Abstract
With the advent of green chemistry, the use of enzymes in industrial processes serves as an alternative to the conventional chemical catalysts. A high demand for sustainable processes for catalysis has brought a significant attention to hunt for novel enzymes. Among various hydrolases, the α-amylase has a gamut of biotechnological applications owing to its pivotal role in starch-hydrolysis. Industrial demand requires enzymes with thermostability and to ameliorate this crucial property, various methods such as protein engineering, directed evolution and enzyme immobilisation strategies are devised. Besides the traditional culture-dependent approach, metagenome from uncultured bacteria serves as a bountiful resource for novel genes/biocatalysts. Exploring the extreme-niches metagenome, advancements in protein engineering and biotechnology tools encourage the mining of novel α-amylase and its stable variants to tap its robust biotechnological and industrial potential. This review outlines α-amylase and its genetics, its catalytic domain architecture and mechanism of action, and various molecular methods to ameliorate its production. It aims to impart understanding on mechanisms involved in thermostability of α-amylase, cover strategies to screen novel genes from futile habitats and some molecular methods to ameliorate its properties.
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References
Aghaei H, Mohammadbagheri Z, Hemasi A, Taghizadeh A (2022) Efficient hydrolysis of starch by α-amylase immobilized on cloisite 30B and modified forms of cloisite 30B by adsorption and covalent methods. Food Chem 373:131425
Ali M, ben, Ghram M, Hmani H, et al (2011) Toward the smallest active subdomain of a TIM-barrel fold: Insights from a truncated α-amylase. Biochem Biophys Res Commun 411:265–270
Alma’abadi A, Behzad H, Alarawi M, et al (2022) Identification of lipolytic enzymes using high-throughput single-cell screening and sorting of a metagenomic library. New Biotechnol 70:102–108
Al-Najada AR, Almulaiky YQ, Aldhahri M et al (2019) Immobilisation of α-amylase on activated amidrazone acrylic fabric: a new approach for the enhancement of enzyme stability and reusability. Sci Rep 9:1–9
Atiroğlu V, Atiroğlu A, Özacar M (2021) Immobilization of α-amylase enzyme on a protein@ metal–organic framework nanocomposite: a new strategy to develop the reusability and stability of the enzyme. Food Chem 349:129127
Ban X, Xie X, Li C et al (2021) The desirable salt bridges in amylases: distribution, configuration and location. Food Chem 354:129475
Bandal JN, Tile VA, Sayyed RZ et al (2021) Statistical based bioprocess design for improved production of amylase from haophilic Bacillus sp. H7 isolated from marine water. Molecules 26:2833
Choure K, Parsai S, Kotoky R et al (2021) Comparative metagenomic analysis of two alkaline hot springs of Madhya Pradesh, India and deciphering the extremophiles for industrial enzymes. Front Genet 12:643423
Datta S, Rajnish KN, Samuel MS et al (2020) Metagenomic applications in microbial diversity, bioremediation, pollution monitoring, enzyme and drug discovery. Review Environ Chem Lett 18:1229–1241
DeCastro M-E, Rodríguez-Belmonte E, González-Siso M-I (2016) Metagenomics of thermophiles with a focus on discovery of novel thermozymes. Front Microbiol 7:1521
Dey TB, Kumar A, Banerjee R et al (2016) Improvement of microbial α-amylase stability: strategic approaches. Process Biochem 51:1380–1390
Elmansy EA, Asker MS, El-Kady EM et al (2018) Production and optimization of α-amylase from thermo-halophilic bacteria isolated from different local marine environments. Bull Natl Res Cent 42:1–9
Elyasi Far B, Dilmaghani A, Yari Khosroushahi A (2020) In silico study and optimization of Bacillus megaterium alpha-amylases production obtained from honey sources. Curr Microbiol 77:2593–2601
Farooq MA, Ali S, Hassan A et al (2021) Biosynthesis and industrial applications of α-amylase: a review. Arch Microbiol 203:1281–1292
