochumGermany
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4
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Senger MR, da Costa Latgé SG, von Ranke NL, de Aquino GAS, Dantas RF, Genta FA, Ferreira SB, Junior FPS. Kinetics and molecular modeling studies on the inhibition mechanism of GH13 α-glycosidases by small molecule ligands. Int J Biol Macromol 2024; 269:132036. [PMID: 38697429 DOI: 10.1016/j.ijbiomac.2024.132036] [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: 02/23/2024] [Revised: 04/17/2024] [Accepted: 04/30/2024] [Indexed: 05/05/2024]
Abstract
Alpha-glucosidase inhibitors play an important role in Diabetes Mellitus (DM) treatment since they prevent postprandial hyperglycemia. The Glycoside Hydrolase family 13 (GH13) is the major family of enzymes acting on substrates containing α-glucoside linkages, such as maltose and amylose/amylopectin chains in starch. Previously, our group identified glycoconjugate 1H-1,2,3-triazoles (GCTs) inhibiting two GH13 α-glycosidases: yeast maltase (MAL12) and porcine pancreatic amylase (PPA). Here, we combined kinetic studies and computational methods on nine GCTs to characterize their inhibitory mechanism. They all behaved as reversible inhibitors, and kinetic models encompassed noncompetitive and various mechanisms of mixed-type inhibition for both enzymes. Most potent inhibitors displayed Ki values of 30 μM for MAL12 (GPESB16) and 37 μM for PPA (GPESB15). Molecular dynamics and docking simulations indicated that on MAL12, GPESB15 and GPESB16 bind in a cavity adjacent to the active site, while on the PPA, GPESB15 was predicted to bind at the entrance of the catalytic site. Notably, despite its putative location within the active site, the binding of GPESB15 does not obstruct the substrate's access to the cleavage site. Our study contributes to paving the way for developing novel therapeutic strategies for managing DM-2 through GH13 α-glycosidases inhibition.
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Affiliation(s)
- Mario Roberto Senger
- Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Samara Graciane da Costa Latgé
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Natalia Lidmar von Ranke
- Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Gabriel Alves Souto de Aquino
- Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael Ferreira Dantas
- Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fernando Ariel Genta
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Sabrina Baptista Ferreira
- Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Floriano Paes Silva Junior
- Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
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5
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Urbániková Ľ, Janeček Š. Trehalose synthases from the subfamily GH13_16 involved in α-glucan biosynthesis - a focus on their maltokinase domain. Int J Biol Macromol 2024; 268:131680. [PMID: 38641282 DOI: 10.1016/j.ijbiomac.2024.131680] [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: 02/21/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
The subfamily GH13_16 trehalose synthase (TreS) converts maltose to trehalose and vice versa. Typically, it consists of three domains, but it may contain a C-terminal extension exhibiting clear sequence features of a maltokinase (MaK). The present in silico study was focused on collection of naturally fused TreS-MaKs and their subsequent detailed bioinformatics analysis. Hence a set of total 3354 unique sequences was compared consisting of 1900 single TreSs, 1426 fused TreS-MaKs and 28 single MaKs. Fused TreS-MaKs were divided into five groups, namely with a standard MaK, with mutations in the maltose-binding site, of the catalytic nucleophile, of the general acid/base and of both catalytic residues. Sequence logos bearing the best conserved sequence regions were prepared for both TreSs and MaKs in an effort to find unique sequence features. In addition, linkers connecting the TreS and MaK parts in the fused enzymes were analysed. This analysis revealed that MaKs in fused enzymes have an extended N-terminal regions compared to single MaKs. Finally, the evolutionary relationships were demonstrated by phylogenetic trees of TreS parts from single TreSs and fused TreS-MaKs from the same organism as well as of single TreSs existing in multiple isoforms in the same organism.
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Affiliation(s)
- Ľubica Urbániková
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia; Institute of Biology and Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, SK-91701 Trnava, Slovakia.
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6
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Niçin RT, Zehir-Şentürk D, Özkan B, Göksungur Y, Şimşek Ö. Optimization of 4,6-α and 4,3-α-Glucanotransferase Production in Lactococcus lactis and Determination of Their Effects on Some Quality Characteristics of Bakery Products. Foods 2024; 13:432. [PMID: 38338567 PMCID: PMC10855804 DOI: 10.3390/foods13030432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
In this study, the production of 4,6-α (4,6-α-GTase) and 4,3-α-glucanotransferase (4,3-α-GTase), expressed previously in Lactococcus lactis, was optimized and these enzymes were used to investigate glycemic index reduction and staling delay in bakery products. HP-SEC analysis showed that the relevant enzymes were able to produce oligosaccharides from potato starch or malto-oligosaccharides. Response Surface Methodology (RSM) was used to optimize enzyme synthesis and the highest enzyme activities of 15.63 ± 1.65 and 19.01 ± 1.75 U/mL were obtained at 1% glucose, pH 6, and 30 °C for 4,6-α-GTase and 4,3-α-GTase enzymes, respectively. SEM analysis showed that both enzymes reduced the size of the starch granules. These enzymes were purified by ultrafiltration and used to produce bread and bun at an enzyme activity of 4 U/g, resulting in a decrease in the specific volume of the bread. It was found that the estimated glycemic index (eGI) of bread formulated with 4,6-α-GTase decreased by 18.01%, and the eGI of bread prepared with 4,3-α-GTase decreased by 13.61%, indicating a potential delay in staling. No significant differences were observed in the sensory properties of the bakery products. This is the first study showing that 4,6-α-GTase and 4,3-α-GTase enzymes have potential in increasing health benefits and improving technological aspects regarding bakery products.
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Affiliation(s)
- Ramazan Tolga Niçin
- Department of Food Engineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, Istanbul 34220, Turkey;
| | - Duygu Zehir-Şentürk
- Department of Food Engineering, Faculty of Engineering, Pamukkale University, Denizli 20160, Turkey; (D.Z.-Ş.); (B.Ö.)
| | - Busenur Özkan
- Department of Food Engineering, Faculty of Engineering, Pamukkale University, Denizli 20160, Turkey; (D.Z.-Ş.); (B.Ö.)
| | - Yekta Göksungur
- Department of Food Engineering, Faculty of Engineering, Ege University, İzmir 35100, Turkey;
| | - Ömer Şimşek
- Department of Food Engineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, Istanbul 34220, Turkey;
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7
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Khator R, Monga V. Recent advances in the synthesis and medicinal perspective of pyrazole-based α-amylase inhibitors as antidiabetic agents. Future Med Chem 2024. [PMID: 38230638 DOI: 10.4155/fmc-2023-0285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024] Open
Abstract
Diabetes is a serious health threat across the globe, claiming millions of lives worldwide. Among the various strategies employed, inhibition of α-amylase is a therapeutic protocol for the management of Type 2 diabetes mellitus. α-Amylase is a crucial enzyme involved in the breakdown of dietary starch into simpler units. However, the clinically used α-amylase inhibitors have various drawbacks. Therefore, design and development of novel α-amylase inhibitors have gained significant attention. The pyrazole motif has been identified as a versatile scaffold in medicinal chemistry, and recent studies have led to the identification of various pyrazole-based α-amylase inhibitors. This review compiles therapeutic implications of pyrazole-appended α-amylase inhibitors; their synthesis, biological activities, structure-activity relationships and molecular docking studies are discussed.
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Affiliation(s)
- Rakesh Khator
- Drug Design & Molecular Synthesis Laboratory, Department of Pharmaceutical Sciences & Natural Products, Central University of Punjab, VPO-Ghudda, 151401, Bathinda, Punjab, India
| | - Vikramdeep Monga
- Drug Design & Molecular Synthesis Laboratory, Department of Pharmaceutical Sciences & Natural Products, Central University of Punjab, VPO-Ghudda, 151401, Bathinda, Punjab, India
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8
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Kumar A, Kumar RR, Chaturvedi V, Kayastha AM. α-Amylase purified and characterized from fenugreek (Trigonella foenum-graecum) showed substantial anti-biofilm activity against Staphylococcus aureus MTCC740. Int J Biol Macromol 2023; 252:126442. [PMID: 37611683 DOI: 10.1016/j.ijbiomac.2023.126442] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
Starch hydrolyzing α-amylase from germinated fenugreek (Trigonella foenum-graecum) has been purified 104-fold to apparent electrophoretic homogeneity with a final specific activity of 297.5 units/mg. SDS-PAGE of the final preparation revealed a single protein band of 47.5 kDa, supported by LC/MS analysis and size-exclusion chromatography on the Superdex 200 (ÄKTA-FPLC). α-Amylase exhibited maximum activity at pH 5.5. An activation energy (Ea) of 9.12 kcal/mol was found to exist in the temperature range of 20 to 90 °C. When substrate concentrations were evaluated between 0.5 and 10 mg/mL, the Km and Vmax values for starch were observed to be 1.12 mg/mL and 384.14 μmol/min/mg, respectively. The major substrate starch exhibited high specificity for fenugreek α-amylase. In the presence of EDTA (5 mM), the activity was lost, however, it could be largely reversed with the addition of calcium. Furthermore, an effort was made to assess the ability of fenugreek seed-derived partially purified (DEAE-cellulose enzyme) and purified α-amylase to disperse inside 48 h-old biofilms of Staphylococcus aureus MTCC740. The outcomes clearly demonstrated that the purified and partially purified α-amylase both exhibited strong biofilm dispersion activity.
