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Hu YT, Hong XZ, Li HM, Yang JK, Shen W, Wang YW, Liu YH. Modifying the amino acids in conformational motion pathway of the α-amylase of Geobacillus stearothermophilus improved its activity and stability. Front Microbiol 2023; 14:1261245. [PMID: 38143856 PMCID: PMC10740195 DOI: 10.3389/fmicb.2023.1261245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/21/2023] [Indexed: 12/26/2023] Open
Abstract
Amino acids along the conformational motion pathway of the enzyme molecule correlated to its flexibility and rigidity. To enhance the enzyme activity and thermal stability, the motion pathway of Geobacillus stearothermophilus α-amylase has been identified and molecularly modified by using the neural relational inference model and deep learning tool. The significant differences in substrate specificity, enzymatic kinetics, optimal temperature, and thermal stability were observed among the mutants with modified amino acids along the pathway. Mutants especially the P44E demonstrated enhanced hydrolytic activity and catalytic efficiency (kcat/KM) than the wild-type enzyme to 95.0% and 93.8% respectively, with the optimum temperature increased to 90°C. This mutation from proline to glutamic acid has increased the number and the radius of the bottleneck of the channels, which might facilitate transporting large starch substrates into the enzyme. The mutation could also optimize the hydrogen bonding network of the catalytic center, and diminish the spatial hindering to the substrate entry and exit from the catalytic center.
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Affiliation(s)
- Yu-Ting Hu
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Xi-Zhi Hong
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Hui-Min Li
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Jiang-Ke Yang
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Wei Shen
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Ya-Wei Wang
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Yi-Han Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
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2
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Baroroh U, Chantika NS, Firdaus ARR, Tohari TR, Subroto T, Ishmayana S, Safari A, Rachman SD, Yusuf M. Accelerated molecular dynamics study to compare the thermostability of Bacillus licheniformis and Aspergillus niger α-amylase. J Biomol Struct Dyn 2023:1-11. [PMID: 37979153 DOI: 10.1080/07391102.2023.2283152] [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: 11/02/2022] [Accepted: 11/06/2023] [Indexed: 11/20/2023]
Abstract
The thermostability of enzymes plays a significant role in the starch hydrolysis process in the industry. The structural difference between thermostable Bacillus licheniformis α-amylase (BLA) and thermolabile Aspergillus niger α-amylase (ANA) is interesting to be explored. This work aimed to study the thermostability-determining factor of BLA as compared to a non-thermostable enzyme, ANA, using molecular dynamics (MD) simulation at a high temperature. A 100 ns of classical MD, which was followed by 200 ns accelerated MD was conducted to explore the conformational changes of the enzyme. It is revealed that the intramolecular interactions through salt bridge interactions and the presence of calcium ions dominates the stability effect of BLA, despite the absence of a disulfide bond in the structure. These results should be useful in designing a thermostable enzyme that can be used in industrial processes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Umi Baroroh
- Department of Biotechnology, Indonesia School of Pharmacy, Bandung, Indonesia
| | - Nindi Salma Chantika
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Ade R R Firdaus
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
| | - Taufik Ramdani Tohari
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
| | - Toto Subroto
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
| | - Safri Ishmayana
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Agus Safari
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Saadah Diana Rachman
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Muhammad Yusuf
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
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3
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Sardiña-Peña AJ, Ballinas-Casarrubias L, Siqueiros-Cendón TS, Espinoza-Sánchez EA, Flores-Holguín NR, Iglesias-Figueroa BF, Rascón-Cruz Q. Thermostability improvement of sucrose isomerase PalI NX-5: a comprehensive strategy. Biotechnol Lett 2023:10.1007/s10529-023-03388-6. [PMID: 37199887 DOI: 10.1007/s10529-023-03388-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/29/2023] [Accepted: 04/27/2023] [Indexed: 05/19/2023]
Abstract
OBJECTIVE To increase the thermal stability of sucrose isomerase from Erwinia rhapontici NX-5, we designed a comprehensive strategy that combines different thermostabilizing elements. RESULTS We identified 19 high B value amino acid residues for site-directed mutagenesis. An in silico evaluation of the influence of post-translational modifications on the thermostability was also carried out. The sucrose isomerase variants were expressed in Pichia pastoris X33. Thus, for the first time, we report the expression and characterization of glycosylated sucrose isomerases. The designed mutants K174Q, L202E and K174Q/L202E, showed an increase in their optimal temperature of 5 °C, while their half-lives increased 2.21, 1.73 and 2.89 times, respectively. The mutants showed an increase in activity of 20.3% up to 25.3%. The Km values for the K174Q, L202E, and K174Q/L202E mutants decreased by 5.1%, 7.9%, and 9.4%, respectively; furthermore, the catalytic efficiency increased by up to 16%. CONCLUSIONS With the comprehensive strategy followed, we successfully obtain engineered mutants more suitable for industrial applications than their counterparts: native (this research) and wild-type from E. rhapontici NX-5, without compromising the catalytic activity of the molecule.
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Affiliation(s)
- A J Sardiña-Peña
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - L Ballinas-Casarrubias
- Laboratorio de Química Analítica III, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - T S Siqueiros-Cendón
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - E A Espinoza-Sánchez
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - N R Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, México
| | - B F Iglesias-Figueroa
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - Q Rascón-Cruz
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México.
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4
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Yuan S, Yan R, Lin B, Li R, Ye X. Improving thermostability of Bacillus amyloliquefaciens alpha-amylase by multipoint mutations. Biochem Biophys Res Commun 2023; 653:69-75. [PMID: 36857902 DOI: 10.1016/j.bbrc.2023.02.064] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 02/26/2023]
Abstract
The medium-temperature alpha-amylase of Bacillus amyloliquefaciens is widely used in the food and washing process. Enhancing the thermostability of alpha-amylases and investigating the mechanism of stability are important for enzyme industry development. The optimal temperature and pH of the wild-type BAA and mutant MuBAA (D28E/V118A/S187D/K370 N) were all 60 °C and 6.0, respectively. The mutant MuBAA showed better thermostability at 50 °C and 60 °C, with a specific activity of 206.61 U/mg, which was 99.1% greater than that of the wild-type. By analyzing predicted structures, the improving thermostability of the mutant MuBAA was mainly related to enhanced stabilization of a loop region in domain B via more calcium-binding sites and intramolecular interactions around Asp187. Furthermore, additional intramolecular interactions around sites 28 and 370 in domain A were also beneficial for improving thermostability. Additionally, the decrease of steric hindrance at the active cavity increased the specific activity of the mutant MuBAA. Improving the thermostability of BAA has theoretical reference values for the modification of alpha-amylases.
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Affiliation(s)
- Susu Yuan
- National Engineering Laboratory for High-efficient Enzyme Expression, Fuzhou, Fujian, China; The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou, Fujian, China; College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Renxiang Yan
- National Engineering Laboratory for High-efficient Enzyme Expression, Fuzhou, Fujian, China; The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou, Fujian, China; College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Biyu Lin
- National Engineering Laboratory for High-efficient Enzyme Expression, Fuzhou, Fujian, China; The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou, Fujian, China; College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Renkuan Li
- National Engineering Laboratory for High-efficient Enzyme Expression, Fuzhou, Fujian, China; The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou, Fujian, China; College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Xiuyun Ye
- National Engineering Laboratory for High-efficient Enzyme Expression, Fuzhou, Fujian, China; The Key Laboratory of Marine Enzyme Engineering of Fujian Province, Fuzhou University, Fuzhou, Fujian, China; College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, China.
