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Akram F, Fatima T, Shabbir I, Haq IU, Ibrar R, Mukhtar H. Abridgement of Microbial Esterases and Their Eminent Industrial Endeavors. Mol Biotechnol 2024:10.1007/s12033-024-01108-7. [PMID: 38461181 DOI: 10.1007/s12033-024-01108-7] [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: 12/02/2023] [Accepted: 02/05/2024] [Indexed: 03/11/2024]
Abstract
Esterases are hydrolases that contribute to the hydrolysis of ester bonds into both water-soluble acyl esters and emulsified glycerol-esters containing short-chain acyl groups. They have garnered significant attention from biotechnologists and organic chemists due to their immense commercial value. Esterases, with their diverse and significant properties, have become highly sought after for various industrial applications. Synthesized ubiquitously by a wide range of living organisms, including animals, plants, and microorganisms, these enzymes have found microbial esterases to be the preferred choice in industrial settings. The cost-effective production of microbial esterases ensures higher yields, unaffected by seasonal variations. Their applications span diverse sectors, such as food manufacturing, leather tanneries, paper and pulp production, textiles, detergents, cosmetics, pharmaceuticals, biodiesel synthesis, bioremediation, and waste treatment. As the global trend shifts toward eco-friendly and sustainable practices, industrial processes are evolving with reduced waste generation, lower energy consumption, and the utilization of biocatalysts derived from renewable and unconventional raw materials. This review explores the background, structural characteristics, thermostability, and multifaceted roles of bacterial esterases in crucial industries, aiming to optimize and analyze their properties for continued successful utilization in diverse industrial processes. Additionally, recent advancements in esterase research are overviewed, showcasing novel techniques, innovations, and promising areas for further exploration.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Taseer Fatima
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ifrah Shabbir
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
- Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Ramesha Ibrar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Hamid Mukhtar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
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Kirchner L, Müller V, Averhoff B. A temperature dependent pilin promoter for production of thermostable enzymes in Thermus thermophilus. Microb Cell Fact 2023; 22:187. [PMID: 37726752 PMCID: PMC10507856 DOI: 10.1186/s12934-023-02192-1] [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: 07/27/2023] [Accepted: 09/02/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Enzymes from thermophiles are of great interest for research and bioengineering due to their stability and efficiency. Thermophilic expression hosts such as Thermus thermophilus [T. thermophilus] can overcome specific challenges experienced with protein production in mesophilic expression hosts, such as leading to better folding, increased protein stability, solubility, and enzymatic activity. However, available inducible promoters for efficient protein production in T. thermophilus HB27 are limited. RESULTS In this study, we characterized the pilA4 promoter region and evaluated its potential as a tool for production of thermostable enzymes in T. thermophilus HB27. Reporter gene analysis using a promoterless β-glucosidase gene revealed that the pilA4 promoter is highly active under optimal growth conditions at 68 °C and downregulated during growth at 80 °C. Furthermore, growth in minimal medium led to significantly increased promoter activity in comparison to growth in complex medium. Finally, we proved the suitability of the pilA4 promoter for heterologous production of thermostable enzymes in T. thermophilus by producing a fully active soluble mannitol-1-phosphate dehydrogenase from Thermoanaerobacter kivui [T. kivui], which is used in degradation of brown algae that are rich in mannitol. CONCLUSIONS Our results show that the pilA4 promoter is an efficient tool for gene expression in T. thermophilus with a high potential for use in biotechnology and synthetic biology applications.
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Affiliation(s)
- Lennart Kirchner
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue- Str. 9, 60438, Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue- Str. 9, 60438, Frankfurt, Germany
| | - Beate Averhoff
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue- Str. 9, 60438, Frankfurt, Germany.
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3
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Ribeiro AL, Sánchez M, Bosch S, Berenguer J, Hidalgo A. Stabilization of Enzymes by Using Thermophiles. Methods Mol Biol 2023; 2704:313-328. [PMID: 37642853 DOI: 10.1007/978-1-0716-3385-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Manufactured steroid compounds have many applications in the pharmaceutical industry. Due to the chemical complexity and chirality of steroids, there is an increasing demand for enzyme-based bioconversion processes to replace those based on chemical synthesis. In this context, thermostability of the involved enzymes is a highly desirable property as both the increased half-life of the enzyme and the enhanced solubility of substrates and products will improve the yield of the reactions. Metagenomic libraries from thermal environments are potential sources of thermostable enzymes of prokaryotic origin, but the number of expected hits could be quite low for enzymes handling substrates such as steroids, rarely found in prokaryotes. An alternative to metagenome screening is the selection of thermostable variants of well-known steroid-processing enzymes. Here we review and detail a protocol for such selection, where error-prone PCR (epPCR) is used to introduce random mutations into a gene to create a variants library for further selection of thermostable variants in the thermophile Thermus thermophilus. The method involves the use of folding interference vectors where the proper folding of the enzyme of interest at high temperature is linked to the folding of a reporter encoding a selectable property such as thermostable resistance to kanamycin, leading to a life-or-death selection of variants of reinforced folding independently of the activity of the enzyme.