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Affiliation(s)
- Avinash Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ravi Ranjan Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Venkatesh Chaturvedi
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Arvind M Kayastha
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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9
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Kumar A, Singh VK, Kayastha AM. Molecular modeling, docking and dynamics studies of fenugreek ( Trigonella foenum-graecum) α-amylase. J Biomol Struct Dyn 2023; 41:9297-9312. [PMID: 36369783 DOI: 10.1080/07391102.2022.2144458] [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: 09/01/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022]
Abstract
α-Amylase catalyses the hydrolysis of glucosidic bonds in polysaccharides such as starch, glycogen and their degradation products. In the present study, the three-dimensional structure of fenugreek (Trigonella foenum-graecum) α-amylase was determined using a homology modeling-based technique. The best predicted model was deposited in PMDB server with PMDB ID PM0084364. The phylogenetic tree was created using the UPGMA method with 8 homologous protein sequences, Trigonella foenum-graecum was utilized as the target protein. Alignment of the phylogenetic tree identified two primary functional groupings (A and B). α-Amylase from the target genome Trigonella foenum-graecum (Acc. No: GHNA01022531.1) was clustered with Medicago truncatula (Acc. No: XP003589186.1), Cicer arietinum (Acc. No: XP004499059.1), Cajanus cajan (Acc. No: XP020231823.1), Vigna angularis (Acc. No: NP001316768.1) and Vigna mungo (Acc. No: P17859.1), in group A cluster, while Hordeum vulgare (Acc. No: Q40015) and Oryza sativa (PDB ID: 3WN6) were in cluster B. The molecular dynamics simulations were performed to understand the molecular basis and mode of action of Trigonella foenum-graecum α-amylase. Additionally, a geometry-based molecular docking technique was used to evaluate potential binding interactions between the modeled structure of α-amylase and maltose. The results show that Trp228, Glu226, Arg199, His308, Tyr165, Asp309, Phe202 and Asp201 from Trigonella foenum-graecum α-amylase enzyme is involved in the binding to the substrate maltose. Our study provides a 3D model of Trigonella foenum-graecum α-amylase and aids in understanding the atomic level molecular underpinnings of the mechanism of α-amylase interaction with substrate maltose. Ca2+ are essential for the stability of domain B since they are connected to it. Ca2+ site ligands are Asp139, Glu130, Thr133, Asp135 and Gly131 residues. HIGHLIGHTSIn silico analysis, gene prediction of α-amylase was carried from Trigonella foenum-graecum.Analysis of the structure of α-amylase was carried out using homology modelling.Calcium binding sites and their interactions with α-amylase were visualised using BIOVIA DISCOVERY STUDIO 2019.The molecular interaction between Trigonella foenum-graecum α-amylase and maltose was studied in silico using a molecular docking-based method.To give the required simulation parameters, RMSD, RMSF, and Total Energy were calculated using BIOVIA DISCOVERY STUDIO 2019.[Figure: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Avinash Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Vinay Kumar Singh
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Arvind M Kayastha
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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Zhao X, Zhang Y, He B, Han Y, Shen B, Zang Y, Wang H. Transcriptional control of carbohydrate catabolism by the CcpA protein in the ruminal bacterium Streptococcus bovis. Appl Environ Microbiol 2023; 89:e0047423. [PMID: 37823652 PMCID: PMC10617382 DOI: 10.1128/aem.00474-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/23/2023] [Indexed: 10/13/2023] Open
Abstract
As a potent, pleiotropic regulatory protein in Gram-positive bacteria, catabolite control protein A (CcpA) mediates the transcriptional control of carbohydrate metabolism in Streptococcus bovis, a lactate-producing bacterium that plays an essential role in rumen acidosis in dairy cows. Although the rumen uptake of carbohydrates is multi-substrate, the focus of S. bovis research thus far has been on the glucose. With the aid of gene deletion, whole-genome sequencing, and transcriptomics, we have unraveled the role of CcpA in carbohydrate metabolism, on the one hand, and acidosis, on the other, and we show that the S. bovis strain S1 encodes "Carbohydrate-Active Enzymes" and that ccpA deletion slows the organism's growth rate and modulates the organic acid fermentation pathways toward lower lactate, higher formate, and acetate in the maltose and cellobiose. Furthermore, this study revealed the different regulatory functions of the CcpA protein in rumen metabolism and acidosis.IMPORTANCEThis study is important as it illustrates the varying regulatory role of the Streptococcus bovis catabolite control protein A protein in carbohydrate metabolism and the onset of acidosis in dairy cattle.
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Affiliation(s)
- Xiujuan Zhao
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ying Zhang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Banglin He
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yu Han
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ben Shen
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yu Zang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hongrong Wang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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Janeček Š. Advances in Amylases-What's Going on? Molecules 2023; 28:7268. [PMID: 37959687 PMCID: PMC10647339 DOI: 10.3390/molecules28217268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
With regard to the CAZy database ( [...].
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia;
- Institute of Biology and Biotechnology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
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12
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Bax HHM, van der Maarel MJEC, Jurak E. Alpha-1,4-transglycosylation Activity of GH57 Glycogen Branching Enzymes Is Higher in the Absence of a Flexible Loop with a Conserved Tyrosine Residue. Polymers (Basel) 2023; 15:2777. [PMID: 37447423 DOI: 10.3390/polym15132777] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Starch-like polymers can be created through the use of enzymatic modification with glycogen branching enzymes (GBEs). GBEs are categorized in the glycoside hydrolase (GH) family 13 and 57. Both GH13 and GH57 GBEs exhibit branching and hydrolytic activity. While GH13 GBEs are also capable of α-1,4-transglycosylation, it is yet unknown whether GH57 share this capability. Among the four crystal structures of GH57 GBEs that have been solved, a flexible loop with a conserved tyrosine was identified to play a role in the branching activity. However, it remains unclear whether this flexible loop is also involved in α-1,4-transglycosylation activity. We hypothesize that GH57 GBEs with the flexible loop and tyrosine are also capable of α-1,4-transglycosylation, similar to GH13 GBEs. The aim of the present study was to characterize the activity of GH57 GBEs to investigate a possible α-1,4-transglycosylation activity. Three GH57 GBEs were selected, one from Thermococcus kodakarensis with the flexible loop and two beta-strands; one from Thermotoga maritima, missing the flexible loop and beta-strands; and one from Meiothermus sp., missing the flexible loop but with the two beta-strands. The analysis of chain length distribution over time of modified maltooctadecaose, revealed, for the first time, that all three GH57 GBEs can generate chains longer than the substrate itself, showing that α-1,4-transglycosylation activity is generally present in GH57 GBEs.
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Affiliation(s)
- Hilda Hubertha Maria Bax
- Bioproduct Engineering, Engineering and Technology Institute Groningen, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | | - Edita Jurak
- Bioproduct Engineering, Engineering and Technology Institute Groningen, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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13
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Acrylic fabric and nanomaterials to enhance α-amylase-based biocatalytic immobilized systems for industrial food applications. Int J Biol Macromol 2023; 233:123539. [PMID: 36740122 DOI: 10.1016/j.ijbiomac.2023.123539] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
An innovative approach for immobilizing α-amylase was used in this investigation. The acrylic fabric was first treated with hexamethylene diamine (HMDA) and then coated with copper ions that were later reduced to copper nanoparticles (CuNPs). The corresponding materials obtained, Cu(II)@HMDA-TA and CuNPs@HMDA-TA, were employed as carriers for α-amylase, respectively. The structural and morphological characteristics of the produced support matrices before and after immobilization were assessed using various techniques, including FTIR, SEM, EDX, TG/DTG, DSC, and zeta potential. The immobilized α-amylase exhibited the highest level of activity at pH 7.0, with immobilization yields observed for CuNPs@HMDA-TA (81.7 %) (60 unit/g support) followed by Cu(II)@HMDA-TA (71.7 %) (49 unit/g support) and 75 % and 61 % of activity yields, and 91.7 % and 85 % of immobilization efficiency, respectively. Meanwhile, biochemical characterizations of the activity of the soluble and immobilized enzymes were carried out and compared. Optimal temperature, pH, kinetics, storage stability, and reusability parameters were optimized for immobilized enzyme activity. The optimal pH and temperature were recorded as 6.0 and 50 °C for soluble α-amylase while the two forms of immobilized α-amylase exhibit a broad pH of 6.0-7.0 and optimal temperature at 60 °C. After recycling 15 times, the immobilized α-amylase on CuNPs@HMDA-TA and Cu(II)@HMDA-TA preserved 63 % and 52 % of their activities, respectively. The two forms of immobilized α-amylase displayed high stability when stored for 6 weeks and preserved 85 % and 76 % of their activities, respectively. Km values were calculated as 1.22, 1.39, and 1.84 mg/mL for soluble, immobilized enzymes on CuNPs@HMDA-TA, and Cu(II)@HMDA-TA, and Vmax values were calculated as 36.25, 29.68, and 21.57 μmol/mL/min, respectively. The total phenolic contents of maize kernels improved 1.4 ± 0.01 fold after treatment by two immobilized α-amylases.
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14
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Improved Stability and Hydrolysates of Hyperthermophilic GH57 Type II Pullulanase from the Deep-Sea Archaeon Thermococcus siculi HJ21 by Truncation. Catalysts 2023. [DOI: 10.3390/catal13030453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Pullulanase (EC 3.2.1.41) belongs to the amylase family and is often used alone or in combination with other amylases in the industrial production of starch-based products. This enzyme is often required in industrial production because of its better stability. We here truncated the pullulanase gene from the deep-sea hydrothermal anaerobic archaeon Thermococcus siculi HJ21 and obtained Pul-HJΔ782, which is a member of the α-amylase family GH57. The results revealed that the optimum temperature for Pul-HJΔ782 was 100 °C, and its thermostability at 100 °C improved after truncation. Less than 15% of its enzyme activity was lost after 1 h of incubation at 100 °C, and 57% activity remained after 5 h of treatment. Truncation significantly improved the overall pH tolerance range of Pul-HJΔ782, and its stability in the pH range 4–8 was over 80% relative activity from an average of 60%. The sequence and structural model of Pul-HJΔ782 was analyzed, and its instability index was reduced significantly. Furthermore, the hydrolysates of the truncated and wild-type pullulanase were analyzed, and the enzymatic digestion efficiency of the truncated Pul-HJΔ782 was higher.