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5
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Sadalage PS, Dar MA, Bhor RD, Bhalerao BM, Kamble PN, Paiva-Santos AC, Nimbalkar MS, Sonawane KD, Pai K, Patil PS, Pawar KD. Optimization of biogenic synthesis of biocompatible platinum nanoparticles with catalytic, enzyme mimetic and antioxidant activities. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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6
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AmyJ33, a truncated amylase with improved catalytic properties. Biotechnol Lett 2022; 44:1447-1463. [DOI: 10.1007/s10529-022-03311-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
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7
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Duan WX, Yang XH, Zhang HF, Feng J, Zhang MY. Chemical Structure, Hypoglycemic Activity, and Mechanism of Action of Selenium Polysaccharides. Biol Trace Elem Res 2022; 200:4404-4418. [PMID: 34843085 PMCID: PMC8628488 DOI: 10.1007/s12011-021-03035-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/14/2021] [Indexed: 12/14/2022]
Abstract
Selenium polysaccharides (Se-polysaccharides) are one of important forms of organic Se, in which selenium (Se) and polysaccharides are joined by covalent bonds. In the present review, recent progress in chemical structure and hypoglycemic activity of Se-polysaccharides is summarized. In particular, the mechanism underlying hypoglycemic capacity of Se-polysaccharides is discussed, and the relationship between hypoglycemic activity and chemical structure is analyzed. Besides, strategies for further research into chemical structure and hypoglycemic activity of Se-polysaccharides are proposed. Hypoglycemic activity of Se-polysaccharides is closely related to their inhibitory effect on α-amylase and α-glucosidase, influence on insulin signal pathway especially IRS-PI3K-Akt signaling pathway, and protection capacity against oxidative stress.
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Affiliation(s)
- Wen-Xia Duan
- Provincial Research Station of Se-Enriched Foods in Hanyin County of Shaanxi Province, International Joint Research Center of Shaanxi Province for Food and Health Sciences, National Engineering Laboratory for Resources Development of Endangered Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
| | - Xiao-Hua Yang
- Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Hua-Feng Zhang
- Provincial Research Station of Se-Enriched Foods in Hanyin County of Shaanxi Province, International Joint Research Center of Shaanxi Province for Food and Health Sciences, National Engineering Laboratory for Resources Development of Endangered Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an, 710062, People's Republic of China.
- Municipal Expert Workstation for Hua-Feng Zhang, Academician and Expert Workstation in Pu'er City of Yunnan Province, Pu'er, 665600, People's Republic of China.
| | - Jing Feng
- Agrarian and Technological Institute, Peoples' Friendship University of Russia, Moscow, 119991, Russia
| | - Meng-Yuan Zhang
- Provincial Research Station of Se-Enriched Foods in Hanyin County of Shaanxi Province, International Joint Research Center of Shaanxi Province for Food and Health Sciences, National Engineering Laboratory for Resources Development of Endangered Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
- Municipal Expert Workstation for Hua-Feng Zhang, Academician and Expert Workstation in Pu'er City of Yunnan Province, Pu'er, 665600, People's Republic of China
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8
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Ahmad A, Rahamtullah, Mishra R. Structural and functional adaptation in extremophilic microbial α-amylases. Biophys Rev 2022; 14:499-515. [PMID: 35528036 PMCID: PMC9043155 DOI: 10.1007/s12551-022-00931-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/12/2022] [Indexed: 01/26/2023] Open
Abstract
Maintaining stable native conformation of a protein under a given ecological condition is the prerequisite for survival of organisms. Extremophilic bacteria and archaea have evolved to adapt under extreme conditions of temperature, pH, salt, and pressure. Molecular adaptations of proteins under these conditions are essential for their survival. These organisms have the capability to maintain stable, native conformations of proteins under extreme conditions. The enzymes produced by the extremophiles are also known as extremozyme, which are used in several industries. Stability and functionality of extremozymes under varying temperature, pH, and solvent conditions are the most desirable requirement of industry. α-Amylase is one of the most important enzymes used in food, pharmaceutical, textile, and detergent industries. This enzyme is produced by diverse microorganisms including various extremophiles. Therefore, understanding its stability is important from fundamental as well as an applied point of view. Each class of extremophiles has a distinctive set of dominant non-covalent interactions which are important for their stability. Static information obtained by comparative analysis of amino acid sequence and atomic resolution structure provides information on the prevalence of particular amino acids or a group of non-covalent interactions. Protein folding studies give the information about thermodynamic and kinetic stability in order to understand dynamic aspect of molecular adaptations. In this review, we have summarized information on amino acid sequence, structure, stability, and adaptability of α-amylases from different classes of extremophiles.
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Affiliation(s)
- Aziz Ahmad
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| | - Rahamtullah
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| | - Rajesh Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
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9
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Wang K, Lv R, Sun S, Dong F, Liu M, Liu J, Nie X. Nanobiocatalyst consisting of immobilized α-amylase on montmorillonite exhibiting enhanced enzymatic performance based on the allosteric effect. Colloids Surf B Biointerfaces 2021; 211:112290. [PMID: 34929483 DOI: 10.1016/j.colsurfb.2021.112290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/23/2021] [Accepted: 12/14/2021] [Indexed: 01/13/2023]
Abstract
Enzyme immobilization on nanostructured substrates is an emerging method for the efficient development of nanobiocatalysts to enhance enzymatic performance. In this study, a novel α-amylase nanobiocatalytic system was constructed based on the allosteric activation of the enzyme and its immobilization on a natural nanostructured mineral montmorillonite. The strategy of allosteric modulation and immobilization, equipped the immobilized α-amylase with higher catalytic activity and greater stability (compared to those of free α-amylase) over a broad range of pH values (4.5-9.0) and temperatures (30-80 °C). Kinetic experiments revealed that although the immobilized α-amylase possessed a considerably lower affinity for its substrate, its catalytic activity was higher than that of free α-amylase, likely owing to allosteric modulation. Thus, this study demonstrates a convenient and environmentally benign immobilization strategy to construct a nanobiocatalytic α-amylase system that exploits the phenomenon of allosteric activation of the enzyme and lays the foundation for further industrial applications.
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Affiliation(s)
- Ke Wang
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycle of Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Rui Lv
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycle of Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Shiyong Sun
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycle of Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China.
| | - Faqin Dong
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycle of Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Mingxue Liu
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycle of Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Jin Liu
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycle of Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Xiaoqin Nie
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycle of Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
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10
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Xie ZB, Zhang KZ, Kang ZH, Yang JG. Saccharomycopsis fibuligera in liquor production: A review. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-021-03743-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Stereoselective synthesis of a 4-⍺-glucoside of valienamine and its X-ray structure in complex with Streptomyces coelicolor GlgE1-V279S. Sci Rep 2021; 11:13413. [PMID: 34183716 PMCID: PMC8238978 DOI: 10.1038/s41598-021-92554-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Glycoside hydrolases (GH) are a large family of hydrolytic enzymes found in all domains of life. As such, they control a plethora of normal and pathogenic biological functions. Thus, understanding selective inhibition of GH enzymes at the atomic level can lead to the identification of new classes of therapeutics. In these studies, we identified a 4-⍺-glucoside of valienamine (8) as an inhibitor of Streptomyces coelicolor (Sco) GlgE1-V279S which belongs to the GH13 Carbohydrate Active EnZyme family. The results obtained from the dose-response experiments show that 8 at a concentration of 1000 µM reduced the enzyme activity of Sco GlgE1-V279S by 65%. The synthetic route to 8 and a closely related 4-⍺-glucoside of validamine (7) was achieved starting from readily available D-maltose. A key step in the synthesis was a chelation-controlled addition of vinylmagnesium bromide to a maltose-derived enone intermediate. X-ray structures of both 7 and 8 in complex with Sco GlgE1-V279S were solved to resolutions of 1.75 and 1.83 Å, respectively. Structural analysis revealed the valienamine derivative 8 binds the enzyme in an E2 conformation for the cyclohexene fragment. Also, the cyclohexene fragment shows a new hydrogen-bonding contact from the pseudo-diaxial C(3)-OH to the catalytic nucleophile Asp 394 at the enzyme active site. Asp 394, in fact, forms a bidentate interaction with both the C(3)-OH and C(7)-OH of the inhibitor. In contrast, compound 7 disrupts the catalytic sidechain interaction network of Sco GlgE1-V279S via steric interactions resulting in a conformation change in Asp 394. These findings will have implications for the design other aminocarbasugar-based GH13-inhibitors and will be useful for identifying more potent and selective inhibitors.
