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Ninck S, Klaus T, Kochetkova TV, Esser SP, Sewald L, Kaschani F, Bräsen C, Probst AJ, Kublanov IV, Siebers B, Kaiser M. Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities. ENVIRONMENTAL MICROBIOME 2024; 19:36. [PMID: 38831353 PMCID: PMC11145796 DOI: 10.1186/s40793-024-00577-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Microbial communities are important drivers of global biogeochemical cycles, xenobiotic detoxification, as well as organic matter decomposition. Their major metabolic role in ecosystem functioning is ensured by a unique set of enzymes, providing a tremendous yet mostly hidden enzymatic potential. Exploring this enzymatic repertoire is therefore not only relevant for a better understanding of how microorganisms function in their natural environment, and thus for ecological research, but further turns microbial communities, in particular from extreme habitats, into a valuable resource for the discovery of novel enzymes with potential applications in biotechnology. Different strategies for their uncovering such as bioprospecting, which relies mainly on metagenomic approaches in combination with sequence-based bioinformatic analyses, have emerged; yet accurate function prediction of their proteomes and deciphering the in vivo activity of an enzyme remains challenging. RESULTS Here, we present environmental activity-based protein profiling (eABPP), a multi-omics approach that extends genome-resolved metagenomics with mass spectrometry-based ABPP. This combination allows direct profiling of environmental community samples in their native habitat and the identification of active enzymes based on their function, even without sequence or structural homologies to annotated enzyme families. eABPP thus bridges the gap between environmental genomics, correct function annotation, and in vivo enzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases from eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia. CONCLUSIONS By reporting enzyme activities within an ecosystem in their native state, we anticipate that eABPP will not only advance current methodological approaches to sequence homology-guided enzyme discovery from environmental ecosystems for subsequent biocatalyst development but also contributes to the ecological investigation of microbial community interactions by dissecting their underlying molecular mechanisms.
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Affiliation(s)
- Sabrina Ninck
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
| | - Thomas Klaus
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Tatiana V Kochetkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60-Let Oktyabrya 7-2, Moscow, 117312, Russia
| | - Sarah P Esser
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Leonard Sewald
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
- Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
- Centre of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60-Let Oktyabrya 7-2, Moscow, 117312, Russia
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany.
| | - Markus Kaiser
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
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2
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Zhuang H, Zheng F, Zhang H, Wang J, Chen J. Efficacious bioconversion of alginate/cellulose to value-added oligosaccharides by alginate-degrading GH5 endoglucanase from Trichoderma asperellum. Int J Biol Macromol 2024; 270:131968. [PMID: 38704059 DOI: 10.1016/j.ijbiomac.2024.131968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/26/2024] [Accepted: 04/27/2024] [Indexed: 05/06/2024]
Abstract
Enzymatic degradation of lignocellulosic biomass provides an eco-friendly approach to produce value-added macromolecules, e.g., bioactive polysaccharides. A novel acidophilic GH5 β-1,4-endoglucanase (termed TaCel5) from Trichoderma asperellum ND-1 was efficiently expressed in Komagataella phaffii (∼1.5-fold increase, 38.42 U/mL). TaCel5 displayed both endoglucanase (486.3 U/mg) and alginate lyase (359.5 U/mg) enzyme activities. It had optimal pH 3.0 and strong pH stability (exceed 86 % activity retained over pH range 3.0-5.0). 80 % activity (both endoglucanase and alginate lyase) was retained in the presence of 15 % ethanol or 3.42 M NaCl. Analysis of action mode revealed that hydrolytic activity of TaCel5 required at least three glucose (cellotriose) residues, yielding mainly cellobiose. Glu241 and Glu352 are essential catalytic residues, while Asp106, Asp277 and Asp317 play auxiliary roles in cellulose degradation. TaCel5 displayed high hydrolysis efficiency for glucan and alginate substrates. ESI-MS analysis indicated that the enzymatic hydrolysates of alginate mainly contained disaccharides and heptasaccharides. This is the first detailed report of a bifunctional GH5 endoglucanase/alginate lyase enzyme from T. asperellum. Thus TaCel5 has strong potential in food and feed industries as a catalyst for bioconversion of cellulose- and alginate-containing waste materials into value-added products oligosaccharides, which was of great benefit both for the economy and environment.
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Affiliation(s)
- Huan Zhuang
- Department of ENT and Head & Neck Surgery, Children's Hospital Zhejiang University School of Medicine, Hangzhou 310051, Zhejiang, China
| | - Fengzhen Zheng
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China.
| | - Hengbin Zhang
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China
| | - Jiaqiang Wang
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China
| | - Jun Chen
- Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310021, China
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3
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Gama Cavalcante AL, Dari DN, Izaias da Silva Aires F, Carlos de Castro E, Moreira Dos Santos K, Sousa Dos Santos JC. Advancements in enzyme immobilization on magnetic nanomaterials: toward sustainable industrial applications. RSC Adv 2024; 14:17946-17988. [PMID: 38841394 PMCID: PMC11151160 DOI: 10.1039/d4ra02939a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024] Open
Abstract
Enzymes are widely used in biofuels, food, and pharmaceuticals. The immobilization of enzymes on solid supports, particularly magnetic nanomaterials, enhances their stability and catalytic activity. Magnetic nanomaterials are chosen for their versatility, large surface area, and superparamagnetic properties, which allow for easy separation and reuse in industrial processes. Researchers focus on the synthesis of appropriate nanomaterials tailored for specific purposes. Immobilization protocols are predefined and adapted to both enzymes and support requirements for optimal efficiency. This review provides a detailed exploration of the application of magnetic nanomaterials in enzyme immobilization protocols. It covers methods, challenges, advantages, and future perspectives, starting with general aspects of magnetic nanomaterials, their synthesis, and applications as matrices for solid enzyme stabilization. The discussion then delves into existing enzymatic immobilization methods on magnetic nanomaterials, highlighting advantages, challenges, and potential applications. Further sections explore the industrial use of various enzymes immobilized on these materials, the development of enzyme-based bioreactors, and prospects for these biocatalysts. In summary, this review provides a concise comparison of the use of magnetic nanomaterials for enzyme stabilization, highlighting potential industrial applications and contributing to manufacturing optimization.
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Affiliation(s)
- Antônio Luthierre Gama Cavalcante
- Departamento de Química Orgânica e Inorgânica, Centro de Ciências, Universidade Federal do Ceará Campus Pici Fortaleza CEP 60455760 CE Brazil
| | - Dayana Nascimento Dari
- Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira Campus das Auroras Redenção CEP 62790970 CE Brazil
| | - Francisco Izaias da Silva Aires
- Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira Campus das Auroras Redenção CEP 62790970 CE Brazil
| | - Erico Carlos de Castro
- Departamento de Química Orgânica e Inorgânica, Centro de Ciências, Universidade Federal do Ceará Campus Pici Fortaleza CEP 60455760 CE Brazil
| | - Kaiany Moreira Dos Santos
- Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira Campus das Auroras Redenção CEP 62790970 CE Brazil
| | - José Cleiton Sousa Dos Santos
- Departamento de Química Orgânica e Inorgânica, Centro de Ciências, Universidade Federal do Ceará Campus Pici Fortaleza CEP 60455760 CE Brazil
- Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira Campus das Auroras Redenção CEP 62790970 CE Brazil
- Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará Campus do Pici, Bloco 940 Fortaleza CEP 60455760 CE Brazil
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Hogg BN, Schnepel C, Finnigan JD, Charnock SJ, Hayes MA, Turner NJ. The Impact of Metagenomics on Biocatalysis. Angew Chem Int Ed Engl 2024; 63:e202402316. [PMID: 38494442 DOI: 10.1002/anie.202402316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/19/2024]
Abstract
In the ever-growing demand for sustainable ways to produce high-value small molecules, biocatalysis has come to the forefront of greener routes to these chemicals. As such, the need to constantly find and optimise suitable biocatalysts for specific transformations has never been greater. Metagenome mining has been shown to rapidly expand the toolkit of promiscuous enzymes needed for new transformations, without requiring protein engineering steps. If protein engineering is needed, the metagenomic candidate can often provide a better starting point for engineering than a previously discovered enzyme on the open database or from literature, for instance. In this review, we highlight where metagenomics has made substantial impact on the area of biocatalysis in recent years. We review the discovery of enzymes in previously unexplored or 'hidden' sequence space, leading to the characterisation of enzymes with enhanced properties that originate from natural selection pressures in native environments.
