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Frima FK, Thufail MA, Madhani IN, Nafisah Z, Shofiyah SS, Ulpiyana A, Puspasari F, Aditama R, Ihsanawati I, Natalia D. Probing the function of C-terminal region of recombinant α-amylase BmaN1 from Bacillus megaterium NL3. Microbiol Spectr 2024:e0335123. [PMID: 39212453 DOI: 10.1128/spectrum.03351-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 06/12/2024] [Indexed: 09/04/2024] Open
Abstract
The α-amylase BmaN1 from Bacillus megaterium NL3 is a member of GH13_45 subfamily that has a conserved C-terminal region of approximately 30 residues. This region features a motif of five aromatic amino acids predicted to play a role in starch binding. This study aimed to unravel the role of the C-terminal region in starch hydrolysis. The full-length and C-terminally truncated forms of BmaN1 (BmaN1∆C) were expressed in Escherichia coli ArcticExpress (DE3), resulting in proteins with molecular weights of 56 kDa and 49 kDa, respectively. They exhibited comparable enzymatic activity in the hydrolysis of soluble starch, displaying versatility across a wide range of pH values, temperatures, and NaCl concentrations. BmaN1 and BmaN1∆C activities were inhibited by acarbose and were reduced by SDS and EDTA. In terms of binding and degrading the starch granules, BmaN1∆C showed lower affinity and activity in comparison to BmaN1. Our study indicates that the C-terminal region of BmaN1 significantly enhances its binding affinity and degrading the raw starches.IMPORTANCEα-Amylase (EC 3.2.1.1) stands as an endo-acting enzyme, essential for catalyzing the hydrolysis of α-1,4 glycosidic bonds within starch molecules. The relevance of α-amylases in biotechnological applications is substantial, constituting approximately 30% of the global enzyme market. Among these enzymes, BmaN1 was the first α-amylase identified to possess distinct catalytic residues within the GH13 family. BmaN1 from B. megaterium NL3 belongs to the GH13_45 subfamily. This subfamily is characterized by a conserved C-terminal region consisting of approximately 30 residues that contains a motif of five aromatic residues predicted to be involved in starch binding. Our study shows that the C-terminal effectively contributes to binding and degrading the raw starch granules. This pioneering research on BmaN1 expands our understanding of α-amylases and holds promise for innovative biotechnological advancements.
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Affiliation(s)
- Fina Khaerunnisa Frima
- Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
- Department of Chemistry, Faculty of Science, Institut Teknologi Sumatera, Lampung Selatan, Indonesia
| | - Muhammad Akbar Thufail
- Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
| | - Indri Novia Madhani
- Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
| | - Zahrotun Nafisah
- Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
| | - Sofi Siti Shofiyah
- Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
- Department of Chemistry, Faculty of Science and Marine, Universitas Oso, Pontianak, Indonesia
| | - Ayra Ulpiyana
- Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
| | - Fernita Puspasari
- Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
| | - Reza Aditama
- Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
| | - Ihsanawati Ihsanawati
- Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
| | - Dessy Natalia
- Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
- Biosciences and Biotechnology Research Center, Institut Teknologi Bandung, Bandung, Indonesia
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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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Barman D, Dkhar MS. Purification and characterization of moderately thermostable raw-starch digesting α-amylase from endophytic Streptomyces mobaraensis DB13 associated with Costus speciosus. J GEN APPL MICROBIOL 2024; 69:293-300. [PMID: 37635076 DOI: 10.2323/jgam.2023.08.001] [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] [Indexed: 08/29/2023]
Abstract
Endophytic actinobacteria are known to produce various enzymes with potential industrial applications. Alpha-amylase is an important class of industrial enzyme with a multi-dimensional utility. The present experiment was designed to characterize a moderately thermostable α-amylase producing endophytic Streptomyces mobaraensis DB13 isolated from Costus speciosus (J. Koenig) Sm. The enzyme was purified using 60% ammonium sulphate precipitation, dialysis, and Sephadex G-100 column chromatography. Based on 12% SDS-PAGE, the molecular weight of the purified α-amylase was estimated to be 55 kDa. The maximum α-amylase activity was achieved at pH 7.0, 50°C and it retained 80% of its activity at both pH 7.0 and 8.0 after incubation for 2 h. The α-mylase activity is strongly enhanced by Ca2+, Mg2+, and inhibited by Ba2+. The activity remains stable in the presence of Tween-80, SDS, PMSF, and Triton X-100; however, β-mercaptoethanol, EDTA, and H2O2 reduced the activity. The kinetic parameters Km and Vmax values for this α-amylase were calculated as 2.53 mM and 29.42 U/mL respectively. The α-amylase had the ability to digest various raw starches at a concentration of 10 mg/mL at pH 7.0, 50°C, where maize and rice are the preferred substrates. The digestion starts after 4 h of incubation, which reaches maximum after 48 h of incubation. These results suggest that S. mobaraensis DB13 is a potential source of moderately thermostable α-amylase enzyme, that effciently hydrolyzes raw starch. It suggesting that this α-amylase is a promising candidate to be use for industrial purposes.
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Affiliation(s)
- Dina Barman
- Microbial Ecology Laboratory, Centre for Advanced Studies in Botany, Department of Botany
- Department of Microbiology, The Assam Royal Global University
| | - Mamtaj S Dkhar
- Microbial Ecology Laboratory, Centre for Advanced Studies in Botany, Department of Botany
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4
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Sequence-structural features and evolution of the α-amylase family GH119 revealed by the in silico analysis of its relatedness to the family GH57. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01349-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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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: 8] [Impact Index Per Article: 4.0] [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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Cakmak U, Tuncay FO, Kolcuoğlu Y. Cold active α-amylase obtained from Cladophora hutchinsiae-Purification, biochemical characterization and some potential applications. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Functional Characterization of Recombinant Raw Starch Degrading α-Amylase from Roseateles terrae HL11 and Its Application on Cassava Pulp Saccharification. Catalysts 2022. [DOI: 10.3390/catal12060647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Exploring new raw starch-hydrolyzing α-amylases and understanding their biochemical characteristics are important for the utilization of starch-rich materials in bio-industry. In this work, the biochemical characteristics of a novel raw starch-degrading α-amylase (HL11 Amy) from Roseateles terrae HL11 was firstly reported. Evolutionary analysis revealed that HL11Amy was classified into glycoside hydrolase family 13 subfamily 32 (GH13_32). It contains four protein domains consisting of domain A, domain B, domain C and carbohydrate-binding module 20 (CMB20). The enzyme optimally worked at 50 °C, pH 4.0 with a specific activity of 6270 U/mg protein and 1030 raw starch-degrading (RSD) U/mg protein against soluble starch. Remarkably, HL11Amy exhibited activity toward both raw and gelatinized forms of various substrates, with the highest catalytic efficiency (kcat/Km) on starch from rice, followed by potato and cassava, respectively. HL11Amy effectively hydrolyzed cassava pulp (CP) hydrolysis, with a reducing sugar yield of 736 and 183 mg/g starch from gelatinized and raw CP, equivalent to 72% and 18% conversion based on starch content in the substrate, respectively. These demonstrated that HL11Amy represents a promising raw starch-degrading enzyme with potential applications in starch modification and cassava pulp saccharification.
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Lekakarn H, Bunterngsook B, Pajongpakdeekul N, Prongjit D, Champreda V. A novel low temperature active maltooligosaccharides-forming amylase from Bacillus koreensis HL12 as biocatalyst for maltooligosaccharide production. 3 Biotech 2022; 12:134. [PMID: 35615748 DOI: 10.1007/s13205-022-03188-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/26/2022] [Indexed: 11/01/2022] Open
Abstract
Maltooligosaccharide-forming amylases (MFAses) are promising enzymes for a variety of industrial applications. In this study, a maltooligosaccharide-forming amylase (BkAmy) isolated from Bacillus koreensis HL12 was first heterologous expressed and characterized. According to structural-sequence alignment, BkAmy contained seven conserved regions which are the signature of a novel GH13 subfamily. The gene was expressed in Pichia pastoris KM71 as an extracellular protein with a volumetric activity of 3.38 U/mL culture medium after 72 h induction by 3% (w/v) of methanol. The recombinant BkAmy migrated as a single protein band with an expected size approximately of 55 kDa. BkAmy exhibited the highest catalytic activity on soluble starch with a specific activity of 42.2 U/mg at 40 °C, pH 7.0. The enzyme exhibited 65% relative activity at 30 °C, indicating its advantage on application at moderate reaction temperature desirable for energy saving and reduction of side unwanted reactions. The enzyme exhibited a specific cleavage pattern by releasing maltose (G2), maltotriose (G3) and maltotetraose (G4) from cassava starch with the highest yield of 363 mg/g substrate equivalent to 36% conversion using 40 U/g substrate at 60 min. The work demonstrates the potential of this enzyme on maltooligosaccharide production from starch to create high value-added products in starch processing industries. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03188-1.