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12
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Solat N, Shafiei M. A novel pH and thermo-tolerant halophilic alpha-amylase from moderate halophile Nesterenkonia sp. strain F: gene analysis, molecular cloning, heterologous expression and biochemical characterization. Arch Microbiol 2021; 203:3641-3655. [PMID: 33993325 DOI: 10.1007/s00203-021-02359-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 10/21/2022]
Abstract
A novel pH and thermo-tolerate halophilic alpha-amylase from moderately halophilic bacterium, Nesterenkonia sp.strain F was cloned and expressed in Escherichia coli. 16S rRNA sequence of the strain shared 99.46% similarities with closely related type species. Also, the genome sequence shared ANI values below 92% and dDDH values below 52% with the closely related type species. Consequently, it is proposed that strain F represents a novel species. The AmyF gene was 1390 bp long and encodes an alpha-amylase of 463 amino acid residues with pI of 4.62. The deduced AmyF shared very low sequence similarity (< 24%) with functionally characterized recombinant halophilic alpha-amylases. The recombinant alpha-amylase was successfully purified from Ni-NTA columns with a molecular mass of about 52 KDa on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme was active over a wide range of temperature (25-75 °C) and pH (4-9) with optimum activity at 45 °C and 7.5, respectively. Also, although it was active over a various concentrations of NaCl and KCl (0-4 M), increasing activity of the enzyme was observed with increasing concentration of these salts. Low concentrations of Ca2+ ion had no activating effect, but high concentrations of the ion (40-200 mM) enhanced activity of AmyF. The enzyme activity was increased by increasing concentrations of Mg2+, Zn2+, Hg2+ and Fe3+. However, it was inhibited only at very high concentrations of these metal ions. Cu2+ did not decrease the amylase activity and the highest activity was observed at 100 mM of the ion. These properties indicate wide potential applications of this recombinant enzyme in starch processing industries. This is the first isolation, cloning and characterization of a gene encoding alpha-amylase from Nesternkonia genus.
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Affiliation(s)
- Nastaran Solat
- Department of Genetics, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Biotechnology and Bioscience Research Center, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Shafiei
- Department of Genetics, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran. .,Biotechnology and Bioscience Research Center, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
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13
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Bioprospecting of Thermophilic Fungal Enzymes and Potential Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Matpan Bekler F, Güven K, Gül Güven R. Purification and characterization of novel α-amylase from Anoxybacillus ayderensis FMB1. BIOCATAL BIOTRANSFOR 2020. [DOI: 10.1080/10242422.2020.1856097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Fatma Matpan Bekler
- Department of Biology, Faculty of Science, Dicle University, Diyarbakır, Turkey
| | - Kemal Güven
- Department of Molecular Biology and Genetics, Faculty of Science, Dicle University, Diyarbakır, Turkey
| | - Reyhan Gül Güven
- Department of Science Teaching, Faculty of Education, Dicle University, Diyarbakır, Turkey
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15
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Baskaran N, Chang YC, Chang CH, Hung SK, Kao CT, Wei Y. Quantify the Protein-Protein Interaction Effects on Adsorption Related Lubricating Behaviors of α-Amylase on a Glass Surface. Polymers (Basel) 2020; 12:E1658. [PMID: 32722491 PMCID: PMC7463787 DOI: 10.3390/polym12081658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/18/2020] [Accepted: 07/22/2020] [Indexed: 11/16/2022] Open
Abstract
Dental ceramic material is one of the widely preferred restorative materials to mimic the natural tooth enamel surface. However, it has continuously been degraded because of low wear resistance during mastication in the oral cavity. The friction involved was reduced by introducing the lubricant saliva protein layers to improve the wear resistance of the dental materials. However, little is understood regarding how the protein-protein interactions (PPI) influence the adsorbed-state structures and lubricating behaviors of saliva proteins on the ceramic material surface. The objective of this study is to quantify the influences of PPI effects on the structural changes and corresponding oral lubrications of adsorbed α-amylase, one of the abundant proteins in the saliva, on the dental ceramic material with glass as a model surface. α-Amylase was first adsorbed to glass surface under varying protein solution concentrations to saturate the surface to vary the PPI effects over a wide range. The areal density of the adsorbed protein was measured as an indicator of the level of PPI effects within the layer, and these values were then correlated with the measurements of the adsorbed protein's secondary structure and corresponding friction coefficient. The decreased friction coefficient value was an indicator of the lubricated surfaces with higher wear resistance. Our results indicate that PPI effects help stabilize the structure of α-amylase adsorbed on glass, and the correlation observed between the friction coefficient and the conformational state of adsorbed α-amylase was apparent. This study thus provides new molecular-level insights into how PPI influences the structure and lubricating behaviors of adsorbed protein, which is critical for the innovations of dental ceramic material designs with improved wear resistance.
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Affiliation(s)
| | | | | | | | | | - Yang Wei
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, 1, Section 3, Zhongxiao East Road, Taipei 10608, Taiwan; (N.B.); (Y.-C.C.); (C.-H.C.); (S.-K.H.); (C.-T.K.)
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16
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Pinto ÉSM, Dorn M, Feltes BC. The tale of a versatile enzyme: Alpha-amylase evolution, structure, and potential biotechnological applications for the bioremediation of n-alkanes. CHEMOSPHERE 2020; 250:126202. [PMID: 32092569 DOI: 10.1016/j.chemosphere.2020.126202] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/10/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
As the primary source of a wide range of industrial products, the study of petroleum-derived compounds is of pivotal importance. However, the process of oil extraction and refinement is among the most environmentally hazardous practices, impacting almost all levels of the ecological chain. So far, the most appropriate strategy to overcome such an issue is through bioremediation, which revolves around the employment of different microorganisms to degrade hazardous compounds, generating less environmental impact and lower monetary costs. In this sense, a myriad of organisms and enzymes are considered possible candidates for the bioremediation process. Amidst the potential candidates is α-amylase, an evolutionary conserved starch-degrading enzyme. Notably, α-amylase was not only seen to degrade n-alkanes, a subclass of alkanes considered the most abundant petroleum-derived compounds but also low-density polyethylene, a dangerous pollutant produced from petroleum. Thus, due to its high conservation in both eukaryotic and prokaryotic lineages, in addition to the capability to degrade different types of hazardous compounds, the study of α-amylase becomes a rising interest. Nevertheless, there are no studies that review all biotechnological applications of α-amylase for bioremediation. In this work, we critically review the potential biotechnological applications of α-amylase, focusing on the biodegradation of petroleum-derived compounds. Evolutionary aspects are discussed, as well for all structural information and all features that could impact on the employment of this protein in the biotechnological industry, such as pH, temperature, and medium conditions. New perspectives and critical assessments are conducted regarding the application of α-amylase in the bioremediation of n-alkanes.
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Affiliation(s)
- Éderson Sales Moreira Pinto
- Laboratory of Structural Bioinformatics and Computational Biology, Center for Biotechnology, Federal University of Rio Grande do Sul, Brazil
| | - Márcio Dorn
- Laboratory of Structural Bioinformatics and Computational Biology, Institute of Informatics, Federal University of Rio Grande do Sul, Brazil; Laboratory of Structural Bioinformatics and Computational Biology, Center for Biotechnology, Federal University of Rio Grande do Sul, Brazil
| | - Bruno César Feltes
- Laboratory of Structural Bioinformatics and Computational Biology, Institute of Informatics, Federal University of Rio Grande do Sul, Brazil.