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Affiliation(s)
- Bethany N Hogg
- Department of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK
| | - Christian Schnepel
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, 11421, Stockholm, SE
| | - James D Finnigan
- Prozomix, Building 4, West End Ind. Estate, Haltwhistle, NE49 9HA, UK
| | - Simon J Charnock
- Prozomix, Building 4, West End Ind. Estate, Haltwhistle, NE49 9HA, UK
| | - Martin A Hayes
- Compound Synthesis and Management, Discovery Sciences, Biopharmaceuticals R&D , AstraZeneca, Mölndal 431 50, Gothenburg, SE
| | - Nicholas J Turner
- Department of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK
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5
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Cowan DA, Albers SV, Antranikian G, Atomi H, Averhoff B, Basen M, Driessen AJM, Jebbar M, Kelman Z, Kerou M, Littlechild J, Müller V, Schönheit P, Siebers B, Vorgias K. Extremophiles in a changing world. Extremophiles 2024; 28:26. [PMID: 38683238 PMCID: PMC11058618 DOI: 10.1007/s00792-024-01341-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the world's attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.
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Affiliation(s)
- D A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa.
| | - S V Albers
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - G Antranikian
- Institute of Technical Biocatalysis, Hamburg University of Technology, 21073, Hamburg, Germany
| | - H Atomi
- Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - B Averhoff
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - M Basen
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - A J M Driessen
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - M Jebbar
- Univ. Brest, CNRS, Ifremer, Laboratoire de Biologie Et d'Écologie Des Écosystèmes Marins Profonds (BEEP), IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Z Kelman
- Institute for Bioscience and Biotechnology Research and the National Institute of Standards and Technology, Rockville, MD, USA
| | - M Kerou
- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - J Littlechild
- Henry Wellcome Building for Biocatalysis, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - V Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - P Schönheit
- Institute of General Microbiology, Christian Albrechts University, Kiel, Germany
| | - B Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, 45117, Essen, Germany
| | - K Vorgias
- Biology Department and RI-Bio3, National and Kapodistrian University of Athens, Athens, Greece
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6
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Salzano F, Aulitto M, Fiorentino G, Cannella D, Peeters E, Limauro D. A novel endo-1,4-β-xylanase from Alicyclobacillus mali FL18: Biochemical characterization and its synergistic action with β-xylosidase in hemicellulose deconstruction. Int J Biol Macromol 2024; 264:130550. [PMID: 38432267 DOI: 10.1016/j.ijbiomac.2024.130550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
A novel endo-1,4-β-xylanase-encoding gene was identified in Alicyclobacillus mali FL18 and the recombinant protein, named AmXyn, was purified and biochemically characterized. The monomeric enzyme worked optimally at pH 6.6 and 80 °C on beechwood xylan with a specific activity of 440.00 ± 0.02 U/mg and a good catalytic efficiency (kcat/KM = 91.89 s-1mLmg-1). In addition, the enzyme did not display any activity on cellulose, suggesting a possible application in paper biobleaching processes. To develop an enzymatic mixture for xylan degradation, the association between AmXyn and the previously characterized β-xylosidase AmβXyl, deriving from the same microorganism, was assessed. The two enzymes had similar temperature and pH optima and showed the highest degree of synergy when AmXyn and AmβXyl were added sequentially to beechwood xylan, making this mixture cost-competitive and suitable for industrial use. Therefore, this enzymatic cocktail was also employed for the hydrolysis of wheat bran residue. TLC and HPAEC-PAD analyses revealed a high conversion rate to xylose (91.56 %), placing AmXyn and AmβXyl among the most promising biocatalysts for the saccharification of agricultural waste.
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Affiliation(s)
- Flora Salzano
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126 Naples, Italy
| | - Martina Aulitto
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126 Naples, Italy
| | - Gabriella Fiorentino
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126 Naples, Italy
| | - David Cannella
- PhotoBiocatalysis Unit, Biomass Transformation lab - BTL, and Crop production and Biostimulation Lab - CPBL, Universitè libre de Brussels, ULB, Belgium
| | - Eveline Peeters
- Department of Bioengineering Sciences Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Danila Limauro
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126 Naples, Italy.
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7
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Wang Y, Qian J, Shi T, Wang Y, Ding Q, Ye C. Application of extremophile cell factories in industrial biotechnology. Enzyme Microb Technol 2024; 175:110407. [PMID: 38341913 DOI: 10.1016/j.enzmictec.2024.110407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/13/2024]
Abstract
Due to the extreme living conditions, extremophiles have unique characteristics in morphology, structure, physiology, biochemistry, molecular evolution mechanism and so on. Extremophiles have superior growth and synthesis capabilities under harsh conditions compared to conventional microorganisms, allowing for unsterilized fermentation processes and thus better performance in low-cost production. In recent years, due to the development and optimization of molecular biology, synthetic biology and fermentation technology, the identification and screening technology of extremophiles has been greatly improved. In this review, we summarize techniques for the identification and screening of extremophiles and review their applications in industrial biotechnology in recent years. In addition, the facts and perspectives gathered in this review suggest that next-generation industrial biotechnology (NGIBs) based on engineered extremophiles holds the promise of simplifying biofuturing processes, establishing open, non-sterilized continuous fermentation production systems, and utilizing low-cost substrates to make NGIBs attractive and cost-effective bioprocessing technologies for sustainable manufacturing.
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Affiliation(s)
- Yuzhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Jinyi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Qiang Ding
- School of Life Sciences, Anhui University, Hefei 230601, PR China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China; Ministry of Education Key Laboratory of NSLSCS.
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8
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Achudhan AB, Kannan P, Gupta A, Saleena LM. A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data. Biochem Genet 2024; 62:621-632. [PMID: 37507643 DOI: 10.1007/s10528-023-10467-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
Metagenomics has now evolved as a promising technology for understanding the microbial population in the environment. By metagenomics, a number of extreme and complex environment has been explored for their microbial population. Using this technology, researchers have brought out novel genes and their potential characteristics, which have robust applications in food, pharmaceutical, scientific research, and other biotechnological fields. A sequencing platform can provide a sequence of microbial populations in any given environment. The sequence needs to be analysed computationally to derive meaningful information. It is presumed that only bioinformaticians with extensive computational skills can process the sequencing data till the downstream end. However, numerous open-source software and online servers are available to analyse the metagenomic data developed for a biologist with less computational skills. This review is focused on bioinformatics tools such as Galaxy, CSI-NGS portal, ANASTASIA and SHAMAN, EBI- metagenomics, IDseq, and MG-RAST for analysing metagenomic data.
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Affiliation(s)
- Arunmozhi Bharathi Achudhan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Priya Kannan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Annapurna Gupta
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Lilly M Saleena
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India.
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Zheng F, Basit A, Wang J, Zhuang H, Chen J, Zhang J. Characterization of a novel acidophilic, ethanol tolerant and halophilic GH12 β-1,4-endoglucanase from Trichoderma asperellum ND-1 and its synergistic hydrolysis of lignocellulosic biomass. Int J Biol Macromol 2024; 254:127650. [PMID: 38287580 DOI: 10.1016/j.ijbiomac.2023.127650] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 10/10/2023] [Accepted: 10/23/2023] [Indexed: 01/31/2024]
Abstract
A novel acidophilic GH5 β-1,4-endoglucanase (TaCel12) from Trichoderma asperellum ND-1 was efficiently expressed in Pichia pastoris (a 1.5-fold increase). Deglycosylated TaCel12 migrated as a single band (26.5 kDa) in SDS-PAGE. TaCel12 was acidophilic with a pH optimum of 4.0 and displayed great pH stability (>80 % activity over pH 3.0-5.0). TaCel12 exhibited considerable activity towards sodium carboxymethyl cellulose and sodium alginate with Vmax values of 197.97 μmol/min/mg and 119.06 μmol/min/mg, respectively. Moreover, TaCel12 maintained >80 % activity in the presence of 20 % ethanol and 4.28 M NaCl. Additionally, Mn2+, Pb2+ and Cu2+ negatively affected TaCel12 activity, while the presence of 5 mM Co2+ significantly increased the enzyme activity. Analysis of action mode revealed that TaCel12 required at least four glucose (cellotetraose) residues for hydrolysis to yield cellobiose and cellotriose. Site-directed mutagenesis results suggested that Glu133 and Glu217 of TaCel12 are crucial catalytic residues, with Asp116 displaying an auxiliary function. Production of soluble sugars from lignocellulose is a crucial step in bioethanol development, and it is noteworthy that TaCel12 could synergistically yield fermentable sugars from corn stover and bagasse, respectively. Thus TaCel12 with excellent properties will be considered a potential biocatalyst for applications in various industries, especially for lignocellulosic biomass conversion.