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Zhang L, Zhong L, Wang J, Zhao Y, Zhang Y, Zheng Y, Dong W, Ye X, Huang Y, Li Z, Cui Z. Efficient hydrolysis of raw starch by a maltohexaose-forming α-amylase from Corallococcus sp. EGB. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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10
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Ben Hlima H, Karray A, Dammak M, Elleuch F, Michaud P, Fendri I, Abdelkafi S. Production and structure prediction of amylases from Chlorella vulgaris. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:51046-51059. [PMID: 33973124 DOI: 10.1007/s11356-021-14357-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Amylases are enzymes required for starch degradation and are naturally produced by many microorganisms. These enzymes are used in several fields such as food processing, beverage, and medicine as well as in the formulation of enzymatic detergents proving their significance in modern biotechnology. In this study, a three-stage growth mode was applied to enhance starch production and amylase detection from Chlorella vulgaris. Stress conditions applied in the second stage of cultivation led to an accumulation of proteins (75% DW) and starch (21% DW) and a decrease in biomass. Amylase activities were detected and they showed high production levels especially on day 3 (35 U/ml) and day 5 (22.5 U/ml) of the second and third stages, respectively. The bioinformatic tools used to seek amylase protein sequences from TSA database of C. vulgaris revealed 7 putative genes encoding for 4 α-amylases, 2 β-amylases, and 1 isoamylase. An in silico investigation showed that these proteins are different in their lengths as well as in their cellular localizations and oligomeric states though they share common features like CSRs of GH13 family or active site of GH14 family. In brief, this study allowed for the production and in silico characterization of amylases from C. vulgaris.
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Affiliation(s)
- Hajer Ben Hlima
- Laboratoire de Génie Enzymatique et de Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038, Sfax, Tunisia
| | - Aida Karray
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3018, Sfax, Tunisia
| | - Mouna Dammak
- Laboratoire de Génie Enzymatique et de Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038, Sfax, Tunisia
| | - Fatma Elleuch
- Laboratoire de Génie Enzymatique et de Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038, Sfax, Tunisia
| | - Philippe Michaud
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut Pascal, F-63000, Clermont-Ferrand, France
| | - Imen Fendri
- Laboratoire de Biotechnologie des Plantes Appliquée à l'Amélioration des Plantes Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
| | - Slim Abdelkafi
- Laboratoire de Génie Enzymatique et de Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038, Sfax, Tunisia.
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Microbial amylolytic enzymes in foods: Technological importance of the Bacillus genus. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Paul JS, Gupta N, Beliya E, Tiwari S, Jadhav SK. Aspects and Recent Trends in Microbial α-Amylase: a Review. Appl Biochem Biotechnol 2021; 193:2649-2698. [PMID: 33715051 DOI: 10.1007/s12010-021-03546-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/26/2021] [Indexed: 10/21/2022]
Abstract
α-Amylases are the oldest and versatile starch hydrolysing enzymes which can replace chemical hydrolysis of starch in industries. It cleaves the α-(1,4)-D-glucosidic linkage of starch and other related polysaccharides to yield simple sugars like glucose, maltose and limit dextrin. α-Amylase covers about 30% shares of the total enzyme market. On account of their superior features, α-amylase is the most widely used among all the existing amylases for hydrolysis of polysaccharides. Endo-acting α-amylase of glycoside hydrolase family 13 is an extensively used biocatalyst and has various biotechnological applications like in starch processing, detergent, textile, paper and pharmaceutical industries. Apart from these, it has some novel applications including polymeric material for drug delivery, bioremediating agent, biodemulsifier and biofilm inhibitor. The present review will accomplish the research gap by providing the unexplored aspects of microbial α-amylase. It will allow the readers to know about the works that have already been done and the latest trends in this field. The manuscript has covered the latest immobilization techniques and the site-directed mutagenesis approaches which are readily being performed to confer the desirable property in wild-type α-amylases. Furthermore, it will state the inadequacies and the numerous obstacles coming in the way of its production during upstream and downstream steps and will also suggest some measures to obtain stable and industrial-grade α-amylase.
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Affiliation(s)
- Jai Shankar Paul
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India
| | - Nisha Gupta
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India
| | - Esmil Beliya
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India.,Department of Botany, Govt. College, Bichhua, Chhindwara, MP, 480111, India
| | - Shubhra Tiwari
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India
| | - Shailesh Kumar Jadhav
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, CG, 492010, India.
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Alpha Amylase from Bacillus pacificus Associated with Brown Algae Turbinaria ornata: Cultural Conditions, Purification, and Biochemical Characterization. Processes (Basel) 2020. [DOI: 10.3390/pr9010016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We aimed in the current study, the identification of a marine bacterial amylase produced by Bacillus pacificus, which was associated with Turbinaria ornata. Cultural conditions were optimized for the highest amylase production on Tryptic soy broth media supplemented with starch 1% at initial pH 9, 55 °C for 24 h. The newly purified amylase was characterized for a possible biotechnological application. Data indicated that the obtained amylase with a molecular weight of 40 kD and the N-terminal sequence of the first 30 amino acids of amBp showed a high degree of homology with known alpha amylase, and was stable at 60 °C of pH 11. Among the tested substrate analogs, amBp was almost fully active on Alylose and Alylopectine (97%), but moderately hydrolyzed glycogen < sucrose < maltose < lactose. Therefore, the current amylase mainly generated maltohexaose from starch. Mg2+ and Zn2+ improved amylase activity up to 170%. While ethylenediamine tetraacetic acid (EDTA) similarly induced the greatest activity with purified amylase, PCMB had the least effect. Regarding all these characteristics, amylase from marine bacterial symbionts amBp has a new promising feature for probable therapeutic, industrial, and nutritional applications.
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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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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 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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Janeček Š, Mareček F, MacGregor EA, Svensson B. Starch-binding domains as CBM families-history, occurrence, structure, function and evolution. Biotechnol Adv 2019; 37:107451. [PMID: 31536775 DOI: 10.1016/j.biotechadv.2019.107451] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/01/2019] [Accepted: 09/15/2019] [Indexed: 01/05/2023]
Abstract
The term "starch-binding domain" (SBD) has been applied to a domain within an amylolytic enzyme that gave the enzyme the ability to bind onto raw, i.e. thermally untreated, granular starch. An SBD is a special case of a carbohydrate-binding domain, which in general, is a structurally and functionally independent protein module exhibiting no enzymatic activity but possessing potential to target the catalytic domain to the carbohydrate substrate to accommodate it and process it at the active site. As so-called families, SBDs together with other carbohydrate-binding modules (CBMs) have become an integral part of the CAZy database (http://www.cazy.org/). The first two well-described SBDs, i.e. the C-terminal Aspergillus-type and the N-terminal Rhizopus-type have been assigned the families CBM20 and CBM21, respectively. Currently, among the 85 established CBM families in CAZy, fifteen can be considered as families having SBD functional characteristics: CBM20, 21, 25, 26, 34, 41, 45, 48, 53, 58, 68, 69, 74, 82 and 83. All known SBDs, with the exception of the extra long CBM74, were recognized as a module consisting of approximately 100 residues, adopting a β-sandwich fold and possessing at least one carbohydrate-binding site. The present review aims to deliver and describe: (i) the SBD identification in different amylolytic and related enzymes (e.g., CAZy GH families) as well as in other relevant enzymes and proteins (e.g., laforin, the β-subunit of AMPK, and others); (ii) information on the position in the polypeptide chain and the number of SBD copies and their CBM family affiliation (if appropriate); (iii) structure/function studies of SBDs with a special focus on solved tertiary structures, in particular, as complexes with α-glucan ligands; and (iv) the evolutionary relationships of SBDs in a tree common to all SBD CBM families (except for the extra long CBM74). Finally, some special cases and novel potential SBDs are also introduced.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia.