Fitter J (2005) Structural and dynamical features contributing to thermostability in α-amylases. Cell Mol Life Sci 62:1925–1937
Gai Y, Chen J, Zhang S et al (2018) Property improvement of α-amylase from Bacillus stearothermophilus by deletion of amino acid residues arginine 179 and glycine 180. Food Technol Biotechnol 56:58–64
Hibbert EG, Dalby PA (2005) Directed evolution strategies for improved enzymatic performance. Microb Cell Fact 4:1–6
Hu X, Yuan X, He N et al (2019) Expression of Bacillus licheniformis α-amylase in Pichia pastoris without antibiotics-resistant gene and effects of glycosylation on the enzymic thermostability. Biotech 9:1–9
Huang L, Shan M, Ma J et al (2019) Directed evolution of α-amylase from Bacillus licheniformis to enhance its acid-stable performance. Biologia (bratisl) 74:1363–1372
Jabbour D, Sorger A, Sahm K, Antranikian G (2013) A highly thermoactive and salt-tolerant α-amylase isolated from a pilot-plant biogas reactor. Appl Microbiol Biotechnol 97:2971–2978
Janecek S, Svensson B, Henrissat B (1997) Domain evolution in the α-amylase family. J Mol Evol 45:322–331
Jensen B, Olsen J (1999) Amylases and their industrial potential. Thermophilic moulds in Biotechnology. Springer, Cham, pp 115–137
Kikani BA, Singh SP (2022) Amylases from thermophilic bacteria: structure and function relationship. Crit Rev Biotechnol 42:325–341
Kuriki T, Hondoh H, Matsuura Y (2005) The conclusive proof that supports the concept of the α-amylase family: structural similarity and common catalytic mechanism. Biologia Bratislava 60:13–16
Ladenstein R, Antranikian G (1998) Proteins from hyperthermophiles: stability and enzymatic catalysis close to the boiling point of water. In: Antranikian G (ed) Biotechnol extremophiles. Springer, Berlin, pp 37–85
Lakshmi SA, Shafreen RB, Balaji K et al (2021) Cloning, expression, homology modelling and molecular dynamics simulation of four domain-containing α-amylase from Streptomyces griseus. J Biomol Struct Dyn 39:2152–2163
Lakshmi SA, Alexpandi R, Shafreen RMB et al (2022) Evaluation of antibiofilm potential of four-domain α-amylase from Streptomyces griseus against exopolysaccharides (EPS) of bacterial pathogens using Danio rerio. Arch Microbiol 204:1–10
Lee J, Xiang L, Byambabaatar S et al (2019) Bacillus licheniformis α-amylase: Structural feature in a biomimetic solution and structural changes in extrinsic conditions. Int J Biol Macromol 127:286–296
Leis B, Angelov A, Mientus M et al (2015) Identification of novel esterase-active enzymes from hot environments by use of the host bacterium Thermus thermophilus. Front Microbiol 6:275
Li Z, Duan X, Chen S, Wu J (2017) Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B. PLoS ONE 12:e0173187
Longwell CK, Labanieh L, Cochran JR (2017) High-throughput screening technologies for enzyme engineering. Curr Opin Biotechnol 48:196–202
López-Gallego F, Fernandez-Lorente G, Rocha-Martín J et al (2020) Multi-point covalent immobilization of enzymes on glyoxyl agarose with minimal physico-chemical modification: stabilization of industrial enzymes. Immobilization of Enzymes and Cells. Springer, New York, pp 93–107
Ma F, Guo T, Zhang Y et al (2021) An ultrahigh-throughput screening platform based on flow cytometric droplet sorting for mining novel enzymes from metagenomic libraries. Environ Microbiol 23:996–1008
MacGregor EA (1988) α-Amylase structure and activity. J Prot Chem 7:399–415
MacGregor EA, Janeček Š, Svensson B (2001) Relationship of sequence and structure to specificity in the α-amylase family of enzymes. Biochimica Et Biophysica Acta (BBA) - Protein Struct Mol Enzym 1546:1–20
Madeira F, Pearce M, Tivey ARN et al (2022) Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res 50(W1):W276–W279
Madhavan A, Arun KB, Binod P et al (2021) Design of novel enzyme biocatalysts for industrial bioprocess: harnessing the power of protein engineering, high throughput screening and synthetic biology. BioresTechnol 325:124617
Mansfeld J, Vriend G, Dijkstra BW et al (1997) Extreme stabilization of a thermolysin-like protease by an engineered disulfide bond. J Biol Chem 272:11152–11156