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Affiliation(s)
- Fengzhen Zheng
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China.
| | - Abdul Basit
- Department of Microbiology, University of Jhang, Jhang 35200, Pakistan
| | - Jiaqiang Wang
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China
| | - Huan Zhuang
- Department of ENT and Head & Neck Surgery, The Children's Hospital Zhejiang University School of Medicine, Zhejiang, Hangzhou 310051, China
| | - Jun Chen
- Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310021, China
| | - Jianfen Zhang
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China
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Yahiaoui B, Bounabi H, Boukerb AM, Gasmi M. Insights into Genomic Features and Potential Biotechnological Applications of Bacillus halotolerans Strain HGR5. Pol J Microbiol 2023; 72:477-490. [PMID: 38103009 PMCID: PMC10725166 DOI: 10.33073/pjm-2023-045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 12/17/2023] Open
Abstract
Algeria is one of the wealthiest countries in terms of hydrothermal sources, with more than two hundred hot springs. However, diverse and little-described microbial communities colonize these habitats, making them an intriguing research subject. This work reports the isolation of bacteria from two hot springs water samples in northeastern Algeria, evaluating their enzymatic activities and effect on plant pathogens. Out of the obtained 72 bacterial isolates and based on the 16S rRNA gene sequence analysis, the strain HGR5 belonging to Bacillus halotolerans had the most interesting activity profile. Interestingly, HGR5 was substantially active against Fusarium graminearum, Phytophthora infestans, and Alternaria alternata. Furthermore, this strain presented a high ability to degrade casein, Tween 80, starch, chitin, cellulose, and xylan. The genome sequence of HGR5 allowed taxonomic validation and screening of specific genetic traits, determining its antagonistic and enzymatic activities. Genome mining revealed that strain HGR5 encloses several secondary metabolite biosynthetic gene clusters (SM-BGCs) involved in metabolite production with antimicrobial properties. Thus, antimicrobial metabolites included bacillaene, fengycin, laterocidine, bacilysin, subtilosin, bacillibactin, surfactin, myxovirescin, dumulmycin, and elansolid A1. HGR5 strain genome was also mined for CAZymes associated with antifungal activity. Finally, the HGR5 strain exhibited the capacity to degrade polycaprolactone (PCL), a model substrate for polyester biodegradation. Overall, these results suggest that this strain may be a promising novel biocontrol agent with interesting plastic-degradation capability, opening the possibilities of its use in various biotechnological applications.
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Affiliation(s)
- Bilal Yahiaoui
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, Ferhat Abbas University, Setif, Algeria
| | - Hadjira Bounabi
- Higher National School of Biotechnology Taoufik Khaznadar, Constantine, Algeria
- Laboratory of Biotechnology, Higher National School of Biotechnology Taoufik Khaznadar, Constantine, Algeria
| | - Amine M. Boukerb
- Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, CBSA UR 4312, Rouen, France
| | - Meriem Gasmi
- Higher National School of Biotechnology Taoufik Khaznadar, Constantine, Algeria
- Laboratory of Biotechnology, Higher National School of Biotechnology Taoufik Khaznadar, Constantine, Algeria
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11
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Burkhardt C, Baruth L, Neele Meyer-Heydecke, Klippel B, Margaryan A, Paloyan A, Panosyan HH, Antranikian G. Mining thermophiles for biotechnologically relevant enzymes: evaluating the potential of European and Caucasian hot springs. Extremophiles 2023; 28:5. [PMID: 37991546 PMCID: PMC10665251 DOI: 10.1007/s00792-023-01321-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/06/2023] [Indexed: 11/23/2023]
Abstract
The development of sustainable and environmentally friendly industrial processes is becoming very crucial and demanding for the rapid implementation of innovative bio-based technologies. Natural extreme environments harbor the potential for discovering and utilizing highly specific and efficient biocatalysts that are adapted to harsh conditions. This review focuses on extremophilic microorganisms and their enzymes (extremozymes) from various hot springs, shallow marine vents, and other geothermal habitats in Europe and the Caucasus region. These hot environments have been partially investigated and analyzed for microbial diversity and enzymology. Hotspots like Iceland, Italy, and the Azores harbor unique microorganisms, including bacteria and archaea. The latest results demonstrate a great potential for the discovery of new microbial species and unique enzymes that can be explored for the development of Circular Bioeconomy.Different screening approaches have been used to discover enzymes that are active at extremes of temperature (up 120 °C), pH (0.1 to 11), high salt concentration (up to 30%) as well as activity in the presence of solvents (up to 99%). The majority of published enzymes were revealed from bacterial or archaeal isolates by traditional activity-based screening techniques. However, the latest developments in molecular biology, bioinformatics, and genomics have revolutionized life science technologies. Post-genomic era has contributed to the discovery of millions of sequences coding for a huge number of biocatalysts. Both strategies, activity- and sequence-based screening approaches, are complementary and contribute to the discovery of unique enzymes that have not been extensively utilized so far.
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Affiliation(s)
- Christin Burkhardt
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Leon Baruth
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Neele Meyer-Heydecke
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Barbara Klippel
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Armine Margaryan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
- Research Institute of Biology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Ani Paloyan
- Scientific and Production Center, "Armbiotechnology" NAS RA, 14 Gyurjyan Str. 0056, Yerevan, Armenia
| | - Hovik H Panosyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
- Research Institute of Biology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Garabed Antranikian
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany.
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12
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Williams GB, Ma H, Khusnutdinova AN, Yakunin AF, Golyshin PN. Harnessing extremophilic carboxylesterases for applications in polyester depolymerisation and plastic waste recycling. Essays Biochem 2023; 67:715-729. [PMID: 37334661 PMCID: PMC10423841 DOI: 10.1042/ebc20220255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023]
Abstract
The steady growth in industrial production of synthetic plastics and their limited recycling have resulted in severe environmental pollution and contribute to global warming and oil depletion. Currently, there is an urgent need to develop efficient plastic recycling technologies to prevent further environmental pollution and recover chemical feedstocks for polymer re-synthesis and upcycling in a circular economy. Enzymatic depolymerization of synthetic polyesters by microbial carboxylesterases provides an attractive addition to existing mechanical and chemical recycling technologies due to enzyme specificity, low energy consumption, and mild reaction conditions. Carboxylesterases constitute a diverse group of serine-dependent hydrolases catalysing the cleavage and formation of ester bonds. However, the stability and hydrolytic activity of identified natural esterases towards synthetic polyesters are usually insufficient for applications in industrial polyester recycling. This necessitates further efforts on the discovery of robust enzymes, as well as protein engineering of natural enzymes for enhanced activity and stability. In this essay, we discuss the current knowledge of microbial carboxylesterases that degrade polyesters (polyesterases) with focus on polyethylene terephthalate (PET), which is one of the five major synthetic polymers. Then, we briefly review the recent progress in the discovery and protein engineering of microbial polyesterases, as well as developing enzyme cocktails and secreted protein expression for applications in the depolymerisation of polyester blends and mixed plastics. Future research aimed at the discovery of novel polyesterases from extreme environments and protein engineering for improved performance will aid developing efficient polyester recycling technologies for the circular plastics economy.
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Affiliation(s)
- Gwion B Williams
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Hairong Ma
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Anna N Khusnutdinova
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Alexander F Yakunin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
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13
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Functional Characterization and Synthetic Application of Is2-SDR, a Novel Thermostable and Promiscuous Ketoreductase from a Hot Spring Metagenome. Int J Mol Sci 2022; 23:ijms232012153. [PMID: 36293010 PMCID: PMC9603792 DOI: 10.3390/ijms232012153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
In a metagenome mining-based search of novel thermostable hydroxysteroid dehydrogenases (HSDHs), enzymes that are able to selectively oxidize/reduce steroidal compounds, a novel short-chain dehydrogenase/reductase (SDR), named Is2-SDR, was recently discovered. This enzyme, found in an Icelandic hot spring metagenome, shared a high sequence similarity with HSDHs, but, unexpectedly, showed no activity in the oxidation of the tested steroid substrates, e.g., cholic acid. Despite that, Is2-SDR proved to be a very active and versatile ketoreductase, being able to regio- and stereoselectively reduce a diversified panel of carbonylic substrates, including bulky ketones, α- and β-ketoesters, and α-diketones of pharmaceutical relevance. Further investigations showed that Is2-SDR was indeed active in the regio- and stereoselective reduction of oxidized steroid derivatives, and this outcome was rationalized by docking analysis in the active site model. Moreover, Is2-SDR showed remarkable thermostability, with an apparent melting temperature (TM) around 75 °C, as determined by circular dichroism analysis, and no significant decrease in catalytic activity, even after 5 h at 80 °C. A broad tolerance to both water-miscible and water-immiscible organic solvents was demonstrated as well, thus, confirming the potential of this new biocatalyst for its synthetic application.