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia
| | - E Ann MacGregor
- 2 Nicklaus Green, Livingston EH54 8RX, West Lothian, United Kingdom
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
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Karim KMR, Husaini A, Sing NN, Tasnim T, Mohd Sinang F, Hussain H, Hossain MA, Roslan H. Characterization and expression in Pichia pastoris of a raw starch degrading glucoamylase (GA2) derived from Aspergillus flavus NSH9. Protein Expr Purif 2019; 164:105462. [PMID: 31351992 DOI: 10.1016/j.pep.2019.105462] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/19/2019] [Accepted: 07/24/2019] [Indexed: 11/25/2022]
Abstract
The Aspergillus flavus NSH9 gene, encoding a pH and thermostable glucoamylase with a starch binding domain (SBD), was expressed in Pichia pastoris to produce recombinant glucoamylase (rGA2). The full-length glucoamylase gene (2039 bp), and cDNA (1839 bp) encode a 612 amino acid protein most similar to glucoamylase from Aspergillus oryzae RIB40; the first 19 amino acids are presumed to be a signal peptide for secretion, and the SBD is at the C-terminal. The cDNA was successfully secreted by Pichia at 8.23 U mL-1, and the rGA2 was found to be: a 80 kDa monomer, stable from pH 3.0-9.0, with optimum catalytic activity at pH 5.0, active at temperatures up to 80°C (rGA2 retained 58% of its activity after 60 min of incubation at 70°C), and metal ions such as Na+, K+, Ca++ and Mg++ enhanced rGA2 enzyme activity. The starch degrading ability of rGA2 was also observed on raw sago starch and where prolonged incubation generated larger, deeper, holes on the starch granules, indicating rGA2 is an excellent candidate for industrial starch processing applications.
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Affiliation(s)
| | - Ahmad Husaini
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota, Samarahan, Sarawak, Malaysia.
| | - Ngieng Ngui Sing
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota, Samarahan, Sarawak, Malaysia
| | - Tasmia Tasnim
- Department of Nutrition and Food Engineering, Daffodil International University, Dhaka, 1207, Bangladesh
| | - Fazia Mohd Sinang
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota, Samarahan, Sarawak, Malaysia
| | - Hasnain Hussain
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota, Samarahan, Sarawak, Malaysia
| | - Md Anowar Hossain
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Hairul Roslan
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota, Samarahan, Sarawak, Malaysia
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Sakwa L, Cripwell RA, Rose SH, Viljoen-Bloom M. Consolidated bioprocessing of raw starch with Saccharomyces cerevisiae strains expressing fungal alpha-amylase and glucoamylase combinations. FEMS Yeast Res 2019; 18:5061630. [PMID: 30085077 DOI: 10.1093/femsyr/foy085] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/27/2018] [Indexed: 01/10/2023] Open
Abstract
Cost-effective consolidated bioprocessing (CBP) of raw starch for biofuel production requires recombinant Saccharomyces cerevisiae strains expressing α-amylases and glucoamylases. Native Aureobasidium pullulans apuA, Aspergillus terreus ateA, Cryptococcus sp. S-2 cryA and Saccharomycopsis fibuligera sfiA genes encoding raw-starch α-amylases were cloned and expressed in the S. cerevisiae Y294 laboratory strain. Recombinant S. cerevisiae Y294[ApuA] and Y294[AteA] strains produced the highest extracellular α-amylase activities (2.17 U mL-1 and 2.98 U mL-1, respectively). Both the ApuA and AteA α-amylases displayed a preference for pH 4 to 5 and retained more than 75% activity after 5 days at 30°C. When ateA was co-expressed with the previously reported Aspergillus. tubingensis glucoamylase gene (glaA), the amylolytic S. cerevisiae Y294[AteA-GlaA] strain produced 45.77 g L-1 ethanol after 6 days. Ethanol production by this strain was improved with the addition of either 2.83 μL STARGEN 002 (54.54 g L-1 ethanol and 70.44% carbon conversion) or 20 μL commercial glucoamylase from Sigma-Aldrich (73.80 g L-1 ethanol and 90.19% carbon conversion). This is the first report of an engineered yeast strain that can replace up to 90% of the enzymes required for raw starch hydrolysis, and thus contributes to the realisation of a CBP yeast for starch-based biofuel production.
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Affiliation(s)
- L Sakwa
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - R A Cripwell
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - S H Rose
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - M Viljoen-Bloom
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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Fang W, Xue S, Deng P, Zhang X, Wang X, Xiao Y, Fang Z. AmyZ1: a novel α-amylase from marine bacterium Pontibacillus sp. ZY with high activity toward raw starches. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:95. [PMID: 31044008 PMCID: PMC6477751 DOI: 10.1186/s13068-019-1432-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 04/12/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Starch is an inexpensive and renewable raw material for numerous industrial applications. However, most starch-based products are not cost-efficient due to high-energy input needed in traditional enzymatic starch conversion processes. Therefore, α-amylase with high efficiency to directly hydrolyze high concentration raw starches at a relatively lower temperature will have a profound impact on the efficient application of starch. RESULTS A novel raw starch digesting α-amylase (named AmyZ1) was screened and cloned from a deep-sea bacterium Pontibacillus sp. ZY. Phylogenetic analysis showed that AmyZ1 was a member of subfamily 5 of glycoside hydrolase family 13. When expressed in Escherichia coli, the recombinant AmyZ1 showed high activity at pH 6.0-7.5 and 25-50 °C. Its optimal pH and temperature were 7.0 and 35 °C, respectively. Similar to most α-amylases, AmyZ1 activity was enhanced (2.4-fold) by 1.0 mM Ca2+. Its half-life time at 35 °C was also extended from about 10 min to 100 min. In comparison, AmyZ1 showed a broad substrate specificity toward raw starches, including those derived from rice, corn, and wheat. The specific activity of AmyZ1 towards raw rice starch was 12,621 ± 196 U/mg, much higher than other reported raw starch hydrolases. When used in raw starch hydrolyzing process, AmyZ1 hydrolyzed 52%, 47% and 38% of 30% (w/v) rice, corn, and wheat starch after 4 h incubation. It can also hydrolyze marine raw starch derived from Chlorella pyrenoidosa, resulting in 50.9 mg/g DW (dry weight of the biomass) of reducing sugars after 4 h incubation at 35 °C. Furthermore, when hydrolyzing raw corn starch using the combination of AmyZ1 and commercial glucoamylase, the hydrolysis rate reached 75% after 4.5 h reaction, notably higher than that obtained in existing starch-processing industries. CONCLUSIONS As a novel raw starch-digesting α-amylase with high specific activity, AmyZ1 efficiently hydrolyzed raw starches derived from both terrestrial and marine environments at near ambient temperature, suggesting its application potential in starch-based industrial processes.
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Affiliation(s)
- Wei Fang
- School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601 Anhui China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601 Anhui China
| | - Saisai Xue
- School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601 Anhui China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601 Anhui China
| | - Pengjun Deng
- School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601 Anhui China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601 Anhui China
| | - Xuecheng Zhang
- School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601 Anhui China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601 Anhui China
| | - Xiaotang Wang
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199 USA
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601 Anhui China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601 Anhui China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, 230601 Anhui China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601 Anhui China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601 Anhui China
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Nguyen HT, Nguyen TT, Pham HTT, Nguyen QTN, Tran MT, Nguyen AH, Phan TN, Bui HTV, Dao HTT, Nguyen ATV. Fate of carotenoid-producing Bacillus aquimaris SH6 colour spores in shrimp gut and their dose-dependent probiotic activities. PLoS One 2018; 13:e0209341. [PMID: 30576365 PMCID: PMC6303041 DOI: 10.1371/journal.pone.0209341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/04/2018] [Indexed: 01/11/2023] Open
Abstract
Bacillus aquimaris SH6 spores produce carotenoids that are beneficial to white-leg shrimp (Litopenaeus vannamei) health. However, the optimal dose and mechanisms behind these effects are not well understood. We investigated the fate of SH6 spores in the gut of L. vannamei. Shrimp were divided into six groups administrated with either feed only (negative control) or SH6 spores at 5 × 106 CFU/g pellet (high dose, SH6 spore-H group), 1 × 106 CFU/g pellet (medium dose, SH6 spore-M group), 2 × 105 CFU/g pellet (low dose, SH6 spore-L group), astaxanthin at 0.5 mg/g pellet (Carophyll group), or carotenoids from SH6 vegetative cells at 5 μg/g pellet (SH6 carotenoid group). The growth rate was highest in SH6 spore-H (3.38%/day), followed by SH6 spore-M (2.84%/day) and SH6 spore-L (2.25%/day), which was significantly higher than the control (1.45%/day), Carophyll (1.53%/day) or SH6 carotenoid (1.57%/day) groups. The astaxanthin levels (1.9-2.0 μg/g shrimp) and red-colour scores (21-22) in SH6 spore-H/M were higher than the control (astaxanthin: 1.2 μg/g shrimp; red score: 20) or SH6 spore-L, but lower than the Carophyll and SH6 carotenoids. Feeding with medium and high doses of SH6 spores after 28 days resulted in respective 1.3-2-fold increases in phenol oxidase activity and 8-9 fold increases in Rho mRNA expression compared to the control and low dose group. The live-counts of SH6 in the gut gradually increased during the 28-day feeding period with SH6 spores at different concentrations, starting from 4.1, 8.2, and 5.4 × 104 CFU/g gut at day 1 and reaching 5.3, 5.1, and 4.4 × 105 CFU/g gut in the SH6-H/M/L groups, respectively, at day 28. Gut microbiota became more diversified, resulting in a 2-8-fold increase in total bacterial live-counts compared to the controls. SH6 spore germination was detected by measuring the mRNA expression of a specific sequence coding for SH6 amylase at 4 h, reaching saturation at 24 h. Our results confirm that SH6 spores colonize and germinate in the gut to improve the microbial diversity and boost the immune system of shrimp, exhibiting beneficial effects at >1 × 106 CFU/g pellet.