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17
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Zhu W, Khalifa I, Wang R, Li C. Persimmon highly galloylated-tannins in vitro mitigated α-amylase and α-glucosidase via statically binding with their catalytic-closed sides and altering their secondary structure elements. J Food Biochem 2020; 44:e13234. [PMID: 32301514 DOI: 10.1111/jfbc.13234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 03/21/2020] [Accepted: 03/25/2020] [Indexed: 12/22/2022]
Abstract
Reticence of α-amylase (α-Amy) and α-glucosidase (α-Glu) is needed due to their mitigation potency on the glucose absorption. In this study, the anti-amylolytic effects of persimmon tannins (PT) on α-Amy and α-Glu and their interaction mechanisms were investigated. It was found that PT inhibited α-Amy and α-Glu with the half inhibitory concentration (IC50 ) values of 0.35 and 0.24 mg/ml, respectively. Fluorescence and FT-IR spectrometry results showed that PT could bind to enzymes and alter their conformations. Molecular docking showed that the structural units of PT interacted with the key sites (amino acids Glu233, Asp197, and Asp300) of α-Amy by H-bonds and π-π interactions, while they bound to the residues closed to the active sites of α-Glu. The whole results implied that PT was a promising mitigator of α-Amy and α-Glu. It might help to understand mechanisms of glycemic response inhibition of PT and develop certain therapeutic strategies against diabetes. PRACTICAL APPLICATIONS: α-Amy and α-Glu are the crucial starch digestive enzymes associated with type II diabetes mellitus in humans. Persimmon is an excellent source of bio-functional tannins which potentially mitigate the type II diabetes. This study showed that PT beneficially decreased the action of the carbohydrate digestion-related enzymes, namely α-Amy and α-Glu via interaction simultaneously, which could be used to formulate a functional food and natural medicine.
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Affiliation(s)
- Wei Zhu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ibrahim Khalifa
- Food Technology Department, Faculty of Agriculture, Benha University, Benha, Egypt
| | - Ruifeng Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chunmei Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Environment Correlative Food Science (Huazhong Agricultural University), Ministry of Education, Wuhan, China
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18
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Wang CH, Lu LH, Huang C, He BF, Huang RB. Simultaneously Improved Thermostability and Hydrolytic Pattern of Alpha-Amylase by Engineering Central Beta Strands of TIM Barrel. Appl Biochem Biotechnol 2020; 192:57-70. [PMID: 32219624 DOI: 10.1007/s12010-020-03308-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/12/2020] [Indexed: 11/26/2022]
Abstract
This study reported simultaneously improved thermostability and hydrolytic pattern of α-amylase from Bacillus subtilis CN7 by rationally engineering the mostly conserved central beta strands in TIM barrel fold. Nine single point mutations and a double mutation were introduced at the 2nd site of the β7 strand and 3rd site of the β5 strand to rationalize the weak interactions in the beta strands of the TIM barrel of α-amylase. All the five active mutants changed the compositions and percentages of maltooligosaccharides in final hydrolytic products compared to the product spectrum of the wild-type. A mutant Y204V produced only maltose, maltotriose, and maltopentaose without any glucose and maltotetraose, indicating a conversion from typical endo-amylase to novel maltooligosaccharide-producing amylase. A mutant V260I enhanced the thermal stability by 7.1 °C. To our best knowledge, this is the first report on the simultaneous improvement of thermostability and hydrolytic pattern of α-amylase by engineering central beta strands of TIM barrel and the novel "beta strands" strategy proposed here may be useful for the protein engineering of other TIM barrel proteins.
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Affiliation(s)
- Cheng-Hua Wang
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China.
| | - Liang-Hua Lu
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China
| | - Cheng Huang
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China
| | - Bing-Fang He
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 210009, China
| | - Ri-Bo Huang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, Nanning, 530007, China
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19
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Salem K, Elgharbi F, Ben Hlima H, Perduca M, Sayari A, Hmida-Sayari A. Biochemical characterization and structural insights into the high substrate affinity of a dimeric and Ca 2+ independent Bacillus subtilis α-amylase. Biotechnol Prog 2020; 36:e2964. [PMID: 31951110 DOI: 10.1002/btpr.2964] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/17/2019] [Accepted: 01/06/2020] [Indexed: 11/10/2022]
Abstract
An extracellular amylase (AmyKS) produced by a newly isolated Bacillus subtilis strain US572 was purified and characterized. AmyKS showed maximal activity at pH 6 and 60°C with a half-life of 10 min at 70°C. It is a Ca2+ independent enzyme and able to hydrolyze soluble starch into oligosaccharides consisting mainly of maltose and maltotriose. When compared to the studied α-amylases, AmyKS presents a high affinity toward soluble starch with a Km value of 0.252 mg ml-1 . Coupled with the size-exclusion chromatography data, MALDI-TOF/MS analysis indicated that the purified amylase is a dimer with a molecular mass of 136,938.18 Da. It is an unusual feature of a non-maltogenic α-amylase. A 3D model and a dimeric model of AmyKS were generated showing the presence of an additional domain suspected to be involved in the dimerization process. This dimer arrangement could explain the high substrate affinity and catalytic efficiency of this enzyme.
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Affiliation(s)
- Karima Salem
- Laboratoire de Biotechnologie Microbienne et d'Ingénierie des Enzymes (LBMIE), Centre de Biotechnologie de Sfax (CBS), Université de Sfax, Sfax, Tunisie
| | - Fatma Elgharbi
- Laboratoire de Biotechnologie Microbienne et d'Ingénierie des Enzymes (LBMIE), Centre de Biotechnologie de Sfax (CBS), Université de Sfax, Sfax, Tunisie
| | - Hajer Ben Hlima
- Unité de Biotechnologie des Algues, ENIS, Université de Sfax, Sfax, Tunisie
| | - Massimiliano Perduca
- Biocrystallography and Nanostructure Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Adel Sayari
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS, Université de Sfax, Sfax, Tunisie
| | - Aïda Hmida-Sayari
- Laboratoire de Biotechnologie Microbienne et d'Ingénierie des Enzymes (LBMIE), Centre de Biotechnologie de Sfax (CBS), Université de Sfax, Sfax, Tunisie
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20
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Production of a novel α-amylase by Bacillus atrophaeus NRC1 isolated from honey: Purification and characterization. Int J Biol Macromol 2020; 148:292-301. [PMID: 31945438 DOI: 10.1016/j.ijbiomac.2020.01.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 01/09/2020] [Accepted: 01/12/2020] [Indexed: 11/23/2022]
Abstract
Different bacterial isolates with amylolytic activity were insulated from various honey samples. The most active isolate was identified by the molecular 16SrRNA sequence technique as Bacillus atrophaeus NRC1. The bacterium showed maximum amylase production under optimum culture conditions at pH 6.0, 40 °C and after 24 h incubation. Two amylase isoenzymes (AmyI and AmyII) from Bacillus atrophaeus NRC1 have been purified to homogeneity by using ammonium sulfate precipitation, Sephacryl S-200 and DEAE-Sepharose chromatography. The major isoenzyme, AmyI, had a specific activity 4635 U/mg proteins with molecular weight of 61 kDa using SDS-PAGE electrophoresis. The maximum activity of AmyI against starch was determined at pH 6.0 and 50 °C. AmyI was stable up to 50 °C after incubation for 30 min, retained 65 and 23% of its activity at 60 and 70 °C, respectively. Pre-incubation with Ca2+, Mg2+ and Ba2+ cations for 30 min enhanced the enzyme activity; while it was completely inhibited by Hg2+. Varied inhibition degree of the enzyme activity was determined with K+, Ni2+, Zn2+, Na2+ and Cu2+ ions. AmyI was inhibited by EDTA, PMSF and SDS, while it was activated by l-Cysteine-HCl and DTT. AmyI had the ability to degrade starch, amylopectin, glycogen, amylose and lacked the affinity towards β-1,4-linked xyloses.