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14
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Liu Y, Luo G, Ngo HH, Zhang S. New approach of bioprocessing towards lignin biodegradation. BIORESOURCE TECHNOLOGY 2022; 361:127730. [PMID: 35932944 DOI: 10.1016/j.biortech.2022.127730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Bio-utilization of lignocellulosic biomass is of huge significance as it can directly replace petroleum resources by producing liquid fuels and organic chemical products in a more sustainable way. However, studies on developing lignin-degrading microbial resources are still very few, which affects on establishing a consolidated bioprocessing of lignocellulosic resource. The main aim of this work is to discover thermostable laccases for lignin thermo-biodegradation by metagenome-mining and biochemical characterization. Results indicate that 124 putative thermostable laccase genes were identified from generated metagenomes. Significantly, 3 rationally selected proteins showed actual activity and structural stability at temperatures up to 60 °C and pH values as low as 4.87. These active recombinant enzymes verify a practical advance in the functional prediction of target proteins, and simultaneous sequence-to-function relationships in this metagenome. In short, the identified thermostable laccase genes in this work could expand range of lignin biocatalysts and contribute to build an efficient lignin biorefinery.
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Affiliation(s)
- Yi Liu
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Gang Luo
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Huu Hao Ngo
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China; Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Shicheng Zhang
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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15
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Escuder-Rodríguez JJ, González-Suarez M, deCastro ME, Saavedra-Bouza A, Becerra M, González-Siso MI. Characterization of a novel thermophilic metagenomic GH5 endoglucanase heterologously expressed in Escherichia coli and Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:76. [PMID: 35799200 PMCID: PMC9264688 DOI: 10.1186/s13068-022-02172-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/24/2022] [Indexed: 01/05/2023]
Abstract
Background Endoglucanases from thermophilic microorganisms are a valuable resource as they can be used in a wide variety of biotechnological applications including the valorisation of biomass and the production of biofuels. In the present work we analysed the metagenome from the hot spring Muiño da Veiga, located in the northwest of Spain (in the Galicia region), in search for novel thermostable endoglucanases. Results Sequence analysis of the metagenome revealed a promising enzyme (Cel776). Predictions on protein structure and conserved amino acid sequences were conducted, as well as expression in heterologous systems with Escherichia coli and Saccharomyces cerevisiae as the host. Cel776Ec was correctly expressed and purified by taking advantage of the His-Tag system, with a yield of 0.346 U/mL in the eluted fraction. Cel776Sc was expressed extracellulary and was easily recovered from the supernatant without the need of further purification, requiring only a concentration step by ultrafiltration, with a significantly higher yield of 531.95 U/mL, revealing a much more suitable system for production of large amounts of the enzyme. Their biochemical characterization revealed biotechnologically interesting enzymes. Both Cel776Ec and Cel776Sc had an optimal temperature of 80 °C and optimal pH of 5. Cel776Ec exhibited high thermostability maintaining its activity for 24 h at 60 °C and maintained its activity longer than Cel776Sc at increasing incubation temperatures. Moreover, its substrate specificity allowed the degradation of both cellulose and xylan. Whereas Cel776Ec was more active in the presence of calcium and magnesium, manganese was found to increase Cel776Sc activity. A stronger inhibitory effect was found for Cel776Ec than Cel776Sc adding detergent SDS to the reaction mix, whereas EDTA only significantly affected Cel776Sc activity. Conclusions Our study reports the discovery of a new promising biocatalyst for its application in processes, such as the production of biofuel and the saccharification of plant biomass, due to its bifunctional enzymatic activity as an endoglucanase and as a xylanase, as well as highlights the advantages of a yeast expression system over bacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02172-4.
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Affiliation(s)
- Juan-José Escuder-Rodríguez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - María González-Suarez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - María-Eugenia deCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - Almudena Saavedra-Bouza
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - Manuel Becerra
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain.
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain.
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16
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Escuder-Rodríguez JJ, DeCastro ME, Saavedra-Bouza A, González-Siso MI, Becerra M. Bioprospecting for Thermozymes and Characterization of a Novel Lipolytic Thermozyme Belonging to the SGNH/GDSL Family of Hydrolases. Int J Mol Sci 2022; 23:5733. [PMID: 35628544 PMCID: PMC9145741 DOI: 10.3390/ijms23105733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
Functional screenings were conducted on two metagenomic libraries from hot springs in order to find novel thermozymes with potential biotechnological applications. These included enzymes acting on plant cell walls such as endoglucanases and exoglucanases, β-glucosidases, xylanases, and β-xylosidases, and broad application enzymes such as proteases and lipolytic hydrolases. Of all the enzymes found by this bioprospection, we selected a novel lipolytic enzyme for further characterization. The protein was found to belong to the SGNH/GDSL family of hydrolases. It was purified and its biochemical parameters determined. We found that the enzyme was most active at 60 °C and pH 9 using pNP-laurate as substrate and was highly thermostable. It also showed preference for short-chained substrates and activation with temperature and with certain detergents such as Tween 80. Proteins of this family of hydrolases are relevant for their broad substrate specificity, that coupled with this protein's high temperature optima, broad pH range, and thermostability further highlights its biotechnological potential.
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Affiliation(s)
| | | | | | - María-Isabel González-Siso
- EXPRELA Group, Advanced Scientific Research Center (CICA), Department of Biology, Faculty of Sciences, Universidade da Coruña, 15071 A Coruña, Spain; (J.-J.E.-R.); (M.-E.D.); (A.S.-B.)
| | - Manuel Becerra
- EXPRELA Group, Advanced Scientific Research Center (CICA), Department of Biology, Faculty of Sciences, Universidade da Coruña, 15071 A Coruña, Spain; (J.-J.E.-R.); (M.-E.D.); (A.S.-B.)
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17
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Hou Q, Pucci F, Pan F, Xue F, Rooman M, Feng Q. Using metagenomic data to boost protein structure prediction and discovery. Comput Struct Biotechnol J 2022; 20:434-442. [PMID: 35070166 PMCID: PMC8760478 DOI: 10.1016/j.csbj.2021.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 11/19/2022] Open
Abstract
Over the past decade, metagenomic sequencing approaches have been providing an ever-increasing amount of protein sequence data at an astonishing rate. These constitute an invaluable source of information which has been exploited in various research fields such as the study of the role of the gut microbiota in human diseases and aging. However, only a small fraction of all metagenomic sequences collected have been functionally or structurally characterized, leaving much of them completely unexplored. Here, we review how this information has been used in protein structure prediction and protein discovery. We begin by presenting some widely used metagenomic databases and analyze in detail how metagenomic data has contributed to the impressive improvement in the accuracy of structure prediction methods in recent years. We then examine how metagenomic information can be exploited to annotate protein sequences. More specifically, we focus on the role of metagenomes in the discovery of enzymes and new CRISPR-Cas systems, and in the identification of antibiotic resistance genes. With this review, we provide an overview of how metagenomic data is currently revolutionizing our understanding of protein science.
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Affiliation(s)
- Qingzhen Hou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250012, China
- National Institute of Health Data Science of China, Shandong University, Shandong 250002, China
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fengming Pan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250012, China
- National Institute of Health Data Science of China, Shandong University, Shandong 250002, China
| | - Fuzhong Xue
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250012, China
- National Institute of Health Data Science of China, Shandong University, Shandong 250002, China
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Qiang Feng
- Shandong Provincial Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Department of Human Microbiome, School of Stomatology, Shandong University, Jinan, Shandong Province 250012, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong Province 266237, China
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18
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Newgas SA, Jeffries JWE, Moody TS, Ward JM, Hailes HC. Discovery of New Carbonyl Reductases Using Functional Metagenomics and Applications in Biocatalysis. Adv Synth Catal 2021; 363:3044-3052. [PMID: 34413714 PMCID: PMC8360200 DOI: 10.1002/adsc.202100199] [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: 02/11/2021] [Revised: 03/22/2021] [Indexed: 12/20/2022]
Abstract
Enzyme discovery for use in the manufacture of chemicals, requiring high stereoselectivities, continues to be an important avenue of research. Here, a sequence directed metagenomics approach is described to identify short chain carbonyl reductases. PCR from a metagenomic template generated 37 enzymes, with an average 25% sequence identity, twelve of which showed interesting activities in initial screens. Six of the most productive enzymes were then tested against a panel of 21 substrates, including bulkier substrates that have been noted as challenging in biocatalytic reductions. Two enzymes were selected for further studies with the Wieland Miescher ketone. Notably, enzyme SDR-17, when co-expressed with a co-factor recycling system produced the anti-(4aR,5S) isomer in excellent isolated yields of 89% and 99% e.e. These results demonstrate the viability of a sequence directed metagenomics approach for the identification of multiple homologous sequences with low similarity, that can yield highly stereoselective enzymes with applicability in industrial biocatalysis.