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Affiliation(s)
- Huong Thi Nguyen
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Thanh Xuan, Hanoi, Vietnam
| | - Tham Thi Nguyen
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Thanh Xuan, Hanoi, Vietnam
| | - Huong Thi Thu Pham
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Thanh Xuan, Hanoi, Vietnam
| | - Que Thi Ngoc Nguyen
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Thanh Xuan, Hanoi, Vietnam
| | - My Thi Tran
- ANABIO Research & Development JSC, Van Khe urban, Ha Dong, Hanoi, Vietnam
| | - Anh Hoa Nguyen
- ANABIO Research & Development JSC, Van Khe urban, Ha Dong, Hanoi, Vietnam
| | - Tuan Nghia Phan
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Thanh Xuan, Hanoi, Vietnam
| | - Ha Thi Viet Bui
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Thanh Xuan, Hanoi, Vietnam
| | - Hien Thi Thanh Dao
- Traditional Pharmacy Department, Hanoi Pharmacy University, Hanoi, Vietnam
| | - Anh Thi Van Nguyen
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi, Thanh Xuan, Hanoi, Vietnam
- * E-mail:
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22
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Cai L, Zheng SW, Shen YJ, Zheng GD, Liu HT, Wu ZY. Complete genome sequence provides insights into the biodrying-related microbial function of Bacillus thermoamylovorans isolated from sewage sludge biodrying material. BIORESOURCE TECHNOLOGY 2018; 260:141-149. [PMID: 29625286 DOI: 10.1016/j.biortech.2018.03.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/24/2018] [Accepted: 03/27/2018] [Indexed: 06/08/2023]
Abstract
To enable the development of microbial agents and identify suitable candidate used for biodrying, the existence and function of Bacillus thermoamylovorans during sewage sludge biodrying merits investigation. This study isolated a strain of B. thermoamylovorans during sludge biodrying, submitted it for complete genome sequencing and analyzed its potential microbial functions. After biodrying, the moisture content of the biodrying material decreased from 66.33% to 50.18%, and B. thermoamylovorans was the ecologically dominant Bacillus, with the primary annotations associated with amino acid transport and metabolism (9.53%) and carbohydrate transport and metabolism (8.14%). It contains 96 carbohydrate-active- enzyme-encoding gene counts, mainly distributed in glycoside hydrolases (33.3%) and glycosyl transferases (27.1%). The virulence factors are mainly associated with biosynthesis of capsule and polysaccharide capsule. This work indicates that among the biodrying microorganisms, B. thermoamylovorans has good potential for degrading recalcitrant and readily degradable components, thus being a potential microbial agent used to improve biodrying.
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Affiliation(s)
- Lu Cai
- Faculty of Architectural, Civil Engineering and Environment, Ningbo University, Ningbo 315211, China.
| | - Sheng-Wei Zheng
- Faculty of Architectural, Civil Engineering and Environment, Ningbo University, Ningbo 315211, China; Institute of Energy and Environmental Protection, Chinese Academy of Agricultural Engineering, Beijing 100125, China
| | - Yu-Jun Shen
- Institute of Energy and Environmental Protection, Chinese Academy of Agricultural Engineering, Beijing 100125, China
| | - Guo-Di Zheng
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Tao Liu
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-Ying Wu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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23
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Amelia TSM, Amirul AAA, Saidin J, Bhubalan K. Identification of Cultivable Bacteria from Tropical Marine Sponges and Their Biotechnological Potentials. Trop Life Sci Res 2018; 29:187-199. [PMID: 30112149 PMCID: PMC6072720 DOI: 10.21315/tlsr2018.29.2.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Marine sponges are acknowledged as bacterial hotspots in the oceanic biome. Aquatic bacteria are being investigated comprehensively for bioactive complexes and secondary metabolites. Cultivable bacteria associated with different species of sea sponges in South China Sea waters adjacent to Bidong Island, Terengganu were identified. Molecular identification was accomplished using 16S rRNA gene cloning and sequencing. Fourteen bacterial species were identified and their phylogenetic relationships were analysed by constructing a neighbour-joining tree with Molecular Evolutionary Genetics Analysis 6. The identified species encompassed four bacterial classes that were Firmicutes, Actinobacteria, Alphaproteobacteria and Gammaproteobacteria known to have been associated with sponges. The potential biotechnological applications of the identified bacteria were compared and reviewed based on relevant past studies. The biotechnological functions of the 14 cultivable isolates have been previously reported, hence reinforcing that bacteria associated with sponges are an abundant resource of scientifically essential compounds. Resilience of psychrotolerant bacteria, Psychrobacter celer, in warm tropical waters holds notable prospects for future research.
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Affiliation(s)
- Tan Suet May Amelia
- School of Marine and Environmental Sciences, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Al-Ashraf Abdullah Amirul
- School of Biological Sciences, Universiti Sains Malaysia, 11800 USM Pulau Pinang, Malaysia
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia (NIBM), Ministry of Science, Technology and Innovation, 11700 Gelugor, Pulau Pinang, Malaysia
- Centre of Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Pulau Pinang, Malaysia
| | - Jasnizat Saidin
- School of Marine and Environmental Sciences, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Kesaven Bhubalan
- School of Marine and Environmental Sciences, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia (NIBM), Ministry of Science, Technology and Innovation, 11700 Gelugor, Pulau Pinang, Malaysia
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
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Cihan AC, Yildiz ED, Sahin E, Mutlu O. Introduction of novel thermostable α-amylases from genus Anoxybacillus and proposing to group the Bacillaceae related α-amylases under five individual GH13 subfamilies. World J Microbiol Biotechnol 2018; 34:95. [PMID: 29904894 DOI: 10.1007/s11274-018-2478-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 06/12/2018] [Indexed: 11/25/2022]
Abstract
Among the thermophilic Bacillaceae family members, α-amylase production of 15 bacilli from genus Anoxybacillus was investigated, some of which are biotechnologically important. These Anoxybacillus α-amylase genes displayed ≥ 91.0% sequence similarities to Anoxybacillus enzymes (ASKA, ADTA and GSX-BL), but relatively lower similarities to Geobacillus (≤ 69.4% to GTA, Gt-amyII), and Bacillus aquimaris (≤ 61.3% to BaqA) amylases, all formerly proposed only in a Glycoside Hydrolase 13 (GH13) subfamily. The phylogenetic analyses of 63 bacilli-originated protein sequences among 93 α-amylases revealed the overall relationships within Bacillaceae amylolytic enzymes. All bacilli α-amylases formed 5 clades different from 15 predefined GH13 subfamilies. Their phylogenetic findings, taxonomic relationships, temperature requirements, and comparisonal structural analyses (including their CSR-I-VII regions, 12 sugar- and 4 calcium-binding sites, presence or absence of the complete catalytic machinery, and their currently unassigned status in a valid GH13 subfamiliy) revealed that these five GH13 α-amylase clades related to familly share some common characteristics, but also display differentiative features from each other and the preclassified ones. Based on these findings, we proposed to divide Bacillaceae related GH13 subfamilies into 5 individual groups: the novel a2 subfamily clustered around α-amylase B2M1-A (Anoxybacillus sp.), the a1, a3 and a4 subfamilies (including the representatives E184aa-A (Anoxybacillus sp.), ATA (Anoxybacillus tepidamans), and BaqA,) all of which were composed from the division of the previously grouped single subfamily around α-amylase BaqA, and the undefinite subfamily formerly defined as xy including Bacillus megaterium NL3.