Markel U, Essani KD, Besirlioglu V et al (2020) Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 49:233–262
Motahar SFS, Khatibi A, Salami M et al (2020) A novel metagenome-derived thermostable and poultry feed compatible α-amylase with enhanced biodegradation properties. Int J Biol Macromol 164:2124–2133
Motahar SFS, Ariaeenejad S, Salami M et al (2021) Improving the quality of gluten-free bread by a novel acidic thermostable α-amylase from metagenomics data. Food Chem 352:129307
Movahedpour A, Asadi M, Khatami SH et al (2022) A brief overview on the application and sources of α-amylase and expression hosts properties in order to production of recombinant α-amylase. Biotechnol Appl Biochem 69:650–659
Nair HP, Bhat SG (2020) Arabian Sea metagenome derived-α-amylase P109 and its potential applications. Ecol Genet Genom 16:100060
Nair HP, Vincent H, Puthusseri RM, Bhat SG (2017) Molecular cloning and characterization of a halotolerant α-amylase from marine metagenomic library derived from Arabian Sea sediments. 3 Biotech 7:1–9
Ngara TR, Zhang H (2018) Recent advances in function-based metagenomic screening. Genom Proteomics Bioinform 16:405–415
Ojha SK, Singh PK, Mishra S et al (2020) Response surface methodology based optimization and scale-up production of amylase from a novel bacterial strain, Bacillus aryabhattai KIIT BE-1. Biotechnol Rep 27:e00506
Pinto ÉSM, Dorn M, Feltes BC (2020) The tale of a versatile enzyme: alpha-amylase evolution, structure, and potential biotechnological applications for the bioremediation of n-alkanes. Chemosphere 250:126202
Rigoldi F, Donini S, Redaelli A et al (2018) Review: engineering of thermostable enzymes for industrial applications. APL Bioeng 2:011501
Robinson SL, Piel J, Sunagawa S (2021) A roadmap for metagenomic enzyme discovery. Nat Product Rep 38:1994–2023
Rodriguez J, Soria F, Geronazzo H, Destefanis H (2016) Modification and characterization of natural aluminosilicates, expanded perlite, and its application to immobilise α–amylase from A. oryzae. J Mol Catal b: Enzym 133:S259–S270
Ruan Y, Zhang R, Xu Y (2022) Directed evolution of maltogenic amylase from Bacillus licheniformis R-53: enhancing activity and thermostability improves bread quality and extends shelf life. Food Chem 381:132222
Saeed AM, El-Shatoury EH, Sayed HAE (2021) Statistical factorial designs for optimum production of thermostable α-amylase by the degradative bacterium Parageobacillus thermoglucosidasius Pharon1 isolated from Sinai. Egypt J Genet Eng Biotechnol 19:1–9
Salt WB, Schenker S (1976) Amylase–its clinical significance: a review of the literature. Medicine 55:269–289
Sanchez AC, Ravanal MC, Andrews BA, Asenjo JA (2019) Heterologous expression and biochemical characterization of a novel cold-active α-amylase from the Antarctic bacteria Pseudoalteromonas sp. 2–3. Protein Expr Purif 155:78–85
Selberg AGA, Gaucher EA, Liberles DA (2021) Ancestral sequence reconstruction: from chemical paleogenetics to maximum likelihood algorithms and beyond. J Mol Evol 89:157–164
Sharma S, Vaid S, Bhat B et al (2019) Thermostable enzymes for industrial biotechnology. advances in enzyme technology. Elsevier, Amsterdam, pp 469–495
Silveira BMP, Barcelos MCS, Vespermann KAC et al (2020) An overview of biotechnological processes in the food industry. Bioprocessing for Biomolecules Production. Wiley, Hoboken, pp 1–19
Sindhu R, Binod P, Madhavan A et al (2017) Molecular improvements in microbial α-amylases for enhanced stability and catalytic efficiency. Bioresour Technol 245:1740–1748
Singh N, Singh V (2022) Singh MP (2022) Microbial degradation of lignocellulosic biomass for bioenergy production: a metagenomic-based approach. Biocatal Biotransform. https://doi.org/10.1080/10242422.2022.2056451
Spence MA, Kaczmarski JA, Saunders JW, Jackson CJ (2021) Ancestral sequence reconstruction for protein engineers. Curr Opin Struct Biol 69:131–141