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Affiliation(s)
- Sophie A. Newgas
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJU.K.
| | - Jack W. E. Jeffries
- Department of Biochemical EngineeringBernard Katz BuildingUniversity College LondonLondonWC1E 6BTU.K.
| | - Thomas S. Moody
- Almac SciencesDepartment of Biocatalysis and Isotope ChemistryAlmac House, 20 Seagoe Industrial EstateCraigavonBT63 5QDNorthern IrelandU.K.
- Arran Chemical CompanyUnit1 Monksland Industrial EstateAthloneN37 DN24Co. RoscommonIreland.
| | - John M. Ward
- Department of Biochemical EngineeringBernard Katz BuildingUniversity College LondonLondonWC1E 6BTU.K.
| | - Helen C. Hailes
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJU.K.
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Reichart NJ, Bowers RM, Woyke T, Hatzenpichler R. High Potential for Biomass-Degrading Enzymes Revealed by Hot Spring Metagenomics. Front Microbiol 2021; 12:668238. [PMID: 33968004 PMCID: PMC8098120 DOI: 10.3389/fmicb.2021.668238] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/29/2021] [Indexed: 12/24/2022] Open
Abstract
Enzyme stability and activity at elevated temperatures are important aspects in biotechnological industries, such as the conversion of plant biomass into biofuels. In order to reduce the costs and increase the efficiency of biomass conversion, better enzymatic processing must be developed. Hot springs represent a treasure trove of underexplored microbiological and protein chemistry diversity. Herein, we conduct an exploratory study into the diversity of hot spring biomass-degrading potential. We describe the taxonomic diversity and carbohydrate active enzyme (CAZyme) coding potential in 71 publicly available metagenomic datasets from 58 globally distributed terrestrial geothermal features. Through taxonomic profiling, we detected a wide diversity of microbes unique to varying temperature and pH ranges. Biomass-degrading enzyme potential included all five classes of CAZymes and we described the presence or absence of genes encoding 19 glycosyl hydrolases hypothesized to be involved with cellulose, hemicellulose, and oligosaccharide degradation. Our results highlight hot springs as a promising system for the further discovery and development of thermo-stable biomass-degrading enzymes that can be applied toward generation of renewable biofuels. This study lays a foundation for future research to further investigate the functional diversity of hot spring biomass-degrading enzymes and their potential utility in biotechnological processing.
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Affiliation(s)
- Nicholas J Reichart
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.,Thermal Biology Institute, Montana State University, Bozeman, MT, United States.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Robert M Bowers
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.,Thermal Biology Institute, Montana State University, Bozeman, MT, United States.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
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20
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Miguel-Ruano V, Rivera I, Rajkovic J, Knapik K, Torrado A, Otero JM, Beneventi E, Becerra M, Sánchez-Costa M, Hidalgo A, Berenguer J, González-Siso MI, Cruces J, Rúa ML, Hermoso JA. Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family. Comput Struct Biotechnol J 2021; 19:1214-1232. [PMID: 33680362 PMCID: PMC7905190 DOI: 10.1016/j.csbj.2021.01.047] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/31/2022] Open
Abstract
A novel esterase, EstD11, has been discovered in a hot spring metagenomic library. It is a thermophilic and thermostable esterase with an optimum temperature of 60°C. A detailed substrate preference analysis of EstD11 was done using a library of chromogenic ester substrate that revealed the broad substrate specificity of EstD11 with significant measurable activity against 16 substrates with varied chain length, steric hindrance, aromaticity and flexibility of the linker between the carboxyl and the alcohol moiety of the ester. The tridimensional structures of EstD11 and the inactive mutant have been determined at atomic resolutions. Structural and bioinformatic analysis, confirm that EstD11 belongs to the family IV, the hormone-sensitive lipase (HSL) family, from the α/β-hydrolase superfamily. The canonical α/β-hydrolase domain is completed by a cap domain, composed by two subdomains that can unmask of the active site to allow the substrate to enter. Eight crystallographic complexes were solved with different substrates and reaction products that allowed identification of the hot-spots in the active site underlying the specificity of the protein. Crystallization and/or incubation of EstD11 at high temperature provided unique information on cap dynamics and a first glimpse of enzymatic activity in vivo. Very interestingly, we have discovered a unique Met zipper lining the active site and the cap domains that could be essential in pivotal aspects as thermo-stability and substrate promiscuity in EstD11.
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Key Words
- CHCA, cyclohexane carboxylic acid
- CMC, critical micellar concentration
- CV, column volume
- Crystal structure
- DMSO, dimethyl sulfoxide
- DSF, Differential scanning fluorimetry
- Enzyme-substrate complex
- FLU, fluorescein
- HSL, hormone-sensitive lipase
- LDAO, N,N-dimethyldodecylamine N-oxide
- MNP, methyl-naproxen
- Metagenomic
- NP, naproxen
- PPL, Porcine Pancreatic Lipase
- Thermophilic esterase
- pNP, 4-nitrophenol
- α/β hydrolase fold
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Affiliation(s)
- Vega Miguel-Ruano
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
| | - Ivanna Rivera
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
| | - Jelena Rajkovic
- Biochemistry Laboratory, CITACA-Agri-Food Research and Transfer Cluster, Campus Auga, University of Vigo, Ourense, Spain
| | - Kamila Knapik
- EXPRELA Group, University A Coruña, Science Faculty, Advanced Scientific Research Center (CICA), A Coruña, Spain
| | - Ana Torrado
- Biochemistry Laboratory, CITACA-Agri-Food Research and Transfer Cluster, Campus Auga, University of Vigo, Ourense, Spain
| | | | | | - Manuel Becerra
- EXPRELA Group, University A Coruña, Science Faculty, Advanced Scientific Research Center (CICA), A Coruña, Spain
| | - Mercedes Sánchez-Costa
- Department of Molecular Biology, Center for Molecular Biology “Severo Ochoa” (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | - Aurelio Hidalgo
- Department of Molecular Biology, Center for Molecular Biology “Severo Ochoa” (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | - José Berenguer
- Department of Molecular Biology, Center for Molecular Biology “Severo Ochoa” (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | - María-Isabel González-Siso
- EXPRELA Group, University A Coruña, Science Faculty, Advanced Scientific Research Center (CICA), A Coruña, Spain
| | | | - María L. Rúa
- Biochemistry Laboratory, CITACA-Agri-Food Research and Transfer Cluster, Campus Auga, University of Vigo, Ourense, Spain
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
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21
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Miao T, Basit A, Wen J, Liu J, Zheng F, Cao Y, Jiang W. High efficient degradation of glucan/glucomannan to cello-/mannan-oligosaccharide by endoglucanase via tetrasaccharide as intermediate. Food Chem 2021; 350:129175. [PMID: 33610847 DOI: 10.1016/j.foodchem.2021.129175] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/27/2020] [Accepted: 01/19/2021] [Indexed: 12/19/2022]
Abstract
Here, we report an efficient endoglucanase from Aureobasidium pullulans (termed ApCel5A) was expressed in Pichia pastoris. ApCel5A shows two different enzyme activities of endoglucanase (1270 U/mg) and mannanase (31.2 U/mg). Through engineering the signal peptide and fed-batch fermentation, the enzyme activity of endoglucanase was improved to 6.63-folds, totally. Its efficient synergism with Celluclast 1.5 L, excellent tolerance to low pH (2.5), cholate and protease suggests potential application in bioresources, food and feed industries. Site-directed mutagenesis experiments present that ApCel5A residues Glu245 and Glu358 are key catalytic sites, while Asp118, Asp122, Asp198 and Asp314 play an auxiliary role. More importantly, ApCel5A display high degradation efficiency of glucan and glucomannan substrates by using tetrasaccharide contained reducing end of glucose residue as an intermediate. This study elucidated the effective methods to improve an endoglucanase expression and detailed catalytic mechanism for degradation of various substrates, which provides a new insight for endoglucanase application.