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Affiliation(s)
- Ana-Luisa Ribeiro
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC). Facultad de Ciencias. Universidad Autónoma de Madrid, Madrid, Spain
| | - Mercedes Sánchez
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC). Facultad de Ciencias. Universidad Autónoma de Madrid, Madrid, Spain
| | - Sandra Bosch
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC). Facultad de Ciencias. Universidad Autónoma de Madrid, Madrid, Spain
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC). Facultad de Ciencias. Universidad Autónoma de Madrid, Madrid, Spain
| | - Aurelio Hidalgo
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC). Facultad de Ciencias. Universidad Autónoma de Madrid, Madrid, Spain.
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Kruglikov A, Wei Y, Xia X. Proteins from Thermophilic Thermus thermophilus Often Do Not Fold Correctly in a Mesophilic Expression System Such as Escherichia coli. ACS OMEGA 2022; 7:37797-37806. [PMID: 36312379 PMCID: PMC9608423 DOI: 10.1021/acsomega.2c04786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Majority of protein structure studies use Escherichia coli (E. coli) and other model organisms as expression systems for other species' genes. However, protein folding depends on cellular environment factors, such as chaperone proteins, cytoplasmic pH, temperature, and ionic concentrations. Because of differences in these factors, especially temperature and chaperones, native proteins in organisms such as extremophiles may fold improperly when they are expressed in mesophilic model organisms. Here we present a methodology of assessing the effects of using E. coli as the expression system on protein structures. We compare these effects between eight mesophilic bacteria and Thermus thermophilus (T. thermophilus), a thermophile, and found that differences are significantly larger for T. thermophilus. More specifically, helical secondary structures in T. thermophilus proteins are often replaced by coil structures in E. coli. Our results show unique directionality in misfolding when proteins in thermophiles are expressed in mesophiles. This indicates that extremophiles, such as thermophiles, require unique protein expression systems in protein folding studies.
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Affiliation(s)
- Alibek Kruglikov
- Department
of Biology, University of Ottawa, Ottawa, Canada K1N 6N5
| | - Yulong Wei
- Department
of Biology, University of Ottawa, Ottawa, Canada K1N 6N5
| | - Xuhua Xia
- Department
of Biology, University of Ottawa, Ottawa, Canada K1N 6N5
- Ottawa
Institute of Systems Biology, University
of Ottawa, Ottawa, Canada K1N 6N5
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Bosch S, Sanchez-Freire E, del Pozo ML, C̆esnik M, Quesada J, Mate DM, Hernández K, Qi Y, Clapés P, Vasić-Rački Đ, Findrik Blažević Z, Berenguer J, Hidalgo A. Thermostability Engineering of a Class II Pyruvate Aldolase from Escherichia coli by in Vivo Folding Interference. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2021; 9:5430-5436. [PMID: 34589311 PMCID: PMC8461973 DOI: 10.1021/acssuschemeng.1c00699] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/21/2021] [Indexed: 06/13/2023]
Abstract
The use of enzymes in industrial processes is often limited by the unavailability of biocatalysts with prolonged stability. Thermostable enzymes allow increased process temperature and thus higher substrate and product solubility, reuse of expensive biocatalysts, resistance against organic solvents, and better "evolvability" of enzymes. In this work, we have used an activity-independent method for the selection of thermostable variants of any protein in Thermus thermophilus through folding interference at high temperature of a thermostable antibiotic reporter protein at the C-terminus of a fusion protein. To generate a monomeric folding reporter, we have increased the thermostability of the moderately thermostable Hph5 variant of the hygromycin B phosphotransferase from Escherichia coli to meet the method requirements. The final Hph17 variant showed 1.5 °C higher melting temperature (T m) and 3-fold longer half-life at 65 °C compared to parental Hph5, with no changes in the steady-state kinetic parameters. Additionally, we demonstrate the validity of the reporter by stabilizing the 2-keto-3-deoxy-l-rhamnonate aldolase from E. coli (YfaU). The most thermostable multiple-mutated variants thus obtained, YfaU99 and YfaU103, showed increases of 2 and 2.9 °C in T m compared to the wild-type enzyme but severely lower retro-aldol activities (150- and 120-fold, respectively). After segregation of the mutations, the most thermostable single variant, Q107R, showed a T m 8.9 °C higher, a 16-fold improvement in half-life at 60 °C and higher operational stability than the wild-type, without substantial modification of the kinetic parameters.