Stavrakis S, Holzner G, Choo J, DeMello A (2019) High-throughput microfluidic imaging flow cytometry. Curr Opin Biotechnol 55:36–43
Svensson B (1994) Protein engineering in the α-amylase family: catalytic mechanism, substrate specificity, and stability. Plant Mol Biol 25:141–157
Sysoev M, Grötzinger SW, Renn D et al (2021) Bioprospecting of novel extremozymes from prokaryotes—the advent of culture-independent methods. Front Microbiol. https://doi.org/10.3389/fmicb.2021.630013
Tan T-C, Mijts BN, Swaminathan K et al (2008) Crystal structure of the polyextremophilic α-amylase AmyB from Halothermothrix orenii: details of a productive enzyme–substrate complex and an N domain with a role in binding raw starch. J Mol Biol 378:852–870
Tan Y, Zhang Y, Han Y et al (2019) Directed evolution of an α1, 3 fucosyltransferase using a single cell ultrahigh throughput screening method. Sci Adv 5:eaaw8451
Tauzin AS, Pereira MR, van Vliet LD et al (2020) Investigating host-microbiome interactions by droplet based microfluidics. Microbiome 8:1–20
van der Helm E, Genee HJ, Sommer MOA (2018) The evolving interface between synthetic biology and functional metagenomics. Nat Chem Biol 14:752–759
van der Maarel MJEC, van der Veen B, Uitdehaag JCM et al (2002) Properties and applications of starch-converting enzymes of the α-amylase family. J Biotechnol 94:137–155
Vidya J, Swaroop S, Singh S et al (2011) Isolation and characterization of a novel α-amylase from a metagenomic library of Western Ghats of Kerala, India. Biologia (bratisl) 66:939–944
Wang H, Gong Y, Xie W et al (2011) Identification and characterization of a novel thermostable gh-57 gene from metagenomic fosmid library of the Juan de Fuca Ridge hydrothemal vent. Appl Biochem Biotechnol 164:1323–1338
Wang C, Huang R, He B, Du Q (2012) Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis. BMC Bioinform 13:1–8
Wu H, Chen Q, Zhang W (2021) Mu W (2021) overview of strategies for developing high thermostability industrial enzymes: discovery, mechanism, modification and challenges. Crit Rev Food Sci Nut. https://doi.org/10.1080/10408398.2021.1970508
Xu Z, Cen Y-K, Zou S-P et al (2020) Recent advances in the improvement of enzyme thermostability by structure modification. Crit Rev Biotechnol 40:83–98
Yang H, Liu L, Shin H et al (2013) Structure-based engineering of histidine residues in the catalytic domain of α-amylase from Bacillus subtilis for improved protein stability and catalytic efficiency under acidic conditions. J Biotechnol 164:59–66
Yang J, Li L, Xiao Y et al (2016) Identification and thermoadaptation engineering of thermostability conferring residue of deep sea bacterial α-amylase AMY121. J Mol Catal b: Enzym 126:56–63
Yin H, Yang Z, Nie X et al (2017) Functional and cooperative stabilization of a two-metal (Ca, Zn) center in α-amylase derived from Flavobacteriaceae species. Sci Rep 7:1–8
Zeng W, Guo L, Xu S et al (2020) High-throughput screening technology in industrial biotechnology. Trends Biotechnol 38:888–906
Zhang H, Zhai W, Lin L et al (2021) In silico rational design and protein engineering of disulfide bridges of an α-amylase from Geobacillus sp. to improve thermostability. Starch-Stärke 73:2000274
Zhao P, Ren S-M, Liu F et al (2021) Protein engineering of thioether monooxygenase to improve its thermostability for enzymatic synthesis of chiral sulfoxide. Mol Catal 509:111625
Zuber H (1988) Temperature adaptation of lactate dehydrogenase Structural, functional and genetic aspects. Biophys Chem 29:171–179
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PS, KM did the analysis and prepared the manuscript; NT and Keshab Chandra Mondal designed the study, reviewed and edited the manuscript.
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Sharma, P., Mondal, K., Mondal, K.C. et al. Hunt for α-amylase from metagenome and strategies to improve its thermostability: a systematic review. World J Microbiol Biotechnol 38, 203 (2022). https://doi.org/10.1007/s11274-022-03396-0
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DOI: https://doi.org/10.1007/s11274-022-03396-0