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Zhu M, Zhai W, Song R, Lin L, Wei W, Wei D. Enhanced Thermostability of Geobacillus stearothermophilus α-Amylase by Rational Design of Disulfide Bond and Application in Corn Starch Liquefaction and Bread Quality Improvement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18928-18942. [PMID: 38053503 DOI: 10.1021/acs.jafc.3c06761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
α-Amylase (EC 3.2.1.1) from Geobacillus stearothermophilus (generally recognized as safe) exhibited thermal inactivation, hampering its further application in starch-based industries. To address this, we performed structural analyses based on molecular dynamics targeting the flexible regions of α-amylase. Subsequently, we rationally designed a thermostable mutant, AmyS1, by introducing disulfide bonds to stabilize the flexible regions. AmyS1 showed excellent thermostability without any stability-activity trade-off, giving a 40-fold longer T1/2 (1359 min) at 90 °C. Thermostability mechanism analysis revealed that the introduction of disulfide bonds in AmyS1 refined weak spots and reconfigured the protein's force network. Moreover, AmyS1 exhibited improved pH compatibility and enhanced corn starch liquefaction at 100 °C with a 5.1-fold increased product concentration. Baking tests confirmed that AmyS1 enhanced bread quality and extended the shelf life. Therefore, mutant AmyS1 is a robust candidate for the starch-based industry.
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Affiliation(s)
- Mengyu Zhu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Wenxin Zhai
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Runfei Song
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Lin Lin
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
- Research Laboratory for Functional Nanomaterial, National Engineering Research Center for Nanotechnology, Shanghai 200241, China
| | - Wei Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
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Liu X, Geng X, Liu W, Lyu Q. Biochemical characterization of an α-fucosidase PsaFuc from the GH29 family. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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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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Mital S, Christie G, Dikicioglu D. Recombinant expression of insoluble enzymes in Escherichia coli: a systematic review of experimental design and its manufacturing implications. Microb Cell Fact 2021; 20:208. [PMID: 34717620 PMCID: PMC8557517 DOI: 10.1186/s12934-021-01698-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/22/2021] [Indexed: 02/06/2023] Open
Abstract
Recombinant enzyme expression in Escherichia coli is one of the most popular methods to produce bulk concentrations of protein product. However, this method is often limited by the inadvertent formation of inclusion bodies. Our analysis systematically reviews literature from 2010 to 2021 and details the methods and strategies researchers have utilized for expression of difficult to express (DtE), industrially relevant recombinant enzymes in E. coli expression strains. Our review identifies an absence of a coherent strategy with disparate practices being used to promote solubility. We discuss the potential to approach recombinant expression systematically, with the aid of modern bioinformatics, modelling, and ‘omics’ based systems-level analysis techniques to provide a structured, holistic approach. Our analysis also identifies potential gaps in the methods used to report metadata in publications and the impact on the reproducibility and growth of the research in this field.
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Affiliation(s)
- Suraj Mital
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Duygu Dikicioglu
- Department of Biochemical Engineering, University College London, London, WC1E 6BT, UK.
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Kikani BA, Singh SP. Amylases from thermophilic bacteria: structure and function relationship. Crit Rev Biotechnol 2021; 42:325-341. [PMID: 34420464 DOI: 10.1080/07388551.2021.1940089] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Amylases hydrolyze starch to diverse products including dextrins and progressively smaller polymers of glucose units. Thermally stable amylases account for nearly 25% of the enzyme market. This review highlights the structural attributes of the α-amylases from thermophilic bacteria. Heterologous expression of amylases in suitable hosts is discussed in detail. Further, specific value maximization approaches, such as protein engineering and immobilization of the amylases are discussed in order to improve its suitability for varied applications on a commercial scale. The review also takes into account of the immobilization of the amylases on nanomaterials to increase the stability and reusability of the enzymes. The function-based metagenomics would provide opportunities for searching amylases with novel characteristics. The review is expected to explore novel amylases for future potential applications.
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Affiliation(s)
- Bhavtosh A Kikani
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, India.,P.D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Changa, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, India
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Chen L, Yi Z, Fang Y, Jin Y, He K, Xiao Y, Zhao D, Luo H, He H, Sun Q, Zhao H. Biochemical and synergistic properties of a novel alpha-amylase from Chinese nong-flavor Daqu. Microb Cell Fact 2021; 20:80. [PMID: 33827572 PMCID: PMC8028695 DOI: 10.1186/s12934-021-01571-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Daqu is the most important fermentation starter for Chinese liquor, with large number of microbes and enzymes being openly enriched in the Daqu system over thousands of years. However, only a few enzymes have been analyzed with crude protein for total liquefying power and saccharifying power of Daqu. Therefore, the complex enzymatic system present in Daqu has not been completely characterized. Moreover, their pivotal and complicated functions in Daqu are completely unknown. Results
In this study, a novel α-amylase NFAmy13B, from GH13_5 subfamily (according to the Carbohydrate-Active enZYmes Database, CAZy) was successfully heterologous expressed by Escherichia coli from Chinese Nong-flavor (NF) Daqu. It exhibited high stability ranging from pH 5.5 to 12.5, and higher specific activity, compared to other GH13_5 fungal α-amylases. Moreover, NFAmy13B did not show activity loss and retained 96% residual activity after pre-incubation at pH 11 for 21 h and pH 12 for 10 h, respectively. Additionally, 1.25 mM Ca2+ significantly improved its thermostability. NFAmy13B showed a synergistic effect on degrading wheat starch with NFAmy13A (GH13_1), another α-amylase from Daqu. Both enzymes could cleave maltotetraose and maltopentaose in same degradation pattern, and only NFAmy13A could efficiently degrade maltotriose. Moreover, NFAmy13B showed higher catalytic efficiency on long-chain starch, while NFAmy13A had higher catalytic efficiency on short-chain maltooligosaccharides. Their different catalytic efficiencies on starch and maltooligosaccharides may be caused by their discrepant substrate-binding region. Conclusions This study mined a novel GH13_5 fungal α-amylase (NFAmy13B) with outstanding alkali resistance from Nong-flavor (NF) Daqu. Furthermore, its synergistic effect with NFAmy13A (GH13_1) on hydrolyzing wheat starch was confirmed, and their possible contribution in NF Daqu was also speculated. Thus, we not only provide a candidate α-amylase for industry, but also a useful strategy for further studying the interactions in the complex enzyme system of Daqu. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01571-w.