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21
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Li Q, Yan Y, Liu X, Zhang Z, Tian J, Wu N. Enhancing thermostability of a psychrophilic alpha-amylase by the structural energy optimization in the trajectories of molecular dynamics simulations. Int J Biol Macromol 2020; 142:624-633. [DOI: 10.1016/j.ijbiomac.2019.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/18/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022]
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22
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Liao SM, Shen NK, Liang G, Lu B, Lu ZL, Peng LX, Zhou F, Du LQ, Wei YT, Zhou GP, Huang RB. Inhibition of α-amylase Activity by Zn2+: Insights from Spectroscopy and Molecular Dynamics Simulations. Med Chem 2019; 15:510-520. [DOI: 10.2174/1573406415666181217114101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/23/2018] [Accepted: 12/12/2018] [Indexed: 02/08/2023]
Abstract
Background:Inhibition of α-amylase activity is an important strategy in the treatment of diabetes mellitus. An important treatment for diabetes mellitus is to reduce the digestion of carbohydrates and blood glucose concentrations. Inhibiting the activity of carbohydrate-degrading enzymes such as α-amylase and glucosidase significantly decreases the blood glucose level. Most inhibitors of α-amylase have serious adverse effects, and the α-amylase inactivation mechanisms for the design of safer inhibitors are yet to be revealed.Objective:In this study, we focused on the inhibitory effect of Zn2+ on the structure and dynamic characteristics of α-amylase from Anoxybacillus sp. GXS-BL (AGXA), which shares the same catalytic residues and similar structures as human pancreatic and salivary α-amylase (HPA and HSA, respectively).Methods:Circular dichroism (CD) spectra of the protein (AGXA) in the absence and presence of Zn2+ were recorded on a Chirascan instrument. The content of different secondary structures of AGXA in the absence and presence of Zn2+ was analyzed using the online SELCON3 program. An AGXA amino acid sequence similarity search was performed on the BLAST online server to find the most similar protein sequence to use as a template for homology modeling. The pocket volume measurer (POVME) program 3.0 was applied to calculate the active site pocket shape and volume, and molecular dynamics simulations were performed with the Amber14 software package.Results:According to circular dichroism experiments, upon Zn2+ binding, the protein secondary structure changed obviously, with the α-helix content decreasing and β-sheet, β-turn and randomcoil content increasing. The structural model of AGXA showed that His217 was near the active site pocket and that Phe178 was at the outer rim of the pocket. Based on the molecular dynamics trajectories, in the free AGXA model, the dihedral angle of C-CA-CB-CG displayed both acute and planar orientations, which corresponded to the open and closed states of the active site pocket, respectively. In the AGXA-Zn model, the dihedral angle of C-CA-CB-CG only showed the planar orientation. As Zn2+ was introduced, the metal center formed a coordination interaction with H217, a cation-π interaction with W244, a coordination interaction with E242 and a cation-π interaction with F178, which prevented F178 from easily rotating to the open state and inhibited the activity of the enzyme.Conclusion:This research may have uncovered a subtle mechanism for inhibiting the activity of α-amylase with transition metal ions, and this finding will help to design more potent and specific inhibitors of α-amylases.
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Affiliation(s)
- Si-Ming Liao
- Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Nai-Kun Shen
- School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, Guangxi, 530008, China
| | - Ge Liang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, China
| | - Bo Lu
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, China
| | - Zhi-Long Lu
- Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Li-Xin Peng
- Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Feng Zhou
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, China
| | - Li-Qin Du
- Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yu-Tuo Wei
- Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Guo-Ping Zhou
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, China
| | - Ri-Bo Huang
- Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
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23
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Sobhy R, Eid M, Zhan F, Liang H, Li B. Toward understanding the in vitro anti-amylolytic effects of three structurally different phytosterols in an aqueous medium using multispectral and molecular docking studies. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.03.098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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24
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Chen A, Xu T, Ge Y, Wang L, Tang W, Li S. Hydrogen-bond-based protein engineering for the acidic adaptation of Bacillus acidopullulyticus pullulanase. Enzyme Microb Technol 2019; 124:79-83. [DOI: 10.1016/j.enzmictec.2019.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/12/2019] [Accepted: 01/29/2019] [Indexed: 01/05/2023]
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25
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El-Sayed AKA, Abou-Dobara MI, El-Fallal AA, Omar NF. Heterologous expression, purification, immobilization and characterization of recombinant α-amylase AmyLa from Laceyella sp. DS3. Int J Biol Macromol 2019; 132:1274-1281. [PMID: 30953727 DOI: 10.1016/j.ijbiomac.2019.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 11/27/2022]
Abstract
AmyLa α-amylase gene from Laceyella sp. DS3 was heterologously expressed in E. coli BL21. E. coli BL21 maximally expressed AmyLa after 4 h of adding 0.02 mM IPTG at 37 °C. The recombinant AmyLa α-amylase was purified 2.19-fold through gel filtration and ion exchange chromatography. We immobilized the purified recombinant AmyLa α-amylase on four carriers; chitosan had the best efficiency. The recombinant free and the immobilized AmyLa α-amylase showed optimum activity in the pH ranges of 6.0-7.0 and 4.0-7.0, respectively and possessed an optimum temperature of 55 °C. The free enzyme had activation energy, Km, and Vmax of 291.5 kJ, 1.5 mg/ml, and 6.06 mg/min, respectively. The immobilized enzyme had activation energy, Km, and Vmax of 309.74 kJ, 6.67 mg/ml, and 50 mg/min, respectively. The immobilized enzyme was calcium-independent and insensitive (relative to the free enzyme) to metals. It could also be reused for seven cycles.
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Affiliation(s)
- Ahmed K A El-Sayed
- Botany and Microbiology Department, Faculty of Science, Damietta University, Egypt
| | | | - Amira A El-Fallal
- Botany and Microbiology Department, Faculty of Science, Damietta University, Egypt
| | - Noha F Omar
- Botany and Microbiology Department, Faculty of Science, Damietta University, Egypt.