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Affiliation(s)
- Ting Miao
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Abdul Basit
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Department of Microbiology and Molecular Genetics, Faculty of Life Sciences, University of Okara, Punjab 56300, Pakistan
| | - Jiaqi Wen
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Junquan Liu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fengzhen Zheng
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yunhe Cao
- State Key Laboratory of Animal Nutrition, China Agricultural, University, Beijing, China.
| | - Wei Jiang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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22
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A multi-omic screening approach for the discovery of thermoactive glycoside hydrolases. Extremophiles 2021; 25:101-114. [PMID: 33416984 DOI: 10.1007/s00792-020-01214-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/21/2020] [Indexed: 01/02/2023]
Abstract
Next-generation sequencing and computational biology have facilitated the implementation of new combinatorial screening approaches to discover novel enzymes of biotechnological interest. In this study, we describe the successful establishment of a multi-omic approach for the identification of thermostable hydrolase-encoding genes by determination of gene expression levels. We applied this combinatorial approach using an anaerobic enrichment culture from an Azorean hot spring sample grown on green coffee beans as recalcitrant substrate. An in-depth analysis of the microbial community resulted in microorganisms capable of metabolizing the selected substrate, such as the genera Caloramator, Dictyoglomus and Thermoanaerobacter as active and abundant microorganisms. To discover glycoside hydrolases, 90,342 annotated genes were screened for specific reaction types. A total number of 106 genes encoding cellulases (EC 3.2.1.4), beta-glucosidases (EC 3.2.1.21) and endo-1,4-beta-mannosidases (EC 3.2.1.78) were selected. Mapping of RNA-Seq reads to the related metagenome led to expression levels for each gene. Amongst those, 14 genes, encoding glycoside hydrolases, showed highest expression values, and were used for further cloning. Four proteins were biochemically characterized and were identified as thermoactive glycoside hydrolases with a broad substrate range. This work demonstrated that a combinatory omic approach is a suitable strategy identifying unique thermoactive enzymes from environmental samples.
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23
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Wohlgemuth R. Biocatalysis - Key enabling tools from biocatalytic one-step and multi-step reactions to biocatalytic total synthesis. N Biotechnol 2020; 60:113-123. [PMID: 33045418 DOI: 10.1016/j.nbt.2020.08.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/07/2020] [Accepted: 08/31/2020] [Indexed: 12/20/2022]
Abstract
In the area of human-made innovations to improve the quality of life, biocatalysis has already had a great impact and contributed enormously to a growing number of catalytic transformations aimed at the detection and analysis of compounds, the bioconversion of starting materials and the preparation of target compounds at any scale, from laboratory small scale to industrial large scale. The key enabling tools which have been developed in biocatalysis over the last decades also provide great opportunities for further development and numerous applications in various sectors of the global bioeconomy. Systems biocatalysis is a modular, bottom-up approach to designing the architecture of enzyme-catalyzed reaction steps in a synthetic route from starting materials to target molecules. The integration of biocatalysis and sustainable chemistry in vitro aims at ideal conversions with high molecular economy and their intensification. Retrosynthetic analysis in the chemical and biological domain has been a valuable tool for target-oriented synthesis while, on the other hand, diversity-oriented synthesis builds on forward-looking analysis. Bioinformatic tools for rapid identification of the required enzyme functions, efficient enzyme production systems, as well as generalized bioprocess design tools, are important for rapid prototyping of the biocatalytic reactions. The tools for enzyme engineering and the reaction engineering of each enzyme-catalyzed one-step reaction are also valuable for coupling reactions. The tools to overcome interaction issues with other components or enzymes are of great interest in designing multi-step reactions as well as in biocatalytic total synthesis.
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Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland; Swiss Coordination Committee on Biotechnology (SKB), Nordstrasse 15, 8021 Zürich, Switzerland.
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24
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Myrtollari K, Katsoulakis N, Zarafeta D, Pavlidis IV, Skretas G, Smonou I. Activity and specificity studies of the new thermostable esterase EstDZ2. Bioorg Chem 2020; 104:104214. [PMID: 32927128 DOI: 10.1016/j.bioorg.2020.104214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/23/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Abstract
In this paper, we study the activity and specificity of EstDZ2, a new thermostable carboxyl esterase of unknown function, which was isolated from a metagenome library from a Russian hot spring. The biocatalytic reaction employing EstDZ2 proved to be an efficient method for the hydrolysis of aryl p-, o- or m-substituted esters of butyric acid and esters of secondary alcohols. Docking studies revealed structural features of the enzyme that led to activity differences among the different substrates.
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Affiliation(s)
- Kamela Myrtollari
- Department of Chemistry, University of Crete, University Campus-Voutes, 70013 Heraklion, Crete, Greece
| | - Nikolaos Katsoulakis
- Department of Chemistry, University of Crete, University Campus-Voutes, 70013 Heraklion, Crete, Greece
| | - Dimitra Zarafeta
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Ioannis V Pavlidis
- Department of Chemistry, University of Crete, University Campus-Voutes, 70013 Heraklion, Crete, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Ioulia Smonou
- Department of Chemistry, University of Crete, University Campus-Voutes, 70013 Heraklion, Crete, Greece.
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25
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Ferrandi EE, Bassanini I, Sechi B, Vanoni M, Tessaro D, Guðbergsdóttir SR, Riva S, Peng X, Monti D. Discovery and Characterization of a Novel Thermostable β-Amino Acid Transaminase from a Meiothermus Strain Isolated in an Icelandic Hot Spring. Biotechnol J 2020; 15:e2000125. [PMID: 32893504 DOI: 10.1002/biot.202000125] [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: 05/29/2020] [Revised: 07/29/2020] [Indexed: 02/02/2023]
Abstract
A Meiothermus strain capable of using β-phenylalanine for growth is isolated by culture enrichment of samples collected in hot environments and the genome is sequenced showing the presence of 22 putative transaminase (TA) sequences. On the basis of phylogenetic and sequence analysis, a TA termed Ms-TA2 is selected for further studies. The enzyme is successfully produced in Escherichia coli Rosetta(DE3) cells, with 70 mg of pure protein obtained from 1 L culture after purification by affinity chromatography. Ms-TA2 shows high activity toward (S)-β-phenylalanine and other (S)-β-amino acids, as well as a preference for α-ketoglutarate and aromatic aldehydes as amino acceptors. Moreover, Ms-TA2 is shown to be a thermostable enzyme by maintaining about 60% of the starting activity after 3 h incubation at 50 °C and showing a melting temperature of about 73 °C. Finally, a homology-based structural model of Ms-TA2 is built and key active site interactions for substrate and cofactor binding are analyzed.
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Affiliation(s)
- Erica E Ferrandi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy.,Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, Denmark
| | - Ivan Bassanini
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy.,Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, Milan, 20133, Italy
| | - Barbara Sechi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy
| | - Marta Vanoni
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy
| | - Davide Tessaro
- Dipartimento di Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, Via Mancinelli 7, Milan, 20131, Italy
| | | | - Sergio Riva
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy
| | - Xu Peng
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, Denmark
| | - Daniela Monti
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy
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26
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Han C, Liu Y, Liu M, Wang S, Wang Q. Improving the thermostability of a thermostable endoglucanase from Chaetomium thermophilum by engineering the conserved noncatalytic residue and N-glycosylation site. Int J Biol Macromol 2020; 164:3361-3368. [PMID: 32888988 DOI: 10.1016/j.ijbiomac.2020.08.225] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/15/2020] [Accepted: 08/29/2020] [Indexed: 12/16/2022]
Abstract
Endoglucanases provide an attractive avenue for the bioconversion of lignocellulosic materials into fermentable sugars to supply cellulosic feedstock for biofuels and other value-added chemicals. Thermostable endoglucanases with high catalytic activity are preferred in practical processes. To improve the thermostability and activity of the thermostable β-1,4-endoglucanase CTendo45 isolated from the thermophilic fungus Chaetomium thermophilum, structure-based rational design was performed by using site-directed mutagenesis. When inactivated mutation of the unique N-glycosylation sequon (N88-E89-T90) was implemented and the conserved Y173 residue was substituted with phenylalanine, a double mutant T90A/Y173F demonstrated enzymatic activity that dramatically increased 2.12- and 1.82-fold towards CMC-Na and β-D-glucan, respectively. Additionally, T90A/Y173F exhibited extraordinary heat endurance after 300 min of incubation at elevated temperatures. This study provides a valid approach to the improvement of enzyme redesign protocols and the properties of this endoglucanase mutant distinguish it as an excellent candidate enzyme for industrial biomass conversion.