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Affiliation(s)
- Lanchai Chen
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, Sichuan, People's Republic of China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, People's Republic of China
| | - Zhuolin Yi
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yang Fang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yanling Jin
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Kaize He
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yao Xiao
- Analytical and Testing Center, Sichuan University of Science and Engineering, Zigong, 643000, China
| | - Dong Zhao
- Wuliangye Group, Yibin, 644007, China
| | - Huibo Luo
- Liquor Making Bio-Technology and Application of Key Laboratory of Sichuan Province, Bioengineering College, Sichuan University of Science and Engineering, Zigong, 643000, China
| | - Hui He
- Department of Liquor Making Engineering, Moutai College, Renhuai, 564501, China
| | - Qun Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, People's Republic of China.
| | - Hai Zhao
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, Sichuan, People's Republic of China.
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A new GH13 subfamily represented by the α-amylase from the halophilic archaeon Haloarcula hispanica. Extremophiles 2019; 24:207-217. [PMID: 31734852 DOI: 10.1007/s00792-019-01147-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 11/05/2019] [Indexed: 01/16/2023]
Abstract
α-Amylase catalyzes the endohydrolysis of α-1,4-glucosidic linkages in starch and related α-glucans. In the CAZy database, most α-amylases have been classified into the family GH13 counting at present more than 80,000 sequences and ~ 30 different enzyme specificities. The family has already been divided into 42 subfamilies, but additional subfamilies are still emerging. The present bioinformatics study was undertaken in an effort to propose a novel GH13 subfamily around the experimentally characterized α-amylase from the halophilic archaeon Haloarcula hispanica, which until now has not been assigned to any GH13 subfamily. The in silico analysis resulted in collecting a convincing group of putative haloarchaeal α-amylase homologues sharing sequence similarities mainly in their conserved sequence regions (CSRs) and forming a cluster in the evolutionary tree, which is well separated from representatives of established GH13 subfamilies. One of the most exclusive sequence features of the novel GH13 subfamily is the tyrosine (Tyr79 in H. hispanica α-amylase numbering) succeeding the glycine at the beginning of the CSR-VI at the β2 strand of the catalytic TIM-barrel. Evolutionarily, the novel GH13 α-amylase subfamily was most closely related to two clusters of GH13 subfamilies with the specificity of α-amylase, i.e. subfamilies GH13_5, 6 and 7 as well as GH13_15, 24, 27 and 28.
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Yin H, Zhang L, Yang Z, Li S, Nie X, Wang Y, Yang C. Contribution of domain B to the catalytic properties of a Flavobacteriaceae α-amylase. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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9
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Yin H, Yang Z, Nie X, Li S, Sun X, Gao C, Wang Z, Zhou G, Xu P, Yang C. Functional and cooperative stabilization of a two-metal (Ca, Zn) center in α-amylase derived from Flavobacteriaceae species. Sci Rep 2017; 7:17933. [PMID: 29263337 PMCID: PMC5738361 DOI: 10.1038/s41598-017-18085-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/06/2017] [Indexed: 11/09/2022] Open
Abstract
Mesophilic α-amylase from Flavobacteriaceae (FSA) is evolutionary closely related to thermophilic archaeal Pyrococcus furiosus α-amylase (PWA), but lacks the high thermostability, despite the conservation of most residues involved in the two-metal (Ca, Zn) binding center of PWA. In this study, a disulfide bond was introduced near the two-metal binding center of FSA (designated mutant EH-CC) and this modification resulted in a slight improvement in thermostability. As expected, E204G mutations in FSA and EH-CC led to the recovery of Ca2+-binding site. Interestingly, both Ca2+- and Zn2+-dependent thermostability were significantly enhanced; 153.1% or 50.8% activities was retained after a 30-min incubation period at 50 °C, in the presence of Ca2+ or Zn2+. The C214S mutation, which affects Zn2+-binding, also remarkably enhanced Zn2+- and Ca2+- dependent thermostability, indicating that Ca2+- and Zn2+-binding sites function cooperatively to maintain protein stability. Furthermore, an isothermal titration calorimetry (ITC) analysis revealed a novel Zn2+-binding site in mutant EH-CC-E204G. This metal ion cooperation provides a possible method for the generation of α-amylases with desired thermal properties by in silico rational design and systems engineering, to generate a Zn2+-binding site adjacent to the conserved Ca2+-binding site.
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Affiliation(s)
- Huijia Yin
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Zhou Yang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Xinyu Nie
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Shannan Li
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Xuyang Sun
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Chao Gao
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Zenghang Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Guangming Zhou
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Chunyu Yang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China.
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