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26
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Chaari F, Chaabouni SE. Fungal β-1,3-1,4-glucanases: production, proprieties and biotechnological applications. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:2657-2664. [PMID: 30430579 DOI: 10.1002/jsfa.9491] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 11/05/2018] [Accepted: 11/10/2018] [Indexed: 06/09/2023]
Abstract
β-1,3-1,4-glucanases (or lichenases; EC 3.2.1.73) comprise one of the main enzymes used in industry during recent decades. These enzymes hydrolyze β-glucans containing β-1,3 and β-1,4 linkages, such as cereal β-glucans and lichenan. The β-1,3-1,4-glucanases are produced by a variety of bacteria, fungi, plants and animals. A large number of microbial β-1,3-1,4-glucanases have potential application in industrial processes, such as feed, food and detergent industries. The present review summarizes the available studies with respect to β-1,3-1,4-glucanases production conditions, enzyme biochemical properties and potential industrial application. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Fatma Chaari
- Laboratory for the Improvement of Plants and Valorization of Agroressources, National School of Engineering of Sfax (ENIS), University of Sfax, Sfax, Tunisia
| | - Semia Ellouz Chaabouni
- Laboratory for the Improvement of Plants and Valorization of Agroressources, National School of Engineering of Sfax (ENIS), University of Sfax, Sfax, Tunisia
- Common Service Unit of Bioreactor Coupled with an Ultrafilter, National School of Engineering, Sfax University, Sfax, Tunisia
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27
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Li J, Gu X, Pan A. Multifunctional α-amylase Amy19 possesses agarase, carrageenase, and cellulase activities. Int J Biol Macromol 2019; 126:585-594. [DOI: 10.1016/j.ijbiomac.2018.12.217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/29/2018] [Accepted: 12/22/2018] [Indexed: 11/28/2022]
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28
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Agirre J, Moroz O, Meier S, Brask J, Munch A, Hoff T, Andersen C, Wilson KS, Davies GJ. The structure of the AliC GH13 α-amylase from Alicyclobacillus sp. reveals the accommodation of starch branching points in the α-amylase family. Acta Crystallogr D Struct Biol 2019; 75:1-7. [PMID: 30644839 PMCID: PMC6333287 DOI: 10.1107/s2059798318014900] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/21/2018] [Indexed: 10/06/2023] Open
Abstract
α-Amylases are glycoside hydrolases that break the α-1,4 bonds in starch and related glycans. The degradation of starch is rendered difficult by the presence of varying degrees of α-1,6 branch points and their possible accommodation within the active centre of α-amylase enzymes. Given the myriad industrial uses for starch and thus also for α-amylase-catalysed starch degradation and modification, there is considerable interest in how different α-amylases might accommodate these branches, thus impacting on the potential processing of highly branched post-hydrolysis remnants (known as limit dextrins) and societal applications. Here, it was sought to probe the branch-point accommodation of the Alicyclobacillus sp. CAZy family GH13 α-amylase AliC, prompted by the observation of a molecule of glucose in a position that may represent a branch point in an acarbose complex solved at 2.1 Å resolution. Limit digest analysis by two-dimensional NMR using both pullulan (a regular linear polysaccharide of α-1,4, α-1,4, α-1,6 repeating trisaccharides) and amylopectin starch showed how the Alicyclobacillus sp. enzyme could accept α-1,6 branches in at least the -2, +1 and +2 subsites, consistent with the three-dimensional structures with glucosyl moieties in the +1 and +2 subsites and the solvent-exposure of the -2 subsite 6-hydroxyl group. Together, the work provides a rare insight into branch-point acceptance in these industrial catalysts.
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Affiliation(s)
- Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Olga Moroz
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Jesper Brask
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | - Astrid Munch
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | - Tine Hoff
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | | | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
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29
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Enhanced acidic adaptation of Bacillus subtilis Ca-independent alpha-amylase by rational engineering of pKa values. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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30
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Parashar D, Satyanarayana T. An Insight Into Ameliorating Production, Catalytic Efficiency, Thermostability and Starch Saccharification of Acid-Stable α-Amylases From Acidophiles. Front Bioeng Biotechnol 2018; 6:125. [PMID: 30324103 PMCID: PMC6172347 DOI: 10.3389/fbioe.2018.00125] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 08/20/2018] [Indexed: 02/03/2023] Open
Abstract
Most of the extracellular enzymes of acidophilic bacteria and archaea are stable at acidic pH with a relatively high thermostability. There is, however, a dearth of information on their acid stability. Although several theories have been postulated, the adaptation of acidophilic proteins to low pH has not been explained convincingly. This review highlights recent developments in understanding the structure and biochemical characteristics, and production of acid-stable and calcium-independent α-amylases by acidophilic bacteria with special reference to that of Bacillus acidicola.
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Affiliation(s)
- Deepak Parashar
- Functional Genomic Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Tulasi Satyanarayana
- Division of Biological Sciences and Engineering, Netaji Subhas Institute of Technology, New Delhi, India
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Wang J, Li Y, Lu F. Molecular cloning and biochemical characterization of an α-amylase family from Aspergillus niger. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Abstract
The dynamic native, functional folded forms of proteins are unstable mainly because they readily unfold into flexible unstructured forms.
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Affiliation(s)
- Romas Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics
- University of Minnesota
- St Paul
- USA
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Sindhu R, Binod P, Madhavan A, Beevi US, Mathew AK, Abraham A, Pandey A, Kumar V. Molecular improvements in microbial α-amylases for enhanced stability and catalytic efficiency. BIORESOURCE TECHNOLOGY 2017; 245:1740-1748. [PMID: 28478894 DOI: 10.1016/j.biortech.2017.04.098] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
α-Amylases is one of the most important industrial enzyme which contributes to 25% of the industrial enzyme market. Though it is produced by plant, animals and microbial source, those from microbial source seems to have potential applications due to their stability and economic viability. However a large number of α-amylases from different sources have been detailed in the literature, only few numbers of them could withstand the harsh industrial conditions. Thermo-stability, pH tolerance, calcium independency and oxidant stability and starch hydrolyzing efficiency are the crucial qualities for α-amylase in starch based industries. Microbes can be genetically modified and fine tuning can be done for the production of enzymes with desired characteristics for specific applications. This review focuses on the native and recombinant α-amylases from microorganisms, their heterologous production and the recent molecular strategies which help to improve the properties of this industrial enzyme.
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Affiliation(s)
- Raveendran Sindhu
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India.
| | - Parameswaran Binod
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Aravind Madhavan
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India
| | - Ummalyma Sabeela Beevi
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Institute of Bioresources and Sustainable Development, Takyelpat, Imphal 795 001, India
| | - Anil Kuruvilla Mathew
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Amith Abraham
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Ashok Pandey
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Center of Innovative and Applied Bioprocessing, Sector 81, Mohali, Punjab, India
| | - Vinod Kumar
- Center of Innovative and Applied Bioprocessing, Sector 81, Mohali, Punjab, India
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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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Rational Engineering of a Cold-Adapted α-Amylase from the Antarctic Ciliate Euplotes focardii for Simultaneous Improvement of Thermostability and Catalytic Activity. Appl Environ Microbiol 2017; 83:AEM.00449-17. [PMID: 28455329 PMCID: PMC5478988 DOI: 10.1128/aem.00449-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/18/2017] [Indexed: 12/04/2022] Open
Abstract
The α-amylases are endo-acting enzymes that hydrolyze starch by randomly cleaving the 1,4-α-d-glucosidic linkages between the adjacent glucose units in a linear amylose chain. They have significant advantages in a wide range of applications, particularly in the food industry. The eukaryotic α-amylase isolated from the Antarctic ciliated protozoon Euplotes focardii (EfAmy) is an alkaline enzyme, different from most of the α-amylases characterized so far. Furthermore, EfAmy has the characteristics of a psychrophilic α-amylase, such as the highest hydrolytic activity at a low temperature and high thermolability, which is the major drawback of cold-active enzymes in industrial applications. In this work, we applied site-directed mutagenesis combined with rational design to generate a cold-active EfAmy with improved thermostability and catalytic efficiency at low temperatures. We engineered two EfAmy mutants. In one mutant, we introduced Pro residues on the A and B domains in surface loops. In the second mutant, we changed Val residues to Thr close to the catalytic site. The aim of these substitutions was to rigidify the molecular structure of the enzyme. Furthermore, we also analyzed mutants containing these combined substitutions. Biochemical enzymatic assays of engineered versions of EfAmy revealed that the combination of mutations at the surface loops increased the thermostability and catalytic efficiency of the enzyme. The possible mechanisms responsible for the changes in the biochemical properties are discussed by analyzing the three-dimensional structural model. IMPORTANCE Cold-adapted enzymes have high specific activity at low and moderate temperatures, a property that can be extremely useful in various applications as it implies a reduction in energy consumption during the catalyzed reaction. However, the concurrent high thermolability of cold-adapted enzymes often limits their applications in industrial processes. The α-amylase from the psychrophilic Antarctic ciliate Euplotes focardii (named EfAmy) is a cold-adapted enzyme with optimal catalytic activity in an alkaline environment. These unique features distinguish it from most α-amylases characterized so far. In this work, we engineered a novel EfAmy with improved thermostability, substrate binding affinity, and catalytic efficiency to various extents, without impacting its pH preference. These characteristics can be considered important properties for use in the food, detergent, and textile industries and in other industrial applications. The enzyme engineering strategy developed in this study may also provide useful knowledge for future optimization of molecules to be used in particular industrial applications.
