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Sadaqat B, Dar MA, Sha C, Abomohra A, Shao W, Yong YC. Thermophilic β-mannanases from bacteria: production, resources, structural features and bioengineering strategies. World J Microbiol Biotechnol 2024; 40:130. [PMID: 38460032 DOI: 10.1007/s11274-024-03912-4] [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: 12/01/2023] [Accepted: 01/29/2024] [Indexed: 03/11/2024]
Abstract
β-mannanases are pivotal enzymes that cleave the mannan backbone to release short chain mannooligosaccharides, which have tremendous biotechnological applications including food/feed, prebiotics and biofuel production. Due to the high temperature conditions in many industrial applications, thermophilic mannanases seem to have great potential to overcome the thermal impediments. Thus, structural analysis of thermostable β-mannanases is extremely important, as it could open up new avenues for genetic engineering, and protein engineering of these enzymes with enhanced properties and catalytic efficiencies. Under this scope, the present review provides a state-of-the-art discussion on the thermophilic β-mannanases from bacterial origin, their production, engineering and structural characterization. It covers broad insights into various molecular biology techniques such as gene mutagenesis, heterologous gene expression, and protein engineering, that are employed to improve the catalytic efficiency and thermostability of bacterial mannanases for potential industrial applications. Further, the bottlenecks associated with mannanase production and process optimization are also discussed. Finally, future research related to bioengineering of mannanases with novel protein expression systems for commercial applications are also elaborated.
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Affiliation(s)
- Beenish Sadaqat
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
- Department of Biochemistry and Structural Biology, Lund University, Box 124, 22100, Lund, Sweden
| | - Mudasir A Dar
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
| | - Chong Sha
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
| | - Abdelfatah Abomohra
- Aquatic Ecophysiology and Phycology, Department of Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, 22609, Germany
| | - Weilan Shao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China.
| | - Yang-Chun Yong
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China.
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Ghaedizadeh S, Zeinali M, Dabirmanesh B, Rasekh B, Khajeh K, Banaei-Moghaddam AM. Rational design engineering of a more thermostable Sulfurihydrogenibium yellowstonense carbonic anhydrase for potential application in carbon dioxide capture technologies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140962. [PMID: 37716447 DOI: 10.1016/j.bbapap.2023.140962] [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: 06/19/2023] [Revised: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 09/18/2023]
Abstract
Implementing hyperthermostable carbonic anhydrases into CO2 capture and storage technologies in order to increase the rate of CO2 absorption from the industrial flue gases is of great importance from technical and economical points of view. The present study employed a combination of in silico tools to further improve thermostability of a known thermostable carbonic anhydrase from Sulfurihydrogenibium yellowstonense. Experimental results showed that our rationally engineered K100G mutant not only retained the overall structure and catalytic efficiency but also showed a 3 °C increase in the melting temperature and a two-fold improvement in the enzyme half-life at 85 °C. Based on the molecular dynamics simulation results, rearrangement of salt bridges and hydrogen interactions network causes a reduction in local flexibility of the K100G variant. In conclusion, our study demonstrated that thermostability can be improved through imposing local structural rigidity by engineering a single-point mutation on the surface of the enzyme.
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Affiliation(s)
- Shima Ghaedizadeh
- Laboratory of Genomics and Epigenomics (LGE), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Majid Zeinali
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry (RIPI), Tehran, Iran.
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Behnam Rasekh
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry (RIPI), Tehran, Iran
| | - Khosrow Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Mohammad Banaei-Moghaddam
- Laboratory of Genomics and Epigenomics (LGE), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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3
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Jia R, Tian S, Yang Z, Sadiq FA, Wang L, Lu S, Zhang G, Li J. Tuning Thermostability and Catalytic Efficiency of Aflatoxin-Degrading Enzyme by Error-prone PCR. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12610-4. [PMID: 37300712 DOI: 10.1007/s00253-023-12610-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/08/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
In our previous work, a recombinant aflatoxin-degrading enzyme derived from Myxococcus fulvus (MADE) was reported. However, the low thermal stability of the enzyme had limitations for its use in industrial applications. In this study, we obtained an improved variant of recombinant MADE (rMADE) with enhanced thermostability and catalytic activity using error-prone PCR. Firstly, we constructed a mutant library containing over 5000 individual mutants. Three mutants with T50 values higher than the wild-type rMADE by 16.5 °C (rMADE-1124), 6.5 °C (rMADE-1795), and 9.8 °C (rMADE-2848) were screened by a high-throughput screening method. Additionally, the catalytic activity of rMADE-1795 and rMADE-2848 was improved by 81.5% and 67.7%, respectively, compared to the wild-type. Moreover, structural analysis revealed that replacement of acidic amino acids with basic amino acids by a mutation (D114H) in rMADE-2848 increased the polar interactions with surrounding residues and resulted in a threefold increase in the t1/2 value of the enzyme and made it more thermaltolerate. KEY POINTS: • Mutant libraries construction of a new aflatoxins degrading enzyme by error-prone PCR. • D114H/N295D mutant improved enzyme activity and thermostability. • The first reported enhanced thermostability of aflatoxins degrading enzyme better for its application.
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Affiliation(s)
- Ru Jia
- School of Life Science, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China.
| | - Senmiao Tian
- School of Life Science, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China
| | - Zhaofeng Yang
- School of Life Science, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China
| | - Faizan Ahmed Sadiq
- Fisheries and Food, Technology & Food Science Unit, Flanders Research Institute for Agriculture, 9090, Melle, Belgium
| | - Lan Wang
- School of Life Science, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China
| | - Simeng Lu
- School of Life Science, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China
| | - Guohua Zhang
- School of Life Science, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China
| | - Jianhui Li
- College of Animal Sciences, Shanxi Agriculture University, Taigu, 030801, China
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4
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Nezhad NG, Rahman RNZRA, Normi YM, Oslan SN, Shariff FM, Leow TC. Recent advances in simultaneous thermostability-activity improvement of industrial enzymes through structure modification. Int J Biol Macromol 2023; 232:123440. [PMID: 36708895 DOI: 10.1016/j.ijbiomac.2023.123440] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
Engineered thermostable microbial enzymes are widely employed to catalyze chemical reactions