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Affiliation(s)
- Sandra Bosch
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Esther Sanchez-Freire
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - María Luisa del Pozo
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Morana C̆esnik
- University
of Zagreb, Faculty of Chemical
Engineering and Technology, Savska c. 16, HR-10000 Zagreb, Croatia
| | - Jaime Quesada
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Diana M. Mate
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Karel Hernández
- Institute
of Advanced Chemistry of Catalonia, Biotransformation and Bioactive
Molecules Group, Spanish National Research Council (IQAC−CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Yuyin Qi
- Prozomix
Ltd., Station Court, Haltwhistle, NE49 9HN Northumberland, United Kingdom
| | - Pere Clapés
- Institute
of Advanced Chemistry of Catalonia, Biotransformation and Bioactive
Molecules Group, Spanish National Research Council (IQAC−CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Đurđa Vasić-Rački
- University
of Zagreb, Faculty of Chemical
Engineering and Technology, Savska c. 16, HR-10000 Zagreb, Croatia
| | - Zvjezdana Findrik Blažević
- University
of Zagreb, Faculty of Chemical
Engineering and Technology, Savska c. 16, HR-10000 Zagreb, Croatia
| | - José Berenguer
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Aurelio Hidalgo
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
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Xing H, Zou G, Liu C, Chai S, Yan X, Li X, Liu R, Yang Y, Zhou Z. Improving the thermostability of a GH11 xylanase by directed evolution and rational design guided by B-factor analysis. Enzyme Microb Technol 2020; 143:109720. [PMID: 33375980 DOI: 10.1016/j.enzmictec.2020.109720] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/20/2020] [Accepted: 11/26/2020] [Indexed: 01/19/2023]
Abstract
Operational stability under high temperature is required for enzyme application in industrial processes. Error-prone PCR and B-factor analysis were employed to enhance the thermostability of a xylanase from GH family 11 in this study. Based on the top 10 mutants screened from the random mutation libraries, mutant Xyn371 was derived from the optimal mutant Xyn370 by integrating the beneficial residues identified in the other 9 screened mutants. Subsequently, a best-saturation mutant Xyn372 originated from Xyn371 was selected with a 60-min half-life at 70 °C (0.5-min half-life for the wild-type enzyme). According to the site-saturated mutagenesis of 10 residues with higher B-factors in Xyn372, mutants Xyn375 and Xyn376 were screened; their half-lives at 70 °C were 410 and 360 min, respectively. The substituted residues located in the "palm" region of the N-terminus and the newly generated hydrogen bonds in the mutants might contribute to improved thermostability. The significantly improved thermostability of mutants will pave the way for applications in different industrial areas.
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Affiliation(s)
- Hongguan Xing
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China; Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Meilong Rd 130, Shanghai, 200237, China
| | - Gen Zou
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
| | - Chunyan Liu
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
| | - Shunxing Chai
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
| | - Xing Yan
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China
| | - Xinliang Li
- CJ, Youtell (Shanghai) Biotech Co., Ltd, Ste 302, Bldg 7, 526 Ruiqing Rd, Shanghai 201201, China
| | - Rui Liu
- CJ, Youtell (Shanghai) Biotech Co., Ltd, Ste 302, Bldg 7, 526 Ruiqing Rd, Shanghai 201201, China
| | - Yi Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Meilong Rd 130, Shanghai, 200237, China
| | - Zhihua Zhou
- CAS-key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Rd 300, Shanghai, 200032, China.
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Song Y, Zhu Z, Zhou W, Zhang YHPJ. High-efficiency transformation of archaea by direct PCR products with its application to directed evolution of a thermostable enzyme. Microb Biotechnol 2020; 14:453-464. [PMID: 32602260 PMCID: PMC7936305 DOI: 10.1111/1751-7915.13613] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/16/2020] [Accepted: 05/31/2020] [Indexed: 01/09/2023] Open
Abstract
Hyperthermophilic archaea with unique biochemical and physiological characteristics are important organisms for fundamental research of life science and have great potential for biotechnological applications. However, low transformation efficiency of foreign DNA molecules impedes developments in genetic modification tools and industrial applications. In this study, we applied prolonged overlap extension PCR (POE-PCR) to generate multimeric DNA molecules and then transformed them into two hyperthermophilic archaea, Thermococcus kodakarensis KOD1 and Pyrococcus yayanosii A1. This study was the first example to demonstrate the enhanced transformation efficiencies of POE-PCR products by a factor of approximately 100 for T. kodakarensis KOD1 and 8 for P. yayanosii A1, respectively, relative to circular shuttle plasmids. Furthermore, directed evolution of a modestly thermophilic enzyme, Methanothermococcus okinawensis 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR), was conducted to obtain more stable ones due to high transformation efficiency of T. kodakarensis (i.e. ~3 × 104 CFU per μg DNA). T. kodakarensis harbouring the most thermostable MoHMGR mutant can grow in the presence of a thermostable antibiotic simvastatin at 85°C and even higher temperatures. This high transformation efficiency technique could not only help develop more hyperthermophilic enzyme mutants via directed evolution but also simplify genetical modification of archaea, which could be novel hosts for industrial biotechnology.
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Affiliation(s)
- Yunhong Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Wei Zhou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
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