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Veleti SK, Petit C, Lindenberger JJ, Ronning DR, Sucheck SJ. Zwitterionic pyrrolidene-phosphonates: inhibitors of the glycoside hydrolase-like phosphorylase Streptomyces coelicolor GlgEI-V279S. Org Biomol Chem 2017; 15:3884-3891. [PMID: 28422240 DOI: 10.1039/c7ob00388a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We synthesized and evaluated new zwitterionic inhibitors against glycoside hydrolase-like phosphorylase Streptomyces coelicolor (Sco) GlgEI-V279S which plays a role in α-glucan biosynthesis. Sco GlgEI-V279S serves as a model enzyme for validated anti-tuberculosis (TB) target Mycobacterium tuberculosis (Mtb) GlgE. Pyrrolidine inhibitors 5 and 6 were designed based on transition state considerations and incorporate a phosphonate on the pyrrolidine moiety to expand the interaction network between the inhibitor and the enzyme active site. Compounds 5 and 6 inhibited Sco GlgEI-V279S with Ki = 45 ± 4 μM and 95 ± 16 μM, respectively, and crystal structures of Sco GlgE-V279S-5 and Sco GlgE-V279S-6 were obtained at a 3.2 Å and 2.5 Å resolution, respectively.
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Affiliation(s)
- Sri Kumar Veleti
- Department of Chemistry and Biochemistry and School of Green Chemistry and Engineering, The University of Toledo, 2801 W. Bancroft Street, Toledo, Ohio 43606, USA.
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Park HS, Jun SC, Han KH, Hong SB, Yu JH. Diversity, Application, and Synthetic Biology of Industrially Important Aspergillus Fungi. ADVANCES IN APPLIED MICROBIOLOGY 2017; 100:161-202. [PMID: 28732553 DOI: 10.1016/bs.aambs.2017.03.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The filamentous fungal genus Aspergillus consists of over 340 officially recognized species. A handful of these Aspergillus fungi are predominantly used for food fermentation and large-scale production of enzymes, organic acids, and bioactive compounds. These industrially important Aspergilli primarily belong to the two major Aspergillus sections, Nigri and Flavi. Aspergillus oryzae (section Flavi) is the most commonly used mold for the fermentation of soybeans, rice, grains, and potatoes. Aspergillus niger (section Nigri) is used in the industrial production of various enzymes and organic acids, including 99% (1.4 million tons per year) of citric acid produced worldwide. Better understanding of the genomes and the signaling mechanisms of key Aspergillus species can help identify novel approaches to enhance these commercially significant strains. This review summarizes the diversity, current applications, key products, and synthetic biology of Aspergillus fungi commonly used in industry.
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Affiliation(s)
- Hee-Soo Park
- Kyungpook National University, Daegu, Republic of Korea
| | | | | | | | - Jae-Hyuk Yu
- University of Wisconsin, Madison, WI, United States
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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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Li Z, Duan X, Chen S, Wu J. Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B. PLoS One 2017; 12:e0173187. [PMID: 28253342 PMCID: PMC5333897 DOI: 10.1371/journal.pone.0173187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/16/2017] [Indexed: 11/29/2022] Open
Abstract
The reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase were improved through site-directed mutagenesis. By using multiple sequence alignment and PoPMuSiC algorithm, Ser187 and Asn188, which located within a long loop in Domain B of Bacillus licheniformis α-amylase, were selected for mutation. In addition, Ala269, which is adjacent to Ser187 and Asn188, was also investigated. Seven mutants carrying the mutations S187D, N188T, N188S, A269K, A269K/S187D, S187D/N188T, and A269K/S187D/N188T were generated and characterized. The most thermostable mutant, A269K/S187D/N188T, exhibited a 9-fold improvement in half-life at 95°C and pH 5.5, compared with that of the wild-type enzyme. Mutant A269K/S187D/N188T also exhibited improved catalytic efficiency. The catalytic efficiency of mutant A269K/S187D/N188T reached 5.87×103±0.17 g·L-1·s-1 at pH 5.5, which is 1.84-fold larger than the corresponding value determined for the wild-type enzyme. Furthermore, the structure analysis showed that immobilization of the loop containing Ser187 and Asn188 plays a significant role in developing the properties of Bacillus licheniformis α-amylase.
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Affiliation(s)
- Zhu Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xuguo Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Department of Food Science and Engineering, College of Light Industry Science and Engineering, Nanjing Forestry University, Nanjing, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- * E-mail:
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Gao Y, Huang M, Sun X, Zhang X, Zhang Y, Zhou X, Cai M. Single-site mutation of C363G or N463T strengthens thermostability improvement of IG181–182 deleted acidic α-amylase from deep-sea thermophile Geobacillus sp. FOOD BIOTECHNOL 2017. [DOI: 10.1080/08905436.2016.1276462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Yanyun Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Mengmeng Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiaoyue Sun
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiaoxu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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Biotechnological Processes in Microbial Amylase Production. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1272193. [PMID: 28280725 PMCID: PMC5322433 DOI: 10.1155/2017/1272193] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 11/27/2016] [Indexed: 01/01/2023]
Abstract
Amylase is an important and indispensable enzyme that plays a pivotal role in the field of biotechnology. It is produced mainly from microbial sources and is used in many industries. Industrial sectors with top-down and bottom-up approaches are currently focusing on improving microbial amylase production levels by implementing bioengineering technologies. The further support of energy consumption studies, such as those on thermodynamics, pinch technology, and environment-friendly technologies, has hastened the large-scale production of the enzyme. Herein, the importance of microbial (bacteria and fungi) amylase is discussed along with its production methods from the laboratory to industrial scales.
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El-Sayed AKA, Abou-Dobara MI, El-Fallal AA, Omar NF. Gene sequence, modeling, and enzymatic characterization of α-amylase AmyLa from the thermophileLaceyellasp. DS3. STARCH-STARKE 2017. [DOI: 10.1002/star.201600255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ahmed K. A. El-Sayed
- Faculty of Science; Department of Botany and Microbiology; Damietta University; New Damietta Egypt
| | - Mohamed I. Abou-Dobara
- Faculty of Science; Department of Botany and Microbiology; Damietta University; New Damietta Egypt
| | - Amira A. El-Fallal
- Faculty of Science; Department of Botany and Microbiology; Damietta University; New Damietta Egypt
| | - Noha F. Omar
- Faculty of Science; Department of Botany and Microbiology; Damietta University; New Damietta Egypt
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44
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Dey TB, Kumar A, Banerjee R, Chandna P, Kuhad RC. Improvement of microbial α-amylase stability: Strategic approaches. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.06.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Suriya J, Bharathiraja S, Krishnan M, Manivasagan P, Kim SK. Marine Microbial Amylases: Properties and Applications. ADVANCES IN FOOD AND NUTRITION RESEARCH 2016; 79:161-177. [PMID: 27770860 DOI: 10.1016/bs.afnr.2016.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Amylases are crucial enzymes which hydrolyze internal glycosidic linkages in starch and produce as primary products dextrins and oligosaccharides. Amylases are classified into α-amylase, β-amylase, and glucoamylase based on their three-dimensional structures, reaction mechanisms, and amino acid sequences. Amylases have innumerable applications in clinical, medical, and analytical chemistries as well as in food, detergent, textile, brewing, and distilling industries. Amylases can be produced from plants, animals, and microbial sources. Due to the advantages in microbial production, it meets commercial needs. The pervasive nature, easy production, and wide range of applications make amylase an industrially pivotal enzyme. This chapter will focus on amylases found in marine microorganisms, their potential industrial applications, and how these enzymes can be improved to the required bioprocessing conditions.