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15
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Li SF, Cheng F, Wang YJ, Zheng YG. Strategies for tailoring pH performances of glycoside hydrolases. Crit Rev Biotechnol 2023; 43:121-141. [PMID: 34865578 DOI: 10.1080/07388551.2021.2004084] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Glycoside hydrolases (GHs) exhibit high activity and stability under harsh conditions, such as high temperatures and extreme pHs, given their wide use in industrial biotechnology. However, strategies for improving the acidophilic and alkalophilic adaptations of GHs are poorly summarized due to the complexity of the mechanisms of these adaptations. This review not only highlights the adaptation mechanisms of acidophilic and alkalophilic GHs under extreme pH conditions, but also summarizes the recent advances in engineering the pH performances of GHs with a focus on four strategies of protein engineering, enzyme immobilization, chemical modification, and medium engineering (additives). The examples described here summarize the methods used in modulating the pH performances of GHs and indicate that methods integrated in different protein engineering techniques or methods are efficient to generate industrial biocatalysts with the desired pH performance and other adapted enzyme properties.
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Affiliation(s)
- Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
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16
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A Novel Subfamily GH13_46 of the α-Amylase Family GH13 Represented by the Cyclomaltodextrinase from Flavobacterium sp. No. 92. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248735. [PMID: 36557873 PMCID: PMC9781549 DOI: 10.3390/molecules27248735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
In the CAZy database, the α-amylase family GH13 has already been divided into 45 subfamilies, with additional subfamilies still emerging. The presented in silico study was undertaken in an effort to propose a novel GH13 subfamily represented by the experimentally characterized cyclomaltodxtrinase from Flavobacterium sp. No. 92. Although most cyclomaltodextrinases have been classified in the subfamily GH13_20. This one has not been assigned any GH13 subfamily as yet. It possesses a non-specified immunoglobulin-like domain at its N-terminus mimicking a starch-binding domain (SBD) and the segment MPDLN in its fifth conserved sequence region (CSR) typical, however, for the subfamily GH13_36. The searches through sequence databases resulted in collecting a group of 108 homologs forming a convincing cluster in the evolutionary tree, well separated from all remaining GH13 subfamilies. The members of the newly proposed subfamily share a few exclusive sequence features, such as the "aromatic" end of the CSR-II consisting of two well-conserved tyrosines with either glycine, serine, or proline in the middle or a glutamic acid succeeding the catalytic proton donor in the CSR-III. Concerning the domain N of the representative cyclomaltodextrinase, docking trials with α-, β- and γ-cyclodextrins have indicated it may represent a new type of SBD. This new GH13 subfamily has been assigned the number GH13_46.
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17
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Zhang J, Li C, Wang G, Cao J, Yang X, Liu X, Sun L. α-Amylase inhibition of a certain dietary polyphenol is predominantly affected by the concentration of α-1, 4-glucosidic bonds in starchy and artificial substrates. Food Res Int 2022; 157:111210. [DOI: 10.1016/j.foodres.2022.111210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 11/04/2022]
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18
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Gaenssle ALO, van der Maarel MJEC, Jurak E. The influence of amylose content on the modification of starches by glycogen branching enzymes. Food Chem 2022; 393:133294. [PMID: 35653995 DOI: 10.1016/j.foodchem.2022.133294] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/10/2022] [Accepted: 05/21/2022] [Indexed: 11/04/2022]
Abstract
Glycogen branching enzymes (GBEs) have been used to generate new branches in starches for producing slowly digestible starches. The aim of this study was to expand the knowledge about the mode of action of these enzymes by identifying structural aspects of starchy substrates affecting the products generated by different GBEs. The structures obtained from incubating five GBEs (three from glycoside hydrolase family (GH) 13 and two from GH57) on five different substrates exhibited minor but statistically significant correlations between the amount of longer chains (degree of polymerization (DP) 9-24) of the product and both the amylose content and the degree of branching of the substrate (Pearson correlation coefficient of ≤-0.773 and ≥0.786, respectively). GH57 GBEs mainly generated large products with long branches (100-700 kDa and DP 11-16) whereas GH13 GBEs produced smaller products with shorter branches (6-150 kDa and DP 3-10).
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Affiliation(s)
- Aline L O Gaenssle
- Bioproduct Engineering, Engineering and Technology Institute Groningen, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Marc J E C van der Maarel
- Bioproduct Engineering, Engineering and Technology Institute Groningen, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Edita Jurak
- Bioproduct Engineering, Engineering and Technology Institute Groningen, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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19
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Liu Z, Wu G, Wu H. Molecular cloning, and optimized production and characterization of recombinant cyclodextrin glucanotransferase from Bacillus sp. T1. 3 Biotech 2022; 12:58. [PMID: 35186655 PMCID: PMC8816995 DOI: 10.1007/s13205-022-03111-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/08/2022] [Indexed: 11/26/2022] Open
Abstract
Cyclodextrin glucosyltransferase (CGTase) is an enzyme which degrades starch to produce cyclodextrins (CDs). In this study, the β-CGTase producing strain T1 was identified as Bacillus sp. by its morphological characteristics and 16S rDNA sequence analysis. The cgt-T1 gene was cloned and expressed in Escherichia coli. CGTase-T1 was purified by Ni-nitrilotriacetic acid agarose column and the molecular weight was determined as approximately 75 kDa using SDS-PAGE analysis. For the expression of soluble proteins, the optimal induction conditions were 10 h at 25 °C with OD600 at 0.8. The purified CGTase-T1 exhibited maximum activity with an optimal pH and temperature of 6.0 and 65 °C. The enzyme was stable in a pH range of 7.0-10.0, retaining over 85% relative activity for 1 h. CGTase-T1 activity can be significantly enhanced by adding 1 mM Ba2+. Using a soluble starch substrate, the kinetic parameters were revealed with K M and k cat/K M values of 2.75 mg mL-1 and 1253.97 s-1 mL mg-1, respectively. Additionally, the four enzyme activities of CGTase-T1 were determined. The highest conversion rate to CDs (40.9%) was achieved from soluble starch after 8 h of enzyme reaction, where mainly β-CD was produced (79.1% of the total CDs yield), indicating that CGTase-T1 potentially has industrial application prospect. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03111-8.
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Affiliation(s)
- Zhenyang Liu
- College of Life Sciences, Yangtze University, 1 South-Loop Road, Jingzhou, 434025 China
| | - Guogan Wu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Bei Zhai Road, Shanghai, 201106 China
| | - Huawei Wu
- College of Life Sciences, Yangtze University, 1 South-Loop Road, Jingzhou, 434025 China
- College of Life Sciences, Yangtze University, 1 South-Loop Road, Jingzhou, 434025 China
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20
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Han X, Ding N, Ban X, Gu Z, Cheng L, Hong Y, Li C, Li Z. Fusion of maltooligosaccharide-forming amylases from two origins for the improvement of maltopentaose synthesis. Food Res Int 2021; 150:110735. [PMID: 34865754 DOI: 10.1016/j.foodres.2021.110735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/02/2021] [Accepted: 09/25/2021] [Indexed: 01/10/2023]
Abstract
Maltopentaose-forming amylases are promising enzymes for their ability to hydrolyze starch and produce functional maltooligosaccharides. Two maltopentaose-forming amylase genes from Bacillus megaterium (BmMFA) and Saccharophagus degradans (SdMFA) were expressed heterologously and their characteristics were analyzed. BmMFA has substantial thermostability and SdMFA owns superior product specificity. The carbohydrate-binding module of SdMFA was fused with BmMFA and the fused protein showed ideal enzymatic properties and displayed potential for industrial production of maltopentaose. Under the optimized conditions, the final product containing 47.41% maltopentaose was obtained with a conversion rate of 92.67% from starch. This study provides a novel strategy for the directed modification of MFAses through protein fusion approach.
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Affiliation(s)
- Xu Han
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Ning Ding
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Xiaofeng Ban
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, PR China
| | - Li Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, PR China
| | - Yan Hong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, PR China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, PR China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, PR China.
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21
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Fort J, Nicolàs-Aragó A, Palacín M. The Ectodomains of rBAT and 4F2hc Are Fake or Orphan α-Glucosidases. Molecules 2021; 26:6231. [PMID: 34684812 PMCID: PMC8537225 DOI: 10.3390/molecules26206231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/22/2022] Open
Abstract
It is known that 4F2hc and rBAT are the heavy subunits of the heteromeric amino acid transporters (HATs). These heavy subunits are N-glycosylated proteins, with an N-terminal domain, one transmembrane domain and a bulky extracellular domain (ectodomain) that belongs to the α-amylase family. The heavy subunits are covalently linked to a light subunit from the SLC7 family, which is responsible for the amino acid transport activity, forming a heterodimer. The functions of 4F2hc and rBAT are related mainly to the stability and trafficking of the HATs in the plasma membrane of vertebrates, where they exert the transport activity. Moreover, 4F2hc is a modulator of integrin signaling, has a role in cell fusion and it is overexpressed in some types of cancers. On the other hand, some mutations in rBAT are found to cause the malfunctioning of the b0,+ transport system, leading to cystinuria. The ectodomains of 4F2hc and rBAT share both sequence and structure homology with α-amylase family members. Very recently, cryo-EM has revealed the structure of several HATs, including the ectodomains of rBAT and 4F2hc. Here, we analyze available data on the ectodomains of rBAT and 4Fhc and their relationship with the α-amylase family. The physiological relevance of this relationship remains largely unknown.