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Affiliation(s)
- Arzu Coleri Cihan
- Faculty of Science, Department of Biology, Ankara University, Tandogan, 06100, Ankara, Turkey.
| | | | - Ergin Sahin
- Faculty of Science, Department of Biology, Ankara University, Tandogan, 06100, Ankara, Turkey
| | - Ozal Mutlu
- Faculty of Arts and Sciences, Department of Biology, Marmara University, Goztepe, 34722, Istanbul, Turkey
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25
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Avwioroko OJ, Anigboro AA, Unachukwu NN, Tonukari NJ. Isolation, identification and in silico analysis of alpha-amylase gene of Aspergillus niger strain CSA35 obtained from cassava undergoing spoilage. Biochem Biophys Rep 2018; 14:35-42. [PMID: 29872732 PMCID: PMC5986626 DOI: 10.1016/j.bbrep.2018.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 11/19/2022] Open
Abstract
In this investigation, a gene (CDF_Amyl) encoding extracellular α-amylase in Aspergillus niger strain CSA35 associated with cassava spoilage was amplified using specific primers and characterized in silico. The gene had a partial nucleotide sequence of 968 bp and encoded a protein of 222 aa residues with a molecular weight and isoelectric point of 25.13 kDa and 4.17, respectively. Its catalytic site was located in the active site domain. BLASTp analysis showed that the protein primary sequence of the α-amylase gene had 98% and 99% homologies with the α-amylase of A. niger and A. oryzae RIB40, respectively. The gene is more closely related to α-amylase genes from fungi than to bacterial, plant, or animal α-amylase genes. Restriction mapping of the gene showed it can be digested with restriction enzymes like NcoI, PstI, SmaI, and BcLI among others but not with EcoRI and EcoRV. Its protein product had a hydrophobicity score of - 0.43 but no transmembrane helix. The CDF_Amyl protein was subcellularly localized in the secretory pathway, an indication of its release into extracellular space after secretion. Also, the 3D structure of the CDF-Amyl protein was barrel-shaped with domains characteristic of α-amylases. The encoded α-amylase Vmax is 6.90 U/mg protein and Km is 6.70 mg/ml. It was concluded that the unique characteristics of the CDF_Amyl gene and its deduced protein could find applications in biotechnological, food and pharmaceutical industries where cloning and further modification of this gene would be required for product development and improvement.
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Affiliation(s)
- Oghenetega J. Avwioroko
- Biochemistry Division, Department of Chemical Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- Corresponding author.
| | - Akpovwehwee A. Anigboro
- Department of Biochemistry, Faculty of Science, Delta State University, P.M.B. 1, Abraka, Nigeria
| | - Nnanna N. Unachukwu
- Bioscience Center, International Institute for Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Nyerhovwo J. Tonukari
- Department of Biochemistry, Faculty of Science, Delta State University, P.M.B. 1, Abraka, Nigeria
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Waghmode S, Dama L, Hingamire T, Bharti N, Doijad S, Suryavanshi M. Draft genome sequence of a biosurfactant producing, Bacillus aquimaris strain SAMM MCC 3014 isolated from Indian Arabian coastline sea water. J Genomics 2017; 5:124-127. [PMID: 29109799 PMCID: PMC5666515 DOI: 10.7150/jgen.21724] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 08/31/2017] [Indexed: 11/19/2022] Open
Abstract
Bacillus aquimaris strain SAMM, a biosurfactant producing moderately halophilic marine bacterium was isolated from Indian Arabian coastline sea water. The strain was found to tolerate up to 2.7 M NaCl indicating osmotic stress sustainable physiological systems. We report here the draft genome sequence of B. aquimaris SAMM, as a candidate bacterium for bioactive surfactant producer. The whole genome sequence with 161 scaffolds, 4,414,932 bp and 44.8% of G+C content for SAMM was obtained using Illumina MiSeq sequencing technology. Annotation was added by the PGAP and RAST prokaryotic genome annotation service and shown 4,247 coding sequences, 123 RNAs genes, classified in 453 subsystems. Several genes encoding enzymatic activities against the high molecular weight polysaccharides, osmotic stress response and siderophore synthesis of potential biotechnological importance were identified in the genome.
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Affiliation(s)
| | - Laxmikant Dama
- Department of Zoology, DBF Dayanand College of Arts and Science, Solapur 413002
| | - Tejashri Hingamire
- Biochemical Science Division, CSIR-National Chemical Laboratory, Homi Bhabha Road, Pune 411008
| | - Nidhi Bharti
- Department of Botany, Savitribai Phule Pune University, Ganeshkhind, Pune 411007
| | - Swapnil Doijad
- Institute of Medical Microbiology, Biomedizinisches Forschungszentrum Seltersberg Schubertstr. 81 Giessen, Germany 35392
| | - Mangesh Suryavanshi
- Microbial Culture Collection, National Centre for Cell Science, Pune 411021
- Yenepoya Research Centre, Yenepoya University, Deralakatte, Mangalore 575018
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27
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Montor-Antonio JJ, Hernández-Heredia S, Ávila-Fernández Á, Olvera C, Sachman-Ruiz B, Del Moral S. Effect of differential processing of the native and recombinant α-amylase from Bacillus amyloliquefaciens JJC33M on specificity and enzyme properties. 3 Biotech 2017; 7:336. [PMID: 28955633 DOI: 10.1007/s13205-017-0954-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/07/2017] [Indexed: 12/07/2022] Open
Abstract
AmyJ33, an α-amylase isolated from Bacillus amyloliquefaciens JJC33M, has been characterized as a non-metalloenzyme that hydrolyzes raw starch. In this work, the gene that codifies for AmyJ33 was isolated and cloned. The recombinant α-amylase (AmyJ33r) produced had a molecular weight of 72 kDa, 25 kDa higher than the native α-amylase (AmyJ33). Our results suggest that the C-terminal was processed in a different way in the native and the recombinant enzyme causing the difference observed in the molecular weight. Additionally, the enzyme activity, specificity and biochemical behavior were affected by this larger C-terminal extra region in AmyJ33r, since the enzyme lost the ability to hydrolyze raw starch compared to the native but increased its thermal stability and pH stability, and modified the profile of activity toward alkaline pH. It is suggested that the catalytic domain in recombinant enzyme, AmyJ33r, could be interfered or blocked by the amino acids involved in the C-terminal additional region producing changes in the enzyme properties.
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Affiliation(s)
- Juan José Montor-Antonio
- División de Estudios de Posgrado, Universidad del Papaloapan, Circuito Central 200, CP 68400 Tuxtepec, Oaxaca Mexico
| | - Sarahi Hernández-Heredia
- Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central 200, CP 68400 Tuxtepec, Oaxaca Mexico
| | - Ángela Ávila-Fernández
- Centro de Investigación, DACS-Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez no. 2838-A. Col. Tamulté, CP 86150 Villahermosa, Centro, Tabasco Mexico
| | - Clarita Olvera
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, CP 62210 Cuernavaca, Morelos Mexico
| | - Bernardo Sachman-Ruiz
- Centro Nacional de Investigación Disciplinaria en Parasitología Veterinaria del Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, CP 62550 Jiutepec, Morelos Mexico
| | - Sandra Del Moral
- División de Estudios de Posgrado, Universidad del Papaloapan, Circuito Central 200, CP 68400 Tuxtepec, Oaxaca Mexico
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Crystal structure of a raw-starch-degrading bacterial α-amylase belonging to subfamily 37 of the glycoside hydrolase family GH13. Sci Rep 2017; 7:44067. [PMID: 28303907 PMCID: PMC5355875 DOI: 10.1038/srep44067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/02/2017] [Indexed: 01/14/2023] Open
Abstract
Subfamily 37 of the glycoside hydrolase family GH13 was recently established on the basis of the discovery of a novel α-amylase, designated AmyP, from a marine metagenomic library. AmyP exhibits raw-starch-degrading activity and consists of an N-terminal catalytic domain and a C-terminal starch-binding domain. To understand this newest subfamily, we determined the crystal structure of the catalytic domain of AmyP, named AmyPΔSBD, complexed with maltose, and the crystal structure of the E221Q mutant AmyPΔSBD complexed with maltotriose. Glu221 is one of the three conserved catalytic residues, and AmyP is inactivated by the E221Q mutation. Domain B of AmyPΔSBD forms a loop that protrudes from domain A, stabilizes the conformation of the active site and increases the thermostability of the enzyme. A new calcium ion is situated adjacent to the -3 subsite binding loop and may be responsible for the increased thermostability of the enzyme after the addition of calcium. Moreover, Tyr36 participates in both stacking and hydrogen bonding interactions with the sugar motif at subsite -3. This work provides the first insights into the structure of α-amylases belonging to subfamily 37 of GH13 and may contribute to the rational design of α-amylase mutants with enhanced performance in biotechnological applications.