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Affiliation(s)
- J Suriya
- School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - S Bharathiraja
- CAS in Marine Biology, Annamalai University, Porto Novo, Tamil Nadu, India
| | - M Krishnan
- School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - P Manivasagan
- Marine Bioprocess Research Center, Pukyong National University, Busan, Republic of Korea.
| | - S-K Kim
- Marine Bioprocess Research Center; Specialized Graduate School Science & Technology Convergence, Pukyong National University, Busan, Republic of Korea.
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Marine Microbiological Enzymes: Studies with Multiple Strategies and Prospects. Mar Drugs 2016; 14:md14100171. [PMID: 27669268 PMCID: PMC5082319 DOI: 10.3390/md14100171] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/04/2016] [Accepted: 09/14/2016] [Indexed: 11/16/2022] Open
Abstract
Marine microorganisms produce a series of promising enzymes that have been widely used or are potentially valuable for our daily life. Both classic and newly developed biochemistry technologies have been broadly used to study marine and terrestrial microbiological enzymes. In this brief review, we provide a research update and prospects regarding regulatory mechanisms and related strategies of acyl-homoserine lactones (AHL) lactonase, which is an important but largely unexplored enzyme. We also detail the status and catalytic mechanism of the main types of polysaccharide-degrading enzymes that broadly exist among marine microorganisms but have been poorly explored. In order to facilitate understanding, the regulatory and synthetic biology strategies of terrestrial microorganisms are also mentioned in comparison. We anticipate that this review will provide an outline of multiple strategies for promising marine microbial enzymes and open new avenues for the exploration, engineering and application of various enzymes.
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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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Song Q, Wang Y, Yin C, Zhang XH. LaaA, a novel high-active alkalophilic alpha-amylase from deep-sea bacterium Luteimonas abyssi XH031(T). Enzyme Microb Technol 2016; 90:83-92. [PMID: 27241296 DOI: 10.1016/j.enzmictec.2016.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/30/2016] [Accepted: 05/06/2016] [Indexed: 10/21/2022]
Abstract
Alpha-amylase is a kind of broadly used industrial enzymes, most of which have been exploited from terrestrial organism. Comparatively, alpha-amylase from marine environment was largely undeveloped. In this study, a novel alkalophilic alpha-amylase with high activity, Luteimonas abyssi alpha-amylase (LaaA), was cloned from deep-sea bacterium L. abyssi XH031(T) and expressed in Escherichia coli BL21. The gene has a length of 1428bp and encodes 475 amino acids with a 35-residue signal peptide. The specific activity of LaaA reached 8881U/mg at the optimum pH 9.0, which is obvious higher than other reported alpha-amylase. This enzyme can remain active at pH levels ranging from 6.0 to 11.0 and temperatures below 45°C, retaining high activity even at low temperatures (almost 38% residual activity at 10°C). In addition, 1mM Na(+), K(+), and Mn(2+) enhanced the activity of LaaA. To investigate the function of potential active sites, R227G, D229K, E256Q/H, H327V and D328V mutants were generated, and the results suggested that Arg227, Asp229, Glu256 and Asp328 were total conserved and essential for the activity of alpha-amylase LaaA. This study shows that the alpha-amylase LaaA is an alkali-tolerant and high-active amylase with strong potential for use in detergent industry.
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Affiliation(s)
- Qinghao Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yan Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Chong Yin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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Truncation of the unique N-terminal domain improved the thermos-stability and specific activity of alkaline α-amylase Amy703. Sci Rep 2016; 6:22465. [PMID: 26926401 PMCID: PMC4772547 DOI: 10.1038/srep22465] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/11/2016] [Indexed: 11/08/2022] Open
Abstract
High pH condition is of special interest for the potential applications of alkaline α-amylase in textile and detergent industries. Thus, there is a continuous demand to improve the amylase's properties to meet the requirements set by specific applications. Here we reported the systematic study of modular domain engineering to improve the specific activity and stability of the alkaline α-amylase from Bacillus pseudofirmus 703. The specific activity of the N-terminal domain truncated mutant (N-Amy) increased by ~35-fold with a significantly improved thermo-stability. Kinetic analysis demonstrated that the Kcat and Kcat/Kmof N-Amy were enhanced by 1300-fold and 425.7-fold, respectively, representing the largest catalytic activity improvement of the engineered α-amylases through the methods of domain deletion, fusion or swapping. In addition, different from the wild-type Amy703, no exogenous Ca(2+) were required for N-Amy to maintain its full catalytic activity, implying its superior potential for many industrial processes. Circular dichroism analysis and structure modeling revealed that the increased compactness and α-helical content were the main contributors for the improved thermo-stability of N-Amy, while the improved catalytic efficiency was mainly attributed by the increased conformational flexibility around the active center.
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Acer Ö, Bekler FM, Pirinççioğlu H, Güven RG, Güven K. Purification and Characterization of Thermostable and Detergent-Stable α-Amylase from Anoxybacillus sp. AH1. Food Technol Biotechnol 2016; 54:70-77. [PMID: 27904395 PMCID: PMC5105632 DOI: 10.17133/ftb.54.01.16.4122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 09/11/2015] [Indexed: 09/29/2022] Open
Abstract
A thermostable and detergent-stable α-amylase from a newly isolated Anoxybacillus sp. AH1 was purified and characterized. Maximum enzyme production (1874.8 U/mL) was obtained at 24 h of incubation. The amylase was purified by using Sephadex G-75 gel filtration, after which an 18-fold increase in specific activity and a yield of 9% were achieved. The molecular mass of the purified enzyme was estimated at 85 kDa by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). The optimum pH and temperature values of the enzyme were 7.0 and 60 °C, respectively. The enzyme was highly stable in the presence of 30% glycerol, retaining 85% of its original activity at 60 °C within 120 min. Km and vmax values were 0.102 µmol and 0.929 µmol/min, respectively, using Lineweaver-Burk plot. The enzyme activity was increased by various detergents, but it was significantly inhibited in the presence of urea. Mg2+ and Ca2+ also significantly activated α-amylase, while Zn2+, Cu2+ and metal ion chelators ethylenediaminetetraacetic acid (EDTA) and 1,10-phenanthroline (phen) greatly inhibited the enzyme activity. α-Amylase activity was enhanced by β-mercaptoethanol (β-ME) and dithiothreitol (DTT) to a great extent, but inhibited by p-chloromercuribenzoic acid (PCMB). Iodoacetamide (IAA) and N-ethylmaleimide (NEM) had a slight, whereas phenylmethylsulfonyl fluoride (PMSF) had a strong inhibitory effect on the amylase activity.
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Affiliation(s)
- Ömer Acer
- Molecular Biology and Genetic Department, Faculty of Science, Dicle University, TR-21280 Diyarbakır, Turkey
| | - Fatma Matpan Bekler
- Molecular Biology and Genetic Department, Faculty of Science, Dicle University, TR-21280 Diyarbakır, Turkey
| | - Hemşe Pirinççioğlu
- Molecular Biology and Genetic Department, Faculty of Science, Dicle University, TR-21280 Diyarbakır, Turkey
| | - Reyhan Gül Güven
- Division of Science Teaching, Ziya Gökalp Faculty of Education, Dicle University, TR-21280 Diyarbakır, Turkey
| | - Kemal Güven
- Molecular Biology and Genetic Department, Faculty of Science, Dicle University, TR-21280 Diyarbakır, Turkey
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