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Affiliation(s)
- Chao Han
- Shandong Key Laboratory for Agricultural Microbiology, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Yifan Liu
- Shandong Key Laboratory for Agricultural Microbiology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Mengyu Liu
- Shandong Key Laboratory for Agricultural Microbiology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Siqi Wang
- Shandong Key Laboratory for Agricultural Microbiology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Qunqing Wang
- Shandong Key Laboratory for Agricultural Microbiology, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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27
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Billot R, Plener L, Jacquet P, Elias M, Chabrière E, Daudé D. Engineering acyl-homoserine lactone-interfering enzymes toward bacterial control. J Biol Chem 2020; 295:12993-13007. [PMID: 32690609 DOI: 10.1074/jbc.rev120.013531] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/17/2020] [Indexed: 12/20/2022] Open
Abstract
Enzymes able to degrade or modify acyl-homoserine lactones (AHLs) have drawn considerable interest for their ability to interfere with the bacterial communication process referred to as quorum sensing. Many proteobacteria use AHL to coordinate virulence and biofilm formation in a cell density-dependent manner; thus, AHL-interfering enzymes constitute new promising antimicrobial candidates. Among these, lactonases and acylases have been particularly studied. These enzymes have been isolated from various bacterial, archaeal, or eukaryotic organisms and have been evaluated for their ability to control several pathogens. Engineering studies on these enzymes were carried out and successfully modulated their capacity to interact with specific AHL, increase their catalytic activity and stability, or enhance their biotechnological potential. In this review, special attention is paid to the screening, engineering, and applications of AHL-modifying enzymes. Prospects and future opportunities are also discussed with a view to developing potent candidates for bacterial control.
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Affiliation(s)
- Raphaël Billot
- Gene&GreenTK, Marseille, France; IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | | | | | - Mikael Elias
- Molecular Biology and Biophysics and Biotechnology Institute, Department of Biochemistry, University of Minnesota, St. Paul, Minnesota, USA
| | - Eric Chabrière
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France.
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28
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Neves Junior A, da Silva Cardoso V, Mansoldo FRP, Cedrola SML, Reis Mansur MCPP, Godoy MG, Vermelho AB. A microplate assay for extracellular hydrolase detection. J Microbiol Methods 2020; 175:105948. [PMID: 32446912 DOI: 10.1016/j.mimet.2020.105948] [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: 04/09/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 10/24/2022]
Abstract
This article presents a new qualitative method to detect enzyme activity replacing the conventional Agar-Petri dishes. This new method is a simple rapid and low-cost technique that uses 24-well microplates. The detection of hydrolases producing microorganisms in bioprospecting studies by qualitative methods is time consuming, costly and requires a large quantity of strains or enzymatic extracts. Tests with different substrate concentrations (0 to 20 g/L) in agar solution for the enzymatic hydrolysis analysis were performed to determine the best substrate concentrations in 24-well microplates. Other quantitative and analytical methods, such as enzymatic assays and thin layer chromatography, were performed to validate this new method and to compare the relationship between enzymatic activity and substrate degradation. Statistically relevant results were observed for amylase, endoglucanase and polygalacturonase enzymes, even when there was a low substrate concentration in agar, where the halo diameter was high. The results also indicated that the concentrations for efficient enzyme index measurements were 4 g/L carboxymethylcellulose for endoglucanase detection and 8 g/L for amylase and polygalacturonase assays. The results were presented according to the traditional methods for detection of enzymatic activity. This new method can be used as a general test for the detection of important industrial hydrolases. It is a faster and less costly alternative for screening microbial enzyme producing microorganisms and is useful for studying the production of microbial enzymes under different growing conditions.
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Affiliation(s)
- Athayde Neves Junior
- Bioinovar Laboratory, Institute of Microbiology Paulo de Góes, Centro de Ciências da Saúde, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Veronica da Silva Cardoso
- Bioinovar Laboratory, Institute of Microbiology Paulo de Góes, Centro de Ciências da Saúde, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Felipe Raposo Passos Mansoldo
- Bioinovar Laboratory, Institute of Microbiology Paulo de Góes, Centro de Ciências da Saúde, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Sabrina Martins Lage Cedrola
- Bioinovar Laboratory, Institute of Microbiology Paulo de Góes, Centro de Ciências da Saúde, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Maria Cristina P P Reis Mansur
- Bioinovar Laboratory, Institute of Microbiology Paulo de Góes, Centro de Ciências da Saúde, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Mateus Gomes Godoy
- LABEM, Institute of Microbiology Paulo de Góes, Centro de Ciências da Saúde, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Alane Beatriz Vermelho
- Bioinovar Laboratory, Institute of Microbiology Paulo de Góes, Centro de Ciências da Saúde, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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29
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Bertuletti S, Ferrandi EE, Marzorati S, Vanoni M, Riva S, Monti D. Insights into the Substrate Promiscuity of Novel Hydroxysteroid Dehydrogenases. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Susanna Bertuletti
- Istituto di Scienze e Tecnologie Chimiche “G. Natta” (SCITEC), CNR Via Mario Bianco 9 20131 Milano Italy
- Università degli Studi di Milano Via Giuseppe Colombo 60 20133 Milano Italy
| | - Erica Elisa Ferrandi
- Istituto di Scienze e Tecnologie Chimiche “G. Natta” (SCITEC), CNR Via Mario Bianco 9 20131 Milano Italy
| | - Stefano Marzorati
- Istituto di Scienze e Tecnologie Chimiche “G. Natta” (SCITEC), CNR Via Mario Bianco 9 20131 Milano Italy
| | - Marta Vanoni
- Istituto di Scienze e Tecnologie Chimiche “G. Natta” (SCITEC), CNR Via Mario Bianco 9 20131 Milano Italy
| | - Sergio Riva
- Istituto di Scienze e Tecnologie Chimiche “G. Natta” (SCITEC), CNR Via Mario Bianco 9 20131 Milano Italy
| | - Daniela Monti
- Istituto di Scienze e Tecnologie Chimiche “G. Natta” (SCITEC), CNR Via Mario Bianco 9 20131 Milano Italy
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30
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Zarafeta D, Galanopoulou AP, Leni ME, Kaili SI, Chegkazi MS, Chrysina ED, Kolisis FN, Hatzinikolaou DG, Skretas G. XynDZ5: A New Thermostable GH10 Xylanase. Front Microbiol 2020; 11:545. [PMID: 32390953 PMCID: PMC7193231 DOI: 10.3389/fmicb.2020.00545] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
Xylanolytic enzymes have a broad range of applications in industrial biotechnology as biocatalytic components of various processes and products, such as food additives, bakery products, coffee extraction, agricultural silage and functional foods. An increasing market demand has driven the growing interest for the discovery of xylanases with specific industrially relevant characteristics, such as stability at elevated temperatures and in the presence of other denaturing factors, which will facilitate their incorporation into industrial processes. In this work, we report the discovery and biochemical characterization of a new thermostable GH10 xylanase, termed XynDZ5, exhibiting only 26% amino acid sequence identity to the closest characterized xylanolytic enzyme. This new enzyme was discovered in an Icelandic hot spring enrichment culture of a Thermoanaerobacterium species using a recently developed bioinformatic analysis platform. XynDZ5 was produced recombinantly in Escherichia coli, purified and characterized biochemically. This analysis revealed that it acts as an endo-1,4-β-xylanase that performs optimally at 65–75°C and pH 7.5. The enzyme is capable of retaining high levels of catalytic efficiency after several hours of incubation at high temperatures, as well as in the presence of significant concentrations of a range of metal ions and denaturing agents. Interestingly, the XynDZ5 biochemical profile was found to be atypical, as it also exhibits significant exo-activity. Computational modeling of its three-dimensional structure predicted a (β/α)8 TIM barrel fold, which is very frequently encountered among family GH10 enzymes. This modeled structure has provided clues about structural features that may explain aspects of its catalytic performance. Our results suggest that XynDZ5 represents a promising new candidate biocatalyst appropriate for several high-temperature biotechnological applications in the pulp, paper, baking, animal-feed and biofuel industries.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Anastasia P Galanopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Evangelia Leni
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Stavroula I Kaili
- Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Magda S Chegkazi
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Dimitris G Hatzinikolaou
- Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