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Sarian FD, Janeček Š, Pijning T, Ihsanawati, Nurachman Z, Radjasa OK, Dijkhuizen L, Natalia D, van der Maarel MJEC. A new group of glycoside hydrolase family 13 α-amylases with an aberrant catalytic triad. Sci Rep 2017; 7:44230. [PMID: 28287181 PMCID: PMC5347038 DOI: 10.1038/srep44230] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/31/2017] [Indexed: 11/09/2022] Open
Abstract
α-Amylases are glycoside hydrolase enzymes that act on the α(1→4) glycosidic linkages in glycogen, starch, and related α-glucans, and are ubiquitously present in Nature. Most α-amylases have been classified in glycoside hydrolase family 13 with a typical (β/α)8-barrel containing two aspartic acid and one glutamic acid residue that play an essential role in catalysis. An atypical α-amylase (BmaN1) with only two of the three invariant catalytic residues present was isolated from Bacillus megaterium strain NL3, a bacterial isolate from a sea anemone of Kakaban landlocked marine lake, Derawan Island, Indonesia. In BmaN1 the third residue, the aspartic acid that acts as the transition state stabilizer, was replaced by a histidine. Three-dimensional structure modeling of the BmaN1 amino acid sequence confirmed the aberrant catalytic triad. Glucose and maltose were found as products of the action of the novel α-amylase on soluble starch, demonstrating that it is active in spite of the peculiar catalytic triad. This novel BmaN1 α-amylase is part of a group of α-amylases that all have this atypical catalytic triad, consisting of aspartic acid, glutamic acid and histidine. Phylogenetic analysis showed that this group of α-amylases comprises a new subfamily of the glycoside hydrolase family 13.
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Affiliation(s)
- Fean D Sarian
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, Indonesia.,Aquatic Biotechnology and Bioproduct Engineering, Engineering and Technology institute Groningen (ENTEG), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, SK-84551 Bratislava, Slovakia.,Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Mehtodius, Nam. J. Herdu 2, SK-91701 Trnava, Slovakia
| | - Tjaard Pijning
- X-Ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Ihsanawati
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, Indonesia
| | - Zeily Nurachman
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, Indonesia
| | - Ocky K Radjasa
- Department of Marine Science, Faculty of Fishery and Marine Science, Diponegoro University, Semarang 50275, Central Java, Indonesia
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Dessy Natalia
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, Indonesia
| | - Marc J E C van der Maarel
- Aquatic Biotechnology and Bioproduct Engineering, Engineering and Technology institute Groningen (ENTEG), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Božić N, Lončar N, Slavić MŠ, Vujčić Z. Raw starch degrading α-amylases: an unsolved riddle. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/amylase-2017-0002] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractStarch is an important food ingredient and a substrate for the production of many industrial products. Biological and industrial processes involve hydrolysis of raw starch, such as digestion by humans and animals, starch metabolism in plants, and industrial starch conversion for obtaining glucose, fructose and maltose syrup or bioethanol. Raw starch degrading α-amylases (RSDA) can directly degrade raw starch below the gelatinization temperature of starch. Knowledge of the structures and properties of starch and RSDA has increased significantly in recent years. Understanding the relationships between structural peculiarities and properties of RSDA is a prerequisite for efficient application in different aspects of human benefit from health to the industry. This review summarizes recent advances on RSDA research with emphasizes on representatives of glycoside hydrolase family GH13. Definite understanding of raw starch digesting ability is yet to come with accumulating structural and functional studies of RSDA.
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Simair AA, Qureshi AS, Khushk I, Ali CH, Lashari S, Bhutto MA, Mangrio GS, Lu C. Production and Partial Characterization of α-Amylase Enzyme from Bacillus sp. BCC 01-50 and Potential Applications. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9173040. [PMID: 28168200 PMCID: PMC5267059 DOI: 10.1155/2017/9173040] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/26/2016] [Accepted: 12/18/2016] [Indexed: 11/20/2022]
Abstract
Amylase is an industrially important enzyme and applied in many industrial processes such as saccharification of starchy materials, food, pharmaceutical, detergent, and textile industries. This research work deals with the optimization of fermentation conditions for α-amylase production from thermophilic bacterial strain Bacillus sp. BCC 01-50 and characterization of crude amylase. The time profile of bacterial growth and amylase production was investigated in synthetic medium and maximum enzyme titer was observed after 60 h. In addition, effects of different carbon sources were tested as a substrate for amylase production and molasses was found to be the best. Various organic and inorganic compounds, potassium nitrate, ammonium chloride, sodium nitrate, urea, yeast extract, tryptone, beef extract, and peptone, were used and beef extract was found to be the best among the nitrogen sources used. Temperature, pH, agitation speed, and size of inoculum were also optimized. Highest enzyme activity was obtained when the strain was cultured in molasses medium for 60 h in shaking incubator (150 rpm) at 50°C and pH 8. Crude amylase showed maximal activity at pH 9 and 65°C. Enzyme remained stable in alkaline pH range 9-10 and 60-70°C. Crude amylase showed great potential for its application in detergent industry and saccharification of starchy materials.
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Affiliation(s)
- Altaf Ahmed Simair
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Abdul Sattar Qureshi
- Institute of Biotechnology and Genetic Engineering, University of Sindh, Jamshoro 76080, Pakistan
| | - Imrana Khushk
- Institute of Biotechnology and Genetic Engineering, University of Sindh, Jamshoro 76080, Pakistan
| | - Chaudhry Haider Ali
- Department of Chemical Engineering, University of Engineering & Technology, KSK Campus, Lahore 54890, Pakistan
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Safia Lashari
- Institute of Biotechnology and Genetic Engineering, University of Sindh, Jamshoro 76080, Pakistan
| | - Muhammad Aqeel Bhutto
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
- Institute of Biotechnology and Genetic Engineering, University of Sindh, Jamshoro 76080, Pakistan
| | - Ghulam Sughra Mangrio
- Institute of Biotechnology and Genetic Engineering, University of Sindh, Jamshoro 76080, Pakistan
| | - Changrui Lu
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
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Mehta D, Satyanarayana T. Bacterial and Archaeal α-Amylases: Diversity and Amelioration of the Desirable Characteristics for Industrial Applications. Front Microbiol 2016; 7:1129. [PMID: 27516755 PMCID: PMC4963412 DOI: 10.3389/fmicb.2016.01129] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/06/2016] [Indexed: 11/13/2022] Open
Abstract
Industrial enzyme market has been projected to reach US$ 6.2 billion by 2020. Major reasons for continuous rise in the global sales of microbial enzymes are because of increase in the demand for consumer goods and biofuels. Among major industrial enzymes that find applications in baking, alcohol, detergent, and textile industries are α-amylases. These are produced by a variety of microbes, which randomly cleave α-1,4-glycosidic linkages in starch leading to the formation of limit dextrins. α-Amylases from different microbial sources vary in their properties, thus, suit specific applications. This review focuses on the native and recombinant α-amylases from bacteria and archaea, their production and the advancements in the molecular biology, protein engineering and structural studies, which aid in ameliorating their properties to suit the targeted industrial applications.
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Affiliation(s)
- Deepika Mehta
- Department of Microbiology, University of Delhi New Delhi, India
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34
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Draft Whole-Genome Sequence of the Type Strain Bacillus aquimaris TF12T. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00640-16. [PMID: 27417832 PMCID: PMC4945792 DOI: 10.1128/genomea.00640-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacillus aquimaris TF12 is a Gram-positive bacteria isolated from a tidal flat of the Yellow Sea in South Korea. We report the draft whole-genome sequence of Bacillus aquimaris TF12, the type strain of a set of bacteria typically associated with marine habitats and with a potentially high biotechnology value.
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Janeček Š, Gabriško M. Remarkable evolutionary relatedness among the enzymes and proteins from the α-amylase family. Cell Mol Life Sci 2016; 73:2707-25. [PMID: 27154042 PMCID: PMC11108405 DOI: 10.1007/s00018-016-2246-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/17/2022]
Abstract
The α-amylase is a ubiquitous starch hydrolase catalyzing the cleavage of the α-1,4-glucosidic bonds in an endo-fashion. Various α-amylases originating from different taxonomic sources may differ from each other significantly in their exact substrate preference and product profile. Moreover, it also seems to be clear that at least two different amino acid sequences utilizing two different catalytic machineries have evolved to execute the same α-amylolytic specificity. The two have been classified in the Cabohydrate-Active enZyme database, the CAZy, in the glycoside hydrolase (GH) families GH13 and GH57. While the former and the larger α-amylase family GH13 evidently forms the clan GH-H with the families GH70 and GH77, the latter and the smaller α-amylase family GH57 has only been predicted to maybe define a future clan with the family GH119. Sequences and several tens of enzyme specificities found throughout all three kingdoms in many taxa provide an interesting material for evolutionarily oriented studies that have demonstrated remarkable observations. This review emphasizes just the three of them: (1) a close relatedness between the plant and archaeal α-amylases from the family GH13; (2) a common ancestry in the family GH13 of animal heavy chains of heteromeric amino acid transporter rBAT and 4F2 with the microbial α-glucosidases; and (3) the unique sequence features in the primary structures of amylomaltases from the genus Borrelia from the family GH77. Although the three examples cannot represent an exhaustive list of exceptional topics worth to be interested in, they may demonstrate the importance these enzymes possess in the overall scientific context.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia.
- Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius in Trnava, Nám. J. Herdu 2, 91701, Trnava, Slovakia.
| | - Marek Gabriško
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia
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Chai KP, Othman NFB, Teh AH, Ho KL, Chan KG, Shamsir MS, Goh KM, Ng CL. Crystal structure of Anoxybacillus α-amylase provides insights into maltose binding of a new glycosyl hydrolase subclass. Sci Rep 2016; 6:23126. [PMID: 26975884 PMCID: PMC4791539 DOI: 10.1038/srep23126] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 02/17/2016] [Indexed: 11/18/2022] Open
Abstract
A new subfamily of glycosyl hydrolase family GH13 was recently proposed for α-amylases from Anoxybacillus species (ASKA and ADTA), Geobacillus thermoleovorans (GTA, Pizzo, and GtamyII), Bacillus aquimaris (BaqA), and 95 other putative protein homologues. To understand this new GH13 subfamily, we report crystal structures of truncated ASKA (TASKA). ASKA is a thermostable enzyme capable of producing high levels of maltose. Unlike GTA, biochemical analysis showed that Ca2+ ion supplementation enhances the catalytic activities of ASKA and TASKA. The crystal structures reveal the presence of four Ca2+ ion binding sites, with three of these binding sites are highly conserved among Anoxybacillus α-amylases. This work provides structural insights into this new GH13 subfamily both in the apo form and in complex with maltose. Furthermore, structural comparison of TASKA and GTA provides an overview of the conformational changes accompanying maltose binding at each subsite.
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Affiliation(s)
- Kian Piaw Chai
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81310 Skudai, Johor, Malaysia
| | - Noor Farhan Binti Othman
- Universiti Kebangsaan Malaysia, Institute of Systems Biology, 43600 UKM Bangi, Selangor, Malaysia
| | - Aik-Hong Teh
- Universiti Sains Malaysia, Centre for Chemical Biology, 11800 Penang, Malaysia
| | - Kok Lian Ho
- Universiti Putra Malaysia, Department of Pathology, Faculty of Medicine and Health Sciences, 43400 Serdang, Selangor, Malaysia
| | - Kok-Gan Chan
- University of Malaya, Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, 50603 Kuala Lumpur, Malaysia
| | - Mohd Shahir Shamsir
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81310 Skudai, Johor, Malaysia
| | - Kian Mau Goh
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81310 Skudai, Johor, Malaysia
| | - Chyan Leong Ng
- Universiti Kebangsaan Malaysia, Institute of Systems Biology, 43600 UKM Bangi, Selangor, Malaysia
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Xu QS, Yan YS, Feng JX. Efficient hydrolysis of raw starch and ethanol fermentation: a novel raw starch-digesting glucoamylase from Penicillium oxalicum. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:216. [PMID: 27777618 PMCID: PMC5069817 DOI: 10.1186/s13068-016-0636-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 10/08/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Starch is a very abundant and renewable carbohydrate and is an important feedstock for industrial applications. The conventional starch liquefaction and saccharification processes are energy-intensive, complicated, and not environmentally friendly. Raw starch-digesting glucoamylases are capable of directly hydrolyzing raw starch to glucose at low temperatures, which significantly simplifies processing and reduces the cost of producing starch-based products. RESULTS A novel raw starch-digesting glucoamylase PoGA15A with high enzymatic activity was purified from Penicillium oxalicum GXU20 and biochemically characterized. The PoGA15A enzyme had a molecular weight of 75.4 kDa, and was most active at pH 4.5 and 65 °C. The enzyme showed remarkably broad pH stability (pH 2.0-10.5) and substrate specificity, and was able to degrade various types of raw starches at 40 °C. Its adsorption ability for different raw starches was consistent with its degrading capacities for the corresponding substrate. The cDNA encoding the enzyme was cloned and heterologously expressed in Pichia pastoris. The recombinant enzyme could quickly and efficiently hydrolyze different concentrations of raw corn and cassava flours (50, 100, and 150 g/L) with the addition of α-amylase at 40 °C. Furthermore, when used in the simultaneous saccharification and fermentation of 150 g/L raw flours to ethanol with the addition of α-amylase, the ethanol yield reached 61.0 g/L with a high fermentation efficiency of 95.1 % after 48 h when raw corn flour was used as the substrate. An ethanol yield of 57.0 g/L and 93.5 % of fermentation efficiency were achieved with raw cassava flour after 36 h. In addition, the starch-binding domain deletion analysis revealed that SBD plays a very important role in raw starch hydrolysis by the enzyme PoGA15A. CONCLUSIONS A novel raw starch-digesting glucoamylase from P. oxalicum, with high enzymatic activity, was biochemically, molecularly, and genetically identified. Its efficient hydrolysis of raw starches and its high efficiency during the direct conversion of raw corn and cassava flours via simultaneous saccharification and fermentation to ethanol suggests that the enzyme has a number of potential applications in industrial starch processing and starch-based ethanol production.
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Affiliation(s)
- Qiang-Sheng Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Yu-Si Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
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38
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A novel GH13 subfamily of α-amylases with a pair of tryptophans in the helix α3 of the catalytic TIM-barrel, the LPDlx signature in the conserved sequence region V and a conserved aromatic motif at the C-terminus. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Overcoming hydrolysis of raw corn starch under industrial conditions with Bacillus licheniformis ATCC 9945a α-amylase. Appl Microbiol Biotechnol 2015; 100:2709-19. [DOI: 10.1007/s00253-015-7101-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 10/22/2022]
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40
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Wu J, Xia B, Li Z, Ye X, Chen Q, Dong W, Zhou J, Huang Y, Cui Z. Molecular cloning and characterization of a novel GH13 saccharifying α‐amylase AmyC fromCorallococcussp. EGB. STARCH-STARKE 2015. [DOI: 10.1002/star.201400258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jiale Wu
- Department of Microbiology, College of Life SciencesKey Laboratory for Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing Agricultural UniversityP. R. China
| | - Bingjie Xia
- Department of Microbiology, College of Life SciencesKey Laboratory for Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing Agricultural UniversityP. R. China
| | - Zhoukun Li
- Department of Microbiology, College of Life SciencesKey Laboratory for Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing Agricultural UniversityP. R. China
| | - Xianfeng Ye
- Department of Microbiology, College of Life SciencesKey Laboratory for Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing Agricultural UniversityP. R. China
| | - Qiongzhen Chen
- Department of Microbiology, College of Life SciencesKey Laboratory for Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing Agricultural UniversityP. R. China
| | - Weiliang Dong
- Department of Microbiology, College of Life SciencesKey Laboratory for Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing Agricultural UniversityP. R. China
| | - Jie Zhou
- Department of Microbiology, College of Life SciencesKey Laboratory for Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing Agricultural UniversityP. R. China
| | - Yan Huang
- Department of Microbiology, College of Life SciencesKey Laboratory for Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing Agricultural UniversityP. R. China
| | - Zhongli Cui
- Department of Microbiology, College of Life SciencesKey Laboratory for Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing Agricultural UniversityP. R. China
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Barman D, Dkhar MS. Amylolytic activity and its parametric optimization of an endophytic bacterium Bacillus subtilis with an ethno-medicinal origin. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Lomthong T, Chotineeranat S, Kitpreechavanich V. Production and characterization of raw starch degrading enzyme from a newly isolated thermophilic filamentous bacterium,Laceyella sacchariLP175. STARCH-STARKE 2014. [DOI: 10.1002/star.201400150] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thanasak Lomthong
- Department of Microbiology, Faculty of Science; Kasetsart University; Bangkok Thailand
| | - Sunee Chotineeranat
- Cassava and Starch Technology Research Unit (CSTRU), National Center for Genetic Engineering and Biotechnology (BIOTEC); Kasetsart University; Bangkok Thailand
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Ranjani V, Janeček Š, Chai KP, Shahir S, Rahman RNZRA, Chan KG, Goh KM. Protein engineering of selected residues from conserved sequence regions of a novel Anoxybacillus α-amylase. Sci Rep 2014; 4:5850. [PMID: 25069018 PMCID: PMC5376179 DOI: 10.1038/srep05850] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/08/2014] [Indexed: 11/08/2022] Open
Abstract
The α-amylases from Anoxybacillus species (ASKA and ADTA), Bacillus aquimaris (BaqA) and Geobacillus thermoleovorans (GTA, Pizzo and GtamyII) were proposed as a novel group of the α-amylase family GH13. An ASKA yielding a high percentage of maltose upon its reaction on starch was chosen as a model to study the residues responsible for the biochemical properties. Four residues from conserved sequence regions (CSRs) were thus selected, and the mutants F113V (CSR-I), Y187F and L189I (CSR-II) and A161D (CSR-V) were characterised. Few changes in the optimum reaction temperature and pH were observed for all mutants. Whereas the Y187F (t1/2 43 h) and L189I (t1/2 36 h) mutants had a lower thermostability at 65°C than the native ASKA (t1/2 48 h), the mutants F113V and A161D exhibited an improved t1/2 of 51 h and 53 h, respectively. Among the mutants, only the A161D had a specific activity, k(cat) and k(cat)/K(m) higher (1.23-, 1.17- and 2.88-times, respectively) than the values determined for the ASKA. The replacement of the Ala-161 in the CSR-V with an aspartic acid also caused a significant reduction in the ratio of maltose formed. This finding suggests the Ala-161 may contribute to the high maltose production of the ASKA.