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Affiliation(s)
- Joana Fort
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (M.P.)
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Adrià Nicolàs-Aragó
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (M.P.)
| | - Manuel Palacín
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (M.P.)
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
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22
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Janíčková Z, Janeček Š. In Silico Analysis of Fungal and Chloride-Dependent α-Amylases within the Family GH13 with Identification of Possible Secondary Surface-Binding Sites. Molecules 2021; 26:molecules26185704. [PMID: 34577174 PMCID: PMC8467227 DOI: 10.3390/molecules26185704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022] Open
Abstract
This study brings a detailed bioinformatics analysis of fungal and chloride-dependent α-amylases from the family GH13. Overall, 268 α-amylase sequences were retrieved from subfamilies GH13_1 (39 sequences), GH13_5 (35 sequences), GH13_15 (28 sequences), GH13_24 (23 sequences), GH13_32 (140 sequences) and GH13_42 (3 sequences). Eight conserved sequence regions (CSRs) characteristic for the family GH13 were identified in all sequences and respective sequence logos were analysed in an effort to identify unique sequence features of each subfamily. The main emphasis was given on the subfamily GH13_32 since it contains both fungal α-amylases and their bacterial chloride-activated counterparts. In addition to in silico analysis focused on eventual ability to bind the chloride anion, the property typical mainly for animal α-amylases from subfamilies GH13_15 and GH13_24, attention has been paid also to the potential presence of the so-called secondary surface-binding sites (SBSs) identified in complexed crystal structures of some particular α-amylases from the studied subfamilies. As template enzymes with already experimentally determined SBSs, the α-amylases from Aspergillus niger (GH13_1), Bacillus halmapalus, Bacillus paralicheniformis and Halothermothrix orenii (all from GH13_5) and Homo sapiens (saliva; GH13_24) were used. Evolutionary relationships between GH13 fungal and chloride-dependent α-amylases were demonstrated by two evolutionary trees—one based on the alignment of the segment of sequences spanning almost the entire catalytic TIM-barrel domain and the other one based on the alignment of eight extracted CSRs. Although both trees demonstrated similar results in terms of a closer evolutionary relatedness of subfamilies GH13_1 with GH13_42 including in a wider sense also the subfamily GH13_5 as well as for subfamilies GH13_32, GH13_15 and GH13_24, some subtle differences in clustering of particular α-amylases may nevertheless be observed.
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Affiliation(s)
- Zuzana Janíčková
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, SK-91701 Trnava, Slovakia;
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
| | - Štefan Janeček
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, SK-91701 Trnava, Slovakia;
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
- Correspondence:
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23
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Gaenssle ALO, Bax HHM, van der Maarel MJEC, Jurak E. GH13 Glycogen branching enzymes can adapt the substrate chain length towards their preferences via α-1,4-transglycosylation. Enzyme Microb Technol 2021; 150:109882. [PMID: 34489035 DOI: 10.1016/j.enzmictec.2021.109882] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022]
Abstract
Glycogen branching enzymes (GBEs; 1,4-α-glucan branching enzyme; E.C. 2.4.1.18) have so far been described to be capable of both α-1,6-transglycosylation (branching) and α-1,4-hydrolytic activity. The aim of the present study was to elucidate the mode of action of three distantly related GBEs from the glycoside hydrolase family 13 by in depth analysis of the activity on a well-defined substrate. For this purpose, the GBEs from R. marinus (RmGBE), P. mobilis (PmGBE1), and B. fibrisolvens (BfGBE) were incubated with a highly pure fraction of a linear substrate of 18 anhydroglucose units. A well-known and characterized branching enzyme from E. coli (EcGBE) was also taken along. Analysis of the chain length distribution over time revealed that, next to hydrolytic and branching activity, all three GBEs were capable of generating chains longer than the substrate, clearly showing α-1,4-transglycosylation activity. Furthermore, the GBEs used those elongated chains for further branching. The sequential activity of elongation and branching enabled the GBEs to modify the substrate to a far larger extent than would have been possible with branching activity alone. Overall, the three GBEs acted ambiguous on the defined substrate. RmGBE appeared to have a strong preference towards transferring chains of nine anhydroglucose units, even during elongation, with a comparably low activity. BfGBE generated an array of elongated chains before using the chains for introducing branches while PmGBE1 exhibited a behaviour intermediate of the other two enzymes. On the basis of the mode of action revealed in this research, an updated model of the mechanism of GBEs was proposed now including the α-1,4-transglycosylation activity.
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Affiliation(s)
- Aline Lucie Odette Gaenssle
- Bioproduct Engineering, Engineering and Technology Institute Groningen, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, the Netherlands
| | - Hilda Hubertha Maria Bax
- Bioproduct Engineering, Engineering and Technology Institute Groningen, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, the Netherlands
| | | | - Edita Jurak
- Bioproduct Engineering, Engineering and Technology Institute Groningen, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, the Netherlands.
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24
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Fan Q, Zhang L, Dong C, Zhong L, Fang X, Huan M, Ye X, Huang Y, Li Z, Cui Z. Novel Malto‐Oligosaccharide‐Producing Amylase AmyAc from
Archangium
sp. Strain AC19 and Its Catalytic Properties. STARCH-STARKE 2021. [DOI: 10.1002/star.202100114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Qiwen Fan
- Key Laboratory of Agricultural Environmental Microbiology Ministry of Agriculture College of Life Science Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Lei Zhang
- Key Laboratory of Agricultural Environmental Microbiology Ministry of Agriculture College of Life Science Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Chaonan Dong
- Key Laboratory of Agricultural Environmental Microbiology Ministry of Agriculture College of Life Science Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Linli Zhong
- Key Laboratory of Agricultural Environmental Microbiology Ministry of Agriculture College of Life Science Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Xiaodong Fang
- Guangzhou Hanyun Pharmaceutical Technology Co. Ltd. Guangzhou 510000 P. R. China
| | - Minghui Huan
- Microbial Research Institute of Liaoning Province Chaoyang P. R. China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology Ministry of Agriculture College of Life Science Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology Ministry of Agriculture College of Life Science Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology Ministry of Agriculture College of Life Science Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology Ministry of Agriculture College of Life Science Nanjing Agricultural University Nanjing 210095 P. R. China
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25
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Sadeghian Motahar SF, Salami M, Ariaeenejad S, Emam‐Djomeh Z, Sheykh Abdollahzadeh Mamaghani A, Kavousi K, Moghadam M, Hosseini Salekdeh G. Synergistic Effect of Metagenome‐Derived Starch‐Degrading Enzymes on Quality of Functional Bread with Antioxidant Activity. STARCH-STARKE 2021. [DOI: 10.1002/star.202100098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | - Maryam Salami
- Department of Food Science and Engineering University College of Agriculture & Natural Resources University of Tehran Karaj Iran
| | - Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology Agricultural Biotechnology Research Institute of Iran (ABRII) Agricultural Research Education and Extension Organization (AREEO) Karaj Iran
| | - Zahra Emam‐Djomeh
- Department of Food Science and Engineering University College of Agriculture & Natural Resources University of Tehran Karaj Iran
| | - Atefeh Sheykh Abdollahzadeh Mamaghani
- Department of Systems and Synthetic Biology Agricultural Biotechnology Research Institute of Iran (ABRII) Agricultural Research Education and Extension Organization (AREEO) Karaj Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB) Institute of Biochemistry and Biophysics (IBB) University of Tehran Tehran Iran
| | - Maryam Moghadam
- Department of Food Science and Engineering University College of Agriculture & Natural Resources University of Tehran Karaj Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems and Synthetic Biology Agricultural Biotechnology Research Institute of Iran (ABRII) Agricultural Research Education and Extension Organization (AREEO) Karaj Iran
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Lin Y, Liao YY, Huang RX, Li AZ, An SQ, Tang JL, Tang DJ. Extracellular Amylase Is Required for Full Virulence and Regulated by the Global Posttranscriptional Regulator RsmA in Xanthomonas campestris Pathovar campestris. PHYTOPATHOLOGY 2021; 111:1104-1113. [PMID: 33245253 DOI: 10.1094/phyto-08-20-0372-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As with many phytopathogenic bacteria, the virulence of Xanthomonas campestris pv. campestris, the causal agent of black rot disease in cruciferous plants, relies on secretion of a suite of extracellular enzymes that includes cellulase (endoglucanase), pectinase, protease, and amylase. Although the role in virulence of a number of these enzymes has been assessed, the contribution of amylase to X. campestris pv. campestris virulence has yet to be established. In this work, we investigated both the role of extracellular amylase in X. campestris pv. campestris virulence and the control of its expression. Deletion of XC3487 (here renamed amyAXcc), a putative amylase-encoding gene from the genome of X. campestris pv. campestris strain 8004, resulted in a complete loss of extracellular amylase activity and significant reduction in virulence. The extracellular amylase activity and virulence of the amyAXcc mutant could be restored to the wild-type level by expressing amyAXcc in trans. These results demonstrated that amyAXcc is responsible for the extracellular amylase activity of X. campestris pv. campestris and indicated that extracellular amylase plays an important role in X. campestris pv. campestris virulence. We also found that the expression of amyAXcc is strongly induced by starch and requires activation by the global posttranscriptional regulator RsmA. RsmA binds specifically to the 5'-untranslated region of amyAXcc transcripts, suggesting that RsmA regulates amyAXcc directly at the posttranscriptional level. Unexpectedly, in addition to posttranscriptional regulation, the use of a transcriptional reporter demonstrated that RsmA also regulates amyAXcc expression at the transcriptional level, possibly by an indirect mechanism.