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Bassanini I, Ferrandi EE, Monti D, Riva S. Studies on the Catalytic Promiscuity of Limonene Epoxide Hydrolases in the Non‐hydrolytic Ring Opening of 1,2‐Epoxides. Chembiochem 2020; 21:1868-1874. [DOI: 10.1002/cbic.201900694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/11/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Ivan Bassanini
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC) – CNR Via Mario Bianco, 9 20131 Milano Italy
- Università degli Studi di MilanoDipartimento di Scienze Farmaceutiche via Mangiagalli 25 20133 Milano Italy
| | - Erica Elisa Ferrandi
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC) – CNR Via Mario Bianco, 9 20131 Milano Italy
| | - Daniela Monti
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC) – CNR Via Mario Bianco, 9 20131 Milano Italy
| | - Sergio Riva
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC) – CNR Via Mario Bianco, 9 20131 Milano Italy
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Merkel AY, Tarnovetskii IY, Podosokorskaya OA, Toshchakov SV. Analysis of 16S rRNA Primer Systems for Profiling of Thermophilic Microbial Communities. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261719060110] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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AidB, a Novel Thermostable N-Acylhomoserine Lactonase from the Bacterium Bosea sp. Appl Environ Microbiol 2019; 85:AEM.02065-19. [PMID: 31604771 DOI: 10.1128/aem.02065-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/04/2019] [Indexed: 11/20/2022] Open
Abstract
Many Gram-negative bacteria employ N-acylhomoserine lactones (AHLs) as quorum-sensing (QS) signal molecules to regulate virulence expression in a density-dependent manner. Quorum quenching (QQ) via enzymatic inactivation of AHLs is a promising strategy to reduce bacterial infections and drug resistance. Herein, a thermostable AHL lactonase (AidB), which could degrade different AHLs, with or without a substitution of carbonyl or hydroxyl at the C-3 position, was identified from the soil bacterium Bosea sp. strain F3-2. Ultrahigh-performance liquid chromatography analysis demonstrated that AidB is an AHL lactonase that hydrolyzes the ester bond of the homoserine lactone (HSL) ring. AidB was thermostable in the range 30 to 80°C and showed maximum activity after preincubation at 60°C for 30 min. The optimum temperature of AidB was 60°C, and the enzyme could be stably stored in double-distilled water (ddH2O) at 4°C or room temperature. AidB homologs were found only in Rhizobiales and Rhodospirillales of the Alphaproteobacteria AidB from Agrobacterium tumefaciens and AidB from Rhizobium multihospitium (with amino acid identities of 50.6% and 52.8% to AidB, respectively) also showed thermostable AHL degradation activity. When introduced into bacteria, plasmid-expressed AidB attenuated pyocyanin production by Pseudomonas aeruginosa PAO1 and the pathogenicity of Pectobacterium carotovorum subsp. carotovorum Z3-3, suggesting that AidB is a potential therapeutic agent by degrading AHLs.IMPORTANCE A quorum-sensing system using AHLs as the signal in many bacterial pathogens is a critical virulence regulator and an attractive target for anti-infective drugs. In this work, we identified a novel AHL lactonase, AidB, from a soil bacterial strain, Bosea sp. F3-2. The expression of aidB reduced the production of AHL signals and QS-dependent virulence factors in Pseudomonas aeruginosa and Pectobacterium carotovorum The homologs of AidB with AHL-degrading activities were found only in several genera belonging to the Alphaproteobacteria Remarkably, AidB is a thermostable enzyme that retained its catalytic activity after treatment at 80°C for 30 min and exhibits reliable storage stability at both 4°C and room temperature. These properties might make it more suitable for practical application.
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Sheldon RA, Brady D. Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis. CHEMSUSCHEM 2019; 12:2859-2881. [PMID: 30938093 DOI: 10.1002/cssc.201900351] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/05/2019] [Accepted: 03/04/2019] [Indexed: 05/21/2023]
Abstract
This Review is aimed at synthetic organic chemists who may be familiar with organometallic catalysis but have no experience with biocatalysis, and seeks to provide an answer to the perennial question: if it is so attractive, why wasn't it extensively used in the past? The development of biocatalysis in industrial organic synthesis is traced from the middle of the last century. Advances in molecular biology in the last two decades, in particular genome sequencing, gene synthesis and directed evolution of proteins, have enabled remarkable improvements in scope and substantially reduced biocatalyst development times and cost contributions. Additionally, improvements in biocatalyst recovery and reuse have been facilitated by developments in enzyme immobilization technologies. Biocatalysis has become eminently competitive with chemocatalysis and the biocatalytic production of important pharmaceutical intermediates, such as enantiopure alcohols and amines, has become mainstream organic synthesis. The synthetic space of biocatalysis has significantly expanded and is currently being extended even further to include new-to-nature biocatalytic reactions.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
- Department of Biotechnology, Delft University of Technology, Section BOC, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
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Koutsandreas T, Ladoukakis E, Pilalis E, Zarafeta D, Kolisis FN, Skretas G, Chatziioannou AA. ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data. Front Genet 2019; 10:469. [PMID: 31178894 PMCID: PMC6543708 DOI: 10.3389/fgene.2019.00469] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 05/01/2019] [Indexed: 01/27/2023] Open
Abstract
Metagenomic analysis of environmental samples provides deep insight into the enzymatic mixture of the corresponding niches, capable of revealing peptide sequences with novel functional properties exploiting the high performance of next-generation sequencing (NGS) technologies. At the same time due to their ever increasing complexity, there is a compelling need for ever larger computational configurations to ensure proper bioinformatic analysis, and fine annotation. With the aiming to address the challenges of such an endeavor, we have developed a novel web-based application named ANASTASIA (automated nucleotide aminoacid sequences translational plAtform for systemic interpretation and analysis). ANASTASIA provides a rich environment of bioinformatic tools, either publicly available or novel, proprietary algorithms, integrated within numerous automated algorithmic workflows, and which enables versatile data processing tasks for (meta)genomic sequence datasets. ANASTASIA was initially developed in the framework of the European FP7 project HotZyme, whose aim was to perform exhaustive analysis of metagenomes derived from thermal springs around the globe and to discover new enzymes of industrial interest. ANASTASIA has evolved to become a stable and extensible environment for diversified, metagenomic, functional analyses for a range of applications overarching industrial biotechnology to biomedicine, within the frames of the ELIXIR-GR project. As a showcase, we report the successful in silico mining of a novel thermostable esterase termed “EstDZ4” from a metagenomic sample collected from a hot spring located in Krisuvik, Iceland.
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Affiliation(s)
- Theodoros Koutsandreas
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,e-NIOS Applications PC, Athens, Greece
| | - Efthymios Ladoukakis
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Eleftherios Pilalis
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,e-NIOS Applications PC, Athens, Greece
| | - Dimitra Zarafeta
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis A Chatziioannou
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,e-NIOS Applications PC, Athens, Greece
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Kumar S, Dangi AK, Shukla P, Baishya D, Khare SK. Thermozymes: Adaptive strategies and tools for their biotechnological applications. BIORESOURCE TECHNOLOGY 2019; 278:372-382. [PMID: 30709766 DOI: 10.1016/j.biortech.2019.01.088] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 05/10/2023]
Abstract
In today's scenario of global climate change, there is a colossal demand for sustainable industrial processes and enzymes from thermophiles. Plausibly, thermozymes are an important toolkit, as they are known to be polyextremophilic in nature. Small genome size and diverse molecular conformational modifications have been implicated in devising adaptive strategies. Besides, the utilization of chemical technology and gene editing attributions according to mechanical necessities are the additional key factor for efficacious bioprocess development. Microbial thermozymes have been extensively used in waste management, biofuel, food, paper, detergent, medicinal and pharmaceutical industries. To understand the strength of enzymes at higher temperatures different models utilize X-ray structures of thermostable proteins, machine learning calculations, neural networks, but unified adaptive measures are yet to be totally comprehended. The present review provides a recent updates on thermozymes and various interdisciplinary applications including the aspects of thermophiles bioengineering utilizing synthetic biology and gene editing tools.
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Affiliation(s)
- Sumit Kumar
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Arun K Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Debabrat Baishya
- Department of Bioengineering and Technology, Institute of Science and Technology, Gauhati University, Guwahati 781014, Assam, India
| | - Sunil K Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India.
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