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Affiliation(s)
- Velayudhan Ranjani
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, 81310 Johor, Malaysia
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
- Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
| | - Kian Piaw Chai
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, 81310 Johor, Malaysia
| | - Shafinaz Shahir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, 81310 Johor, Malaysia
| | - Raja Noor Zaliha Raja Abdul Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, 81310 Johor, Malaysia
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Lu Z, Tian C, Li A, Zhang G, Ma Y. Identification and characterization of a novel alkaline α-amylase Amy703 belonging to a new clade from Bacillus pseudofirmus. ACTA ACUST UNITED AC 2014; 41:783-93. [DOI: 10.1007/s10295-014-1420-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/12/2014] [Indexed: 11/25/2022]
Abstract
Abstract
Alkaline α-amylases are of great interest in desizing processes and detergent industries. Here, an alkaline α-amylase gene amy703 from an alkaliphilic Bacillus pseudofirmus strain was cloned and sequenced. Its encoding product, Amy703, might represent a new clade of α-amylase family, because it shared only 35 % highest identity with all amylases characterized up to date and was not clustered into any subfamilies with amylase activity in glycoside hydrolase family 13. Heterologous expression and characterization of Amy703 showed that it is a metalloenzyme with maximal activity at 40 °C and pH 9.0. Its activity was significantly enhanced by 2- and 2.48-fold at the presence of 10 mM Ca2+ and Mg2+, respectively, while Hg2+ was a strong inhibitor of Amy703. Amy703 has a higher affinity (K m = 3.92 mg/ml) for soluble starch compared to many other alkaline amylases. The computer modeling of its structure indicated that Amy703 contains typical amylase domains and a loop region appearing to bind the substrates. Site-directed mutagenesis suggested that a conserved residue Glu550 was essential for the activity of Amy703, and proposed it working together with other two residues to constitute a catalytic triad (Asp521, Glu550, and Asp615).
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Affiliation(s)
- Zhenghui Lu
- grid.34418.3a 0000000107279022 Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences Hubei University 430062 Wuhan China
| | - Chaoguang Tian
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
| | - Aiying Li
- grid.411407.7 0000000417602614 The College of Life Sciences Central China Normal University 430079 Wuhan China
| | - Guimin Zhang
- grid.34418.3a 0000000107279022 Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences Hubei University 430062 Wuhan China
| | - Yanhe Ma
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
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Tamamura N, Saburi W, Mukai A, Morimoto N, Takehana T, Koike S, Matsui H, Mori H. Enhancement of hydrolytic activity of thermophilic alkalophilic α-amylase from Bacillus sp. AAH-31 through optimization of amino acid residues surrounding the substrate binding site. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Janeček Š, Svensson B, MacGregor EA. α-Amylase: an enzyme specificity found in various families of glycoside hydrolases. Cell Mol Life Sci 2014; 71:1149-70. [PMID: 23807207 PMCID: PMC11114072 DOI: 10.1007/s00018-013-1388-z] [Citation(s) in RCA: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/27/2013] [Accepted: 05/27/2013] [Indexed: 10/26/2022]
Abstract
α-Amylase (EC 3.2.1.1) represents the best known amylolytic enzyme. It catalyzes the hydrolysis of α-1,4-glucosidic bonds in starch and related α-glucans. In general, the α-amylase is an enzyme with a broad substrate preference and product specificity. In the sequence-based classification system of all carbohydrate-active enzymes, it is one of the most frequently occurring glycoside hydrolases (GH). α-Amylase is the main representative of family GH13, but it is probably also present in the families GH57 and GH119, and possibly even in GH126. Family GH13, known generally as the main α-amylase family, forms clan GH-H together with families GH70 and GH77 that, however, contain no α-amylase. Within the family GH13, the α-amylase specificity is currently present in several subfamilies, such as GH13_1, 5, 6, 7, 15, 24, 27, 28, 36, 37, and, possibly in a few more that are not yet defined. The α-amylases classified in family GH13 employ a reaction mechanism giving retention of configuration, share 4-7 conserved sequence regions (CSRs) and catalytic machinery, and adopt the (β/α)8-barrel catalytic domain. Although the family GH57 α-amylases also employ the retaining reaction mechanism, they possess their own five CSRs and catalytic machinery, and adopt a (β/α)7-barrel fold. These family GH57 attributes are likely to be characteristic of α-amylases from the family GH119, too. With regard to family GH126, confirmation of the unambiguous presence of the α-amylase specificity may need more biochemical investigation because of an obvious, but unexpected, homology with inverting β-glucan-active hydrolases.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia,
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Marques JM, da Silva TF, Vollu RE, Blank AF, Ding GC, Seldin L, Smalla K. Plant age and genotype affect the bacterial community composition in the tuber rhizosphere of field-grown sweet potato plants. FEMS Microbiol Ecol 2014; 88:424-35. [PMID: 24597529 DOI: 10.1111/1574-6941.12313] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 02/21/2014] [Accepted: 02/23/2014] [Indexed: 11/30/2022] Open
Abstract
The hypothesis that sweet potato genotypes containing different starch yields in their tuberous roots can affect the bacterial communities present in the rhizosphere (soil adhering to tubers) was tested in this study. Tuberous roots of field-grown sweet potato of genotypes IPB-149 (commercial genotype), IPB-052, and IPB-137 were sampled three and six months after planting and analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analysis of 16S rRNA genes PCR-amplified from total community DNA. The statistical analysis of the DGGE fingerprints showed that both plant age and genotypes influenced the bacterial community structure in the tuber rhizosphere. Pyrosequencing analysis showed that the IPB-149 and IPB-052 (both with high starch content) displayed similar bacterial composition in the tuber rhizosphere, while IPB-137 with the lowest starch content was distinct. In comparison with bulk soil, higher 16S rRNA gene copy numbers (qPCR) and numerous genera with significantly increased abundance in the tuber rhizosphere of IPB-137 (Sphingobium, Pseudomonas, Acinetobacter, Stenotrophomonas, Chryseobacterium) indicated a stronger rhizosphere effect. The genus Bacillus was strongly enriched in the tuber rhizosphere samples of all sweet potato genotypes studied, while other genera showed a plant genotype-dependent abundance. This is the first report on the molecular identification of bacteria being associated with the tuber rhizosphere of different sweet potato genotypes.
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Affiliation(s)
- Joana M Marques
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Domain C of thermostable α-amylase of Geobacillus thermoleovorans mediates raw starch adsorption. Appl Microbiol Biotechnol 2014; 98:4503-19. [DOI: 10.1007/s00253-013-5459-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 11/28/2013] [Accepted: 12/08/2013] [Indexed: 10/25/2022]
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Mok SC, Teh AH, Saito JA, Najimudin N, Alam M. Crystal structure of a compact α-amylase from Geobacillus thermoleovorans. Enzyme Microb Technol 2013; 53:46-54. [PMID: 23683704 DOI: 10.1016/j.enzmictec.2013.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 11/17/2022]
Abstract
A truncated form of an α-amylase, GTA, from thermophilic Geobacillus thermoleovorans CCB_US3_UF5 was biochemically and structurally characterized. The recombinant GTA, which lacked both the N- and C-terminal transmembrane regions, functioned optimally at 70°C and pH 6.0. While enzyme activity was not enhanced by the addition of CaCl2, GTA's thermostability was significantly improved in the presence of CaCl2. The structure, in complex with an acarbose-derived pseudo-hexasaccharide, consists of the typical three domains and binds one Ca(2+) ion. This Ca(2+) ion was strongly bound and not chelated by EDTA. A predicted second Ca(2+)-binding site, however, was disordered. With limited subsites, two novel substrate-binding residues, Y147 and Y182, may help increase substrate affinity. No distinct starch-binding domain is present, although two regions rich in aromatic residues have been observed. GTA, with a smaller domain B and several shorter loops compared to other α-amylases, has one of the most compact α-amylase folds that may contribute greatly to its tight Ca(2+) binding and thermostability.
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Affiliation(s)
- Sook-Chen Mok
- Centre for Chemical Biology, Universiti Sains Malaysia, 11800 Penang, Malaysia
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