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Affiliation(s)
- Yan Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, and College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Yong-Yan Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, and College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Ru-Xia Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, and College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Ai-Zhou Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, and College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Shi-Qi An
- National Biofilms Innovation Centre, Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, and College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Dong-Jie Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, and College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
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Fatimah H, Siti Aisyah R, Ma NL, Rased NM, Mohamad NFAC, Nur Syakinah Nafisa F, Azila A, Zakeri HA. Aspergillus niger trehalase enzyme induced morphological and protein alterations on Acanthamoeba cyst and molecular docking studies. J Parasit Dis 2021; 45:459-473. [PMID: 34295046 PMCID: PMC8254846 DOI: 10.1007/s12639-020-01332-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/25/2020] [Indexed: 11/30/2022] Open
Abstract
The cytotoxicity of Acanthamoeba is yet to fully illustrate due to recalcitrant of Acanthamoeba during cyst stage. The formation of the trehalose layer at the cyst stage protects the inner components of this opportunist protozoan parasite. Trehalase from the Aspergillus niger (AnTre) activity on the cyst of Acanthamoeba was determined based on AnTre dose-response, morphological and protein changes. The interaction of the AnTre and trehalose was also visualized through docking simulation. Vacuolation of the cyst can be seen when observed under light microscopy. Membrane integrity assessment suggested possible hydrolization of the AnTre enzyme to trehalose membranes which based on acridine orange and propidium iodide staining. Surface morphology based on scanning electron microscopy revealed the formation of bulging structure that was also proved through cross sectioning observed by transmission electron microscopy. Loss of internal structure of the cysts was clearly observed. Other morphological distinction where loss of rigid shape due to the destruction of the endo- and ecto cyst layers. However, the protein profile exhibits change of trehalose layer as responses to AnTre treatment. The observed biological results were also supported by interaction simulation based on molecular docking between trehalose and AnTre enzyme. In conclusion, this enzymatic approach could be developed into selective and effective mechanism to control Acanthamoeba without affecting the host especially mammals due to the absence of trehalose elements in the tissues of mammals.
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Affiliation(s)
- H. Fatimah
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu Malaysia
| | - R. Siti Aisyah
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu Malaysia
| | - N. L. Ma
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu Malaysia
| | - Nurhidayana M. Rased
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu Malaysia
| | - Nor F. A. C. Mohamad
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu Malaysia
| | - F. Nur Syakinah Nafisa
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu Malaysia
| | - A. Azila
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu Malaysia
| | - Hazlina A. Zakeri
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu Malaysia
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Effect of Leu 277 on Disproportionation and Hydrolysis Activity in Bacillus stearothermophilus NO2 Cyclodextrin Glucosyltransferase. Appl Environ Microbiol 2021; 87:e0315120. [PMID: 33837009 DOI: 10.1128/aem.03151-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The disproportionation activity of cyclodextrin glucosyltransferase (CGTase; EC 2.4.1.19) can be used to convert small molecules into glycosides, thereby enhancing their solubility and stability. However, CGTases also exhibit a competing hydrolysis activity. The +2 subsite of the substrate binding cleft plays an important role in both the disproportionation and hydrolysis activities, but almost all known mutations at this site decrease disproportionation activity. In this study, Leu277 of the CGTase from Bacillus stearothermophilus NO2, located near both the +2 subsite and the catalytic acid/base Glu253, was modified to assess the effect of side chain size at this position on disproportionation and hydrolysis activities. The best mutant, L277M, exhibited a reduced Km for the acceptor substrate maltose (0.48 mM versus 0.945 mM) and an increased kcat/Km (1,175 s-1 mM-1 versus 686.1 s-1 mM-1), compared with those of the wild-type enzyme. The disproportionation-to-hydrolysis ratio of L277M was 2.4-fold greater than that of the wild type. Existing structural data were combined with a multiple-sequence alignment and Gly282 mutations to examine the mechanism behind the effects of the Leu277mutations. The Gly282 mutations were included to aid a molecular dynamics (MD) analysis and the comparison of crystal structures. They reveal that changes to a hydrophobic cluster near Glu253 and the hydrophobicity of the +2 subsite combine to produce the observed effects. IMPORTANCE In this study, mutations that enhance the disproportionation to hydrolysis ratio of a CGTase have been discovered. For example, the disproportionation-to-hydrolysis ratio of the L277M mutant of Bacillus stearothermophilus NO2 CGTase was 2.4-fold greater than that of the wild type. The mechanism behind the effects of these mutations is explained. This paper opens up other avenues for future research into the disproportionation and hydrolysis activities of CGTases. Productive mutations are no longer limited to the acceptor subsite, since mutations that indirectly affect the acceptor subsite also enhance enzymatic activity.
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Jiang H, Xie X, Ban X, Gu Z, Cheng L, Hong Y, Li C, Li Z. Flexible Loop in Carbohydrate-Binding Module 48 Allosterically Modulates Substrate Binding of the 1,4-α-Glucan Branching Enzyme. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5755-5763. [PMID: 33988022 DOI: 10.1021/acs.jafc.1c00293] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The 1,4-α-glucan branching enzyme (GBE, EC 2.4.1.18) catalyzes the formation of α-1,6 branching points in starch and plays a key role in synthesis. To obtain mechanistic insights into the catalytic action of the enzyme, we first determined the crystal structure of GBE from Rhodothermus obamensis STB05 (RoGBE) to a resolution of 2.39 Å (PDB ID: 6JOY). The structure consists of three domains: domain A, domain C, and the carbohydrate-binding module 48 (CBM48). An engineered truncated mutant lacking the CBM48 domain (ΔCBM48) showed significantly reduced ligand binding affinity and enzyme activity. Comparison of the structures of RoGBE with other GBEs showed that CBM48 of RoGBE had a longer flexible loop. Truncation of the flexible loops resulted in reduced binding affinity and activity, thereby substantiating the importance of the optimum loop structure for catalysis. In essence, our study shows that CBM48, especially the flexible loop, plays an important role in substrate binding and enzymatic activity of RoGBE. Further, based on the structural analysis, kinetics, and activity assays on wild type and mutants, as well as homology modeling, we proposed a mechanistic model (called the "lid model") to illustrate how the flexible loop triggers substrate binding, ultimately leading to catalysis.
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Affiliation(s)
- Haimin Jiang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiaofang Xie
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiaofeng Ban
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
| | - Li Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
| | - Yan Hong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. 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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31
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da Costa-Latgé SG, Bates P, Dillon R, Genta FA. Characterization of Glycoside Hydrolase Families 13 and 31 Reveals Expansion and Diversification of α-Amylase Genes in the Phlebotomine Lutzomyia longipalpis and Modulation of Sandfly Glycosidase Activities by Leishmania Infection. Front Physiol 2021; 12:635633. [PMID: 33897451 PMCID: PMC8063059 DOI: 10.3389/fphys.2021.635633] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/26/2021] [Indexed: 11/13/2022] Open
Abstract
Sugar-rich food sources are essential for sandflies to meet their energy demands, achieving more prolonged survival. The digestion of carbohydrates from food is mainly realized by glycoside hydrolases (GH). To identify genes coding for α-glycosidases and α-amylases belonging to Glycoside Hydrolase Family 13 (GH13) and Glycoside Hydrolase Family 31 (GH31) in Lutzomyia longipalpis, we performed an HMMER search against its genome using known sequences from other dipteran species. The sequences retrieved were classified based on BLASTP best hit, analysis of conserved regions by alignment with sequences of proteins with known structure, and phylogenetic analysis comparing with orthologous proteins from other dipteran species. Using RT-PCR analysis, we evaluated the expression of GH13 and GH31 genes, in the gut and rest of the body of females, in four different conditions: non-fed, sugar-fed, blood-fed, and Leishmania mexicana infected females. L. longipalpis has GH13/31 genes that code for enzymes involved in various aspects of sugar metabolism, as carbohydrate digestion, storage, and mobilization of glycogen reserves, proteins involved in transport, control of N-glycosylation quality, as well as others with a putative function in the regulation of myogenesis. These proteins are representatives of GH13 and GH31 families, and their roles seem to be conserved. Most of the enzymes seem to be active with conserved consense sequences, including the expected catalytic residues. α-amylases also demonstrated the presence of calcium and chloride binding sites. L. longipalpis genome shows an expansion in the α-amylase gene family, with two clusters. In contrast, a retraction in the number of α-glucosidases occurred. The expansion of α-amylases is probably related to the specialization of these proteins for different substrates or inhibitors, which might correlate with the higher diversity of plant foods available in the natural habitat of L. longipalpis. The expression of α-glucosidase genes is higher in blood-fed females, suggesting their role in blood digestion. Besides that, in blood-fed females infected with the parasite Leishmania mexicana, these genes were also modulated. Glycoside Hydrolases from families 13 and 31 are essential for the metabolism of L. longipalpis, and GH13 enzymes seem to be involved in the interaction between sandflies and Leishmania.
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Affiliation(s)
| | - Paul Bates
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| | - Rod Dillon
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
- National Institute of Science and Technology for Molecular Entomology, Rio de Janeiro, Brazil
| | - Fernando Ariel Genta
- Laboratory of Insect Biochemistry and Physiology, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- National Institute of Science and Technology for Molecular Entomology, Rio de Janeiro, Brazil
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Wei X, Li J, Xiao J, Huang D. Gene duplication and subsequent functional diversification of maltase in fig wasp (Chalcidoidea, Hymenoptera). Int J Biol Macromol 2021; 182:482-491. [PMID: 33838190 DOI: 10.1016/j.ijbiomac.2021.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/29/2021] [Accepted: 04/05/2021] [Indexed: 10/21/2022]
Abstract
Maltase can catalyze the hydrolysis of α-1,4-glucosidic linkages and release α-d-glucoses that are used as a source of energy by insects. Maltase has been extensively studied in Lepidoptera and Diptera, while the characterization and evolutionary history of maltase are largely unknown in Hymenoptera. Here, we undertook a bioinformatics study and identified 105 maltase genes in 12 fig wasp species. Together with the maltase genes of Nasonia vitripennis and Apis mellifera, phylogenetic analysis showed that all the maltase genes were clustered into three clades. Clade I and III included maltase genes from all the fig wasp species, while clade II contained the maltase genes from non-pollinating fig wasps (NPFWs) only. Interestingly, the maltase genes located in clade II were intronless. Fig pollinators and NPFWs had lineage-specific gene expansion in clade I and II respectively, which were mainly derived from tandem duplications. The three clades displayed distinct gene structures. Furthermore, maltase showed significant functional divergence among the three clades and the critical amino acid sites were detected. These sites could be responsible for the ligand-binding preference and hydrolytic specificity. Overall, our results demonstrated that maltase might contribute to the discrepancy of life histories and feeding regimes between fig pollinators and NPFWs.
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Affiliation(s)
- Xianqin Wei
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiaxing Li
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jinhua Xiao
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Dawei Huang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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33
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Shofiyah SS, Yuliani D, Widya N, Sarian FD, Puspasari F, Radjasa OK, Ihsanawati, Natalia D. Isolation, expression, and characterization of raw starch degrading α-amylase from a marine lake Bacillus megaterium NL3. Heliyon 2020; 6:e05796. [PMID: 33426327 PMCID: PMC7776835 DOI: 10.1016/j.heliyon.2020.e05796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/23/2020] [Accepted: 12/18/2020] [Indexed: 01/05/2023] Open
Abstract
A land-locked marine lake Kakaban with its significant ecological paramaters provides a unique habitat for bacteria with novel biotechnology potential that uses a diverse array of catalytic agents, including α-amylase. Aiming at the isolation of raw starch degrading α-amylase from marine biodiversity, a gene encoding BmaN2 from a sea anemone associated bacterium Bacillus megaterium NL3 was cloned and expressed in Escherichia coli ArcticExpress (DE3). It comprises an open reading frame of 1,563 nucleotides encoding BmaN2 of 520 amino acids and belongs to the glycoside hydrolase family 13 subfamily 36 (GH13_36). This α-amylase has a maximum activity at pH 6.0 and 60 °C with a specific activity of 28.7 U mg-1. The BmaN2 activity is enhanced strongly by Ca2+ but inhibited by EDTA. BmaN2 also exhibits high catalytic efficiency on soluble starch with k cat /K M value of 14.1 mL mg-1 s-1. Despite no additional starch-binding domain, BmaN2 is able to hydrolyze various raw starches, such as wheat, corn, cassava, potato, rice, sago, and canna, in which granular wheat is the preferred substrate for BmaN2. These characteristics indicate that BmaN2 is a promising raw starch degrading enzyme within the subfamily GH13_36.
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Affiliation(s)
- Sofi Siti Shofiyah
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
- Marine Science Program Study, Faculty of Marine Science, OSO University, Pontianak, 78113, Indonesia
| | - Dewi Yuliani
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Nurul Widya
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Fean D. Sarian
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Fernita Puspasari
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Ocky Karna Radjasa
- Center for Tropical Coastal and Marine Studies, Diponegoro University, Widya Puraya, Semarang, 50275, Indonesia
- Indonesian Institute of Sciences, Gatot Subroto 10, Jakarta, Indonesia
| | - Ihsanawati
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Dessy Natalia
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
- University Center of Excellence for Nutraceuticals, Biosciences and Biotechnology Research Center, Bandung, Indonesia
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Production and characterization of psychrophilic α-amylase from a psychrophilic bacterium, Shewanella sp. ISTPL2. ACTA ACUST UNITED AC 2020. [DOI: 10.1515/amylase-2020-0001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractA psychrophilic and halophilic bacterial isolate, Shewanella sp. ISTPL2, procured from the pristine Pangong Lake, Ladakh, Jammu and Kashmir, India, was used for the production and characterization of the psychrophilic and alkalophilic α-amylase enzyme. The α-amylase is a critical enzyme that catalyses the hydrolysis of α-1,4-glycosidic bonds of starch molecules and is predominately utilized in biotechnological applications. The highest enzyme activity of partially purified extracellular α-amylase was 10,064.20 U/mL after 12 h of incubation in a shake flask at pH 6.9 and 10 °C. Moreover, the maximum intracellular α-amylase enzyme activity (259.62 U/mL) was also observed at 6 h of incubation. The extracellular α-amylase was refined to the homogeneity with the specific enzyme activity of 36,690.47 U/mg protein corresponding to 6.87-fold purification. The optimized pH and temperature for the α-amylase were found to be pH 8 and 4 °C, respectively, suggesting its stability at alkaline conditions and low or higher temperatures. The amylase activity was highly activated by Cu2+, Fe2+ and Ca2+, while inhibited by Cd2+, Co2+ and Na2+. As per our knowledge, the current study reports the highest activity of a psychrophilic α-amylase enzyme providing prominent biotechnological potential.
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35
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Sweeney RP, Danby PM, Geissner A, Karimi R, Brask J, Withers SG. Development of an active site titration reagent for α-amylases. Chem Sci 2020; 12:683-687. [PMID: 34163800 PMCID: PMC8178983 DOI: 10.1039/d0sc05380e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/03/2020] [Indexed: 01/12/2023] Open
Abstract
α-Amylases are among the most widely used classes of enzymes in industry and considerable effort has gone into optimising their activities. Efforts to find better amylase mutants, such as through high-throughput screening, would be greatly aided by access to precise and robust active site titrating agents for quantitation of active mutants in crude cell lysates. While active site titration reagents designed for retaining β-glycosidases quantify these enzymes down to nanomolar levels, convenient titrants for α-glycosidases are not available. We designed such a reagent by incorporating a highly reactive fluorogenic leaving group onto unsaturated cyclitol ethers, which have been recently shown to act as slow substrates for retaining glycosidases that operate via a covalent 'glycosyl'-enzyme intermediate. By appending this warhead onto the appropriate oligosaccharide, we developed efficient active site titration reagents for α-amylases that effect quantitation down to low nanomolar levels.
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Affiliation(s)
- Ryan P Sweeney
- Department of Chemistry, The University of British Columbia 2036 Main Mall Vancouver BC V6T 1Z1 Canada
| | - Phillip M Danby
- Department of Chemistry, The University of British Columbia 2036 Main Mall Vancouver BC V6T 1Z1 Canada
| | - Andreas Geissner
- Department of Chemistry, The University of British Columbia 2036 Main Mall Vancouver BC V6T 1Z1 Canada
| | - Ryan Karimi
- Department of Chemistry, The University of British Columbia 2036 Main Mall Vancouver BC V6T 1Z1 Canada
| | - Jesper Brask
- Novozymes Krogshoejvej 36 2880 Bagsvaerd Denmark
| | - Stephen G Withers
- Department of Chemistry, The University of British Columbia 2036 Main Mall Vancouver BC V6T 1Z1 Canada
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36
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Chengyao X, Yan Q, Chaonan D, Xiaopei C, Yanxin W, Ding L, Xianfeng Y, Jian H, Yan H, Zhongli C, Zhoukun L. Enzymatic properties of an efficient glucan branching enzyme and its potential application in starch modification. Protein Expr Purif 2020; 178:105779. [PMID: 33115653 DOI: 10.1016/j.pep.2020.105779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/02/2020] [Accepted: 10/21/2020] [Indexed: 11/29/2022]
Abstract
Glucan branching enzymes (GBEs, EC 2.4.1.18) catalyze the formation of α-1,6-linked branch in starch, which is important for the starch modification with prospective properties. In this study, the aqGBE gene encoding an efficient glucan branching enzyme was cloned from Aquabacterium sp. strain A7-Y and successfully expressed in Escherichia coli BL21 (DE3). The specific activity of the purified recombinant enzyme rAqGBE was 2850 U/mg with potato starch as the optimal substrate, and the Km and Vmax values of rAqGBE were 1.18 mg/mL and 588.2 μmol/min/mg, respectively. Enzymological characterization showed that rAqGBE exhibits its optimal activity under the condition of 40 °C and pH 7.0, respectively, which is independent of calcium ions. Otherwise, rAqGBE-treated potato starch showed different chain length distribution compared with control, the numbers of short chains (degree of polymerization, DP < 7) and long chains (DP > 25) increased from 4.5% to 9.6% and 6.1%-15.7% after enzymatic treatment, respectively. In starch anti-ageing assay, with minimum usage of 0.8 mg rAqGBE per g starch, the rAqGBE-treated potato starch exhibited reduced retrogradation properties. Our results indicate that the branching enzyme AqGBE may therefore be a promising tool for the enzymatic modification of starch.
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Affiliation(s)
- Xia Chengyao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Qiao Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Dong Chaonan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Chen Xiaopei
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Wang Yanxin
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Li Ding
- Institute of Veterinary Immunology &Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China
| | - Ye Xianfeng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Han Jian
- College of Agriculture, Xinjiang Agricultural University, XinJiang, 830052, China
| | - Huang Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Cui Zhongli
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Li Zhoukun
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, PR China.
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Imamura K, Matsuura T, Nakagawa A, Kitamura S, Kusunoki M, Takaha T, Unno H. Structural analysis and reaction mechanism of the disproportionating enzyme (D-enzyme) from potato. Protein Sci 2020; 29:2085-2100. [PMID: 32808707 PMCID: PMC7513719 DOI: 10.1002/pro.3932] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 11/06/2022]
Abstract
Starch produced by plants is a stored form of energy and is an important dietary source of calories for humans and domestic animals. Disproportionating enzyme (D-enzyme) catalyzes intramolecular and intermolecular transglycosylation reactions of α-1, 4-glucan. D-enzyme is essential in starch metabolism in the potato. We present the crystal structures of potato D-enzyme, including two different types of complex structures: a primary Michaelis complex (substrate binding mode) for 26-meric cycloamylose (CA26) and a covalent intermediate for acarbose. Our study revealed that the acarbose and CA26 reactions catalyzed by potato D-enzyme involve the formation of a covalent intermediate with the donor substrate. HPAEC of reaction substrates and products revealed the activity of the potato D-enzyme on acarbose and CA26 as donor substrates. The structural and chromatography analyses provide insight into the mechanism of the coupling reaction of CA and glucose catalyzed by the potato D-enzyme. The enzymatic reaction mechanism does not involve residual hydrolysis. This could be particularly useful in preventing unnecessary starch degradation leading to reduced crop productivity. Optimization of this mechanism would be important for improvements of starch storage and productivity in crops.
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Affiliation(s)
- Kayo Imamura
- Laboratory of Enzyme Chemistry, Graduate School of Agriculture and Biological ScienceOsaka Prefecture UniversityOsakaJapan
| | | | | | - Shinichi Kitamura
- Laboratory of Biophysical Chemistry, Graduate School of Agriculture and Biological ScienceOsaka Prefecture UniversityOsakaJapan
- Present address:
Laboratory of Advanced Food Process EngineeringOsaka Prefecture University, 1‐2, Gakuen‐cho, Nakaku, Osaka, Sakai 599‐8570Japan
| | | | - Takeshi Takaha
- Biochemical Research LaboratoriesEzaki Glico Co., LtdOsakaJapan
- Present address:
Sanawa Starch Co., Ltd. 594 Unate, Kashihara, Nara 634‐8585Japan
| | - Hideaki Unno
- Graduate School of EngineeringNagasaki UniversityNagasakiJapan
- Organization for Marine Science and TechnologyNagasaki UniversityNagasakiJapan
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Janíčková Z, Janeček Š. Fungal α-amylases from three GH13 subfamilies: their sequence-structural features and evolutionary relationships. Int J Biol Macromol 2020; 159:763-772. [DOI: 10.1016/j.ijbiomac.2020.05.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 01/12/2023]
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A detailed in silico analysis of the amylolytic family GH126 and its possible relatedness to family GH76. Carbohydr Res 2020; 494:108082. [PMID: 32634753 DOI: 10.1016/j.carres.2020.108082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/13/2020] [Accepted: 06/14/2020] [Indexed: 11/21/2022]
Abstract
The glycoside hydrolase (GH) family 126 was established based on the X-ray structure determination of the amylolytic enzyme CPF_2247 from Clostridium perfringens genome. Its original identification as a putative carbohydrate-active enzyme was based on its low, yet significant sequence identity to members of the family GH8, which are inverting endo-β-1,4-glucanases. As the family GH8 forms the clan GH-M with GH48, the CPF_2247 protein also exhibits similarities with members of the family GH48. The original screening of the CPF_2247 on carbohydrate substrates demonstrated its activity on glycogen and amylose, thus classifying this protein as an "α-amylase". It should be pointed out, however, there are apparent inconsistencies concerning the exact enzyme specificity of the "amylase" CPF_2247, since it exhibits both the endo- and exo-fashion of action. The family GH126 currently counts ~1000 amino acid sequences solely from Bacteria; all belonging to the phylum Firmicutes. The present study delivers the first detailed bioinformatics study of 117 selected amino acid sequences from the family GH126, featuring the insightful sequence-structure comparison with the aim to define seven conserved sequence regions and elucidate the evolutionary relationships within the family. In addition, a comparative structural analysis of the GH126 members with representatives of other GH families adopting the same (α/α)6-barrel catalytic domain fold indicates the possible sharing a catalytic residue between the families GH126 and GH76.
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Huang P, Wu S, Yang S, Yan Q, Jiang Z. Structural basis of carbohydrate binding in domain C of a type I pullulanase fromPaenibacillus barengoltzii. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:447-457. [DOI: 10.1107/s205979832000409x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 03/24/2020] [Indexed: 11/10/2022]
Abstract
Pullulanase (EC 3.2.1.41) is a well known starch-debranching enzyme that catalyzes the cleavage of α-1,6-glycosidic linkages in α-glucans such as starch and pullulan. Crystal structures of a type I pullulanase fromPaenibacillus barengoltzii(PbPulA) and ofPbPulA in complex with maltopentaose (G5), maltohexaose (G6)/α-cyclodextrin (α-CD) and β-cyclodextrin (β-CD) were determined in order to better understand substrate binding to this enzyme.PbPulA belongs to glycoside hydrolase (GH) family 13 subfamily 14 and is composed of three domains (CBM48, A and C). Three carbohydrate-binding sites identified inPbPulA were located in CBM48, near the active site and in domain C, respectively. The binding site in CBM48 was specific for β-CD, while that in domain C has not been reported for other pullulanases. The domain C binding site had higher affinity for α-CD than for G6; a small motif (FGGEH) seemed to be one of the major determinants for carbohydrate binding in this domain. Structure-based mutations of several surface-exposed aromatic residues in CBM48 and domain C had a debilitating effect on the activity of the enzyme. These results suggest that both CBM48 and domain C play a role in binding substrates. The crystal forms described contribute to the understanding of pullulanase domain–carbohydrate interactions.
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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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Ban X, Dhoble AS, Li C, Gu Z, Hong Y, Cheng L, Holler TP, Kaustubh B, Li Z. Bacterial 1,4-α-glucan branching enzymes: characteristics, preparation and commercial applications. Crit Rev Biotechnol 2020; 40:380-396. [DOI: 10.1080/07388551.2020.1713720] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Xiaofeng Ban
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
| | - Abhishek S. Dhoble
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
| | - Caiming Li
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
| | - Zhengbiao Gu
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
| | - Yan Hong
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
| | - Li Cheng
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
| | - Tod P. Holler
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Bhalerao Kaustubh
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
| | - Zhaofeng Li
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, People’s Republic of China
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Improvement of the Thermostability and Activity of Pullulanase from Anoxybacillus sp. WB42. Appl Biochem Biotechnol 2020; 191:942-954. [DOI: 10.1007/s12010-020-03249-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/08/2020] [Indexed: 12/14/2022]
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Li P, Huang Z, She Y, Qin S, Gao W, Cao Y, Liu X. An assessment of the interaction for three Chrysanthemum indicum flavonoids and α-amylase by surface plasmon resonance. Food Sci Nutr 2020; 8:620-628. [PMID: 31993185 PMCID: PMC6977516 DOI: 10.1002/fsn3.1349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 10/12/2019] [Accepted: 10/15/2019] [Indexed: 11/23/2022] Open
Abstract
This study evaluated the interaction of Chrysanthemum indicum (CI) flavonoids (luteolin, acacetin, and buddleoside) with α-amylase. Surface plasmon resonance (SPR) assay showed their equilibrium dissociation constants (KD ) are 1.9695 ± 0.12, 2.9240 ± 0.20, and 3.2966 ± 0.08 mM at pH 6.0, respectively. Furthermore, their binding affinities were influenced by KCl, MgCl2, and CaCl2. Enzymatic kinetic studies revealed that three flavonoids exhibited noncompetitive α-amylase inhibitory activity. The inhibitory sequence is luteolin > acacetin > buddleoside, which was in accordance with the results of binding affinity from SPR. 1,1-diphenyl-2-picryl hydrazyl radical assay demonstrated that antioxidant activities of three flavonoids were inhibited significantly with α-amylase. Meanwhile, the study reveals that hydroxyl on C'-4, C'-5, and C-7 of flavonoids play an important role on the interaction of three flavonoids with α-amylase. Also, SPR could be used as sensor for rapid screening inhibitors of α-amylase and provide useful information for the application of C. indicum flavonoids in food and pharmaceutical area.
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Affiliation(s)
- Pao Li
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
| | - Zhao Huang
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
| | - Yin She
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
| | - Si Qin
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
- Hunan Co‐Innovation Center for Utilization of Botanical Functional IngredientsChangshaChina
| | - Wanru Gao
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
| | - Yanan Cao
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
| | - Xia Liu
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
- Hunan Co‐Innovation Center for Utilization of Botanical Functional IngredientsChangshaChina
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Bashary R, Vyas M, Nayak SK, Suttee A, Verma S, Narang R, Khatik GL. An Insight of Alpha-amylase Inhibitors as a Valuable Tool in the Management of Type 2 Diabetes Mellitus. Curr Diabetes Rev 2020; 16:117-136. [PMID: 31237215 DOI: 10.2174/1573399815666190618093315] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/14/2019] [Accepted: 05/05/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Among the millions of people around the world, the most prevalent metabolic disorder is diabetes mellitus. Due to the drawbacks which are associated with commercially available antidiabetic agents, new therapeutic approaches are needed to be considered. Alpha-amylase is a membrane- bound enzyme which is responsible for the breakdown of polysaccharides such as starch to monosaccharides which can be absorbed. METHODS We searched the scientific database using alpha-amylase, diabetes, antidiabetic agents as the keywords. Here in, only peer-reviewed research articles were collected which were useful to our current work. RESULTS To overcome the research gap, the alpha-amylase enzyme is regarded as a good target for antidiabetic agents to design the drug and provide an alternate approach for the treatment of type 2 diabetes mellitus. Basically, alpha-amylase inhibitors are classified into two groups: proteinaceous inhibitors, and non-proteinaceous inhibitors. Recently, non-proteinaceous inhibitors are being explored which includes chalcones, flavones, benzothiazoles, etc. as the potential antidiabetic agents. CONCLUSION Herein, we discuss various potential antidiabetic agents which are strategically targeted alpha-amylase enzyme. These are having lesser side effects as compared to other antidiabetic agents, and are proposed to prevent the digestion and absorption of glucose leading to a decrease in the blood glucose level.
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Affiliation(s)
- Roqia Bashary
- Department of Pharmaceutical Chemistry, Kabul University, Kabul, Afghanistan
| | - Manish Vyas
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, 144411, India
| | - Surendra Kumar Nayak
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, 144411, India
| | - Ashish Suttee
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, 144411, India
| | - Surajpal Verma
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, 144411, India
| | - Rakesh Narang
- Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra, Haryana, 136119, India
| | - Gopal L Khatik
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, 144411, India
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Yang Y, Zhu Y, Obaroakpo JU, Zhang S, Lu J, Yang L, Ni D, Pang X, Lv J. Identification of a novel type I pullulanase from Fervidobacterium nodosum Rt17-B1, with high thermostability and suitable optimal pH. Int J Biol Macromol 2020; 143:424-433. [DOI: 10.1016/j.ijbiomac.2019.10.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/09/2019] [Accepted: 10/11/2019] [Indexed: 01/06/2023]
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Zhang Z, Jin T, Xie X, Ban X, Li C, Hong Y, Cheng L, Gu Z, Li Z. Structure of maltotetraose-forming amylase from Pseudomonas saccharophila STB07 provides insights into its product specificity. Int J Biol Macromol 2019; 154:1303-1313. [PMID: 31751711 DOI: 10.1016/j.ijbiomac.2019.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/25/2019] [Accepted: 11/02/2019] [Indexed: 11/27/2022]
Abstract
The maltooligosaccharide-forming amylases (MFAses) degrade starch into maltooligosaccharides which potentially benefit human diet and grow popular in food processing, but little has been studied about their product specificity and structures. We focused on this topic and provide evidence through an X-ray crystal structure of the maltotetraose (G4)-forming amylase from Pseudomonas saccharophila STB07 (MFAps), as well as co-crystal structures of MFAps with G4 and with pseudo-maltoheptaose (pseudo-G7) determined at up to 1.1 Å resolution. G4 and pseudo-G7 occupy active cleft subsites -4 to -1 and -4 to +3 respectively. Binding induces conformational changes in the active sites except Asp193, working as the base catalyst. Comparison of the MFAps structure with those of other α-amylases revealed obvious differences in the loop structures providing dominant interactions between protein and substrate in the non-reducing side of the active sites cleft. These structures at the non-reducing end may govern the G4 specificity of MFAps and also be relevant to its exo-type action pattern.
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Affiliation(s)
- Ziqian Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Tengchuan Jin
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA; School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027, People's Republic of China.
| | - Xiaofang Xie
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Yan Hong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, 214122, People's Republic of China.
| | - Li Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, 214122, People's Republic of China.
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, 214122, People's Republic of China.
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A new GH13 subfamily represented by the α-amylase from the halophilic archaeon Haloarcula hispanica. Extremophiles 2019; 24:207-217. [PMID: 31734852 DOI: 10.1007/s00792-019-01147-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 11/05/2019] [Indexed: 01/16/2023]
Abstract
α-Amylase catalyzes the endohydrolysis of α-1,4-glucosidic linkages in starch and related α-glucans. In the CAZy database, most α-amylases have been classified into the family GH13 counting at present more than 80,000 sequences and ~ 30 different enzyme specificities. The family has already been divided into 42 subfamilies, but additional subfamilies are still emerging. The present bioinformatics study was undertaken in an effort to propose a novel GH13 subfamily around the experimentally characterized α-amylase from the halophilic archaeon Haloarcula hispanica, which until now has not been assigned to any GH13 subfamily. The in silico analysis resulted in collecting a convincing group of putative haloarchaeal α-amylase homologues sharing sequence similarities mainly in their conserved sequence regions (CSRs) and forming a cluster in the evolutionary tree, which is well separated from representatives of established GH13 subfamilies. One of the most exclusive sequence features of the novel GH13 subfamily is the tyrosine (Tyr79 in H. hispanica α-amylase numbering) succeeding the glycine at the beginning of the CSR-VI at the β2 strand of the catalytic TIM-barrel. Evolutionarily, the novel GH13 α-amylase subfamily was most closely related to two clusters of GH13 subfamilies with the specificity of α-amylase, i.e. subfamilies GH13_5, 6 and 7 as well as GH13_15, 24, 27 and 28.
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Plaza-Vinuesa L, Hernandez-Hernandez O, Moreno FJ, de Las Rivas B, Muñoz R. Unravelling the diversity of glycoside hydrolase family 13 α-amylases from Lactobacillus plantarum WCFS1. Microb Cell Fact 2019; 18:183. [PMID: 31655584 PMCID: PMC6815381 DOI: 10.1186/s12934-019-1237-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/17/2019] [Indexed: 11/10/2022] Open
Abstract
Background α-Amylases specifically catalyse the hydrolysis of the internal α-1, 4-glucosidic linkages of starch. Glycoside hydrolase (GH) family 13 is the main α-amylase family in the carbohydrate-active database. Lactobacillus plantarum WCFS1 possesses eleven proteins included in GH13 family. Among these, proteins annotated as maltose-forming α-amylase (Lp_0179) and maltogenic α-amylase (Lp_2757) were included. Results In this study, Lp_0179 and Lp_2757 L. plantarum α-amylases were structurally and biochemically characterized. Lp_2757 displayed structural features typical of GH13_20 subfamily which were absent in Lp_0179. Genes encoding Lp_0179 (Amy2) and Lp_2757 were cloned and overexpressed in Escherichia coli BL21(DE3). Purified proteins showed high hydrolytic activity on pNP-α-D-maltopyranoside, being the catalytic efficiency of Lp_0179 remarkably higher. In relation to the hydrolysis of starch-related carbohydrates, Lp_0179 only hydrolysed maltopentaose and dextrin, demonstrating that is an exotype glucan hydrolase. However, Lp_2757 was also able to hydrolyze cyclodextrins and other non-cyclic oligo- and polysaccharides, revealing a great preference towards α-1,4-linkages typical of maltogenic amylases. Conclusions The substrate range as well as the biochemical properties exhibited by Lp_2757 maltogenic α-amylase suggest that this enzyme could be a very promising enzyme for the hydrolysis of α-1,4 glycosidic linkages present in a broad number of starch-carbohydrates, as well as for the investigation of an hypothetical transglucosylation activity under appropriate reaction conditions.
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Affiliation(s)
- Laura Plaza-Vinuesa
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición, ICTAN (CSIC), Juan de la Cierva 3, 28006, Madrid, Spain
| | - Oswaldo Hernandez-Hernandez
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI (UAM+CSIC), Nicolás Cabrera 9, 28049, Madrid, Spain
| | - F Javier Moreno
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI (UAM+CSIC), Nicolás Cabrera 9, 28049, Madrid, Spain
| | - Blanca de Las Rivas
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición, ICTAN (CSIC), Juan de la Cierva 3, 28006, Madrid, Spain
| | - Rosario Muñoz
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición, ICTAN (CSIC), Juan de la Cierva 3, 28006, Madrid, Spain.
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Pan S, Yao T, Du L, Wei Y. Site-saturation mutagenesis at amino acid 329 of Klebsiella pneumoniae halophilic α-amylase affects enzymatic properties. J Biosci Bioeng 2019; 129:155-159. [PMID: 31575478 DOI: 10.1016/j.jbiosc.2019.09.002] [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: 07/11/2019] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 11/25/2022]
Abstract
Halophilic α-amylases possess optimal activity in high salt concentrations. Therefore, they can be used in many extreme conditions in industrialised production. In the present work, a halophilic α-amylase (KP) from Klebsiella pneumoniae was characterised, and it exhibited a high specific activity of 3512 U/mg under optimal conditions of 2 M NaCl at 50°C and pH 6.5, but only 97 U/mg in the absence of salt. Furthermore, threonine at position 329 (Thr-329) was found to be related to the non-halophilic properties of KP according to PCR-based site-saturation mutagenesis. The activity of a mutant KP in which this threonine was replaced by aspartic acid was improved 14.6-fold compared with the native enzyme under salt-free conditions, and was increased by 14.8% in the absence of salt. Additionally, the optimal enzymatic properties of KP, including pH and temperature, were altered very little by the amino acid replacement. A further three halophilic α-amylases displayed similar mutational results. The findings provide a reference for bidirectional transformation of KP and similar halophilic enzymes.
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Affiliation(s)
- Shiyou Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Tiantian Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Liqin Du
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Yutuo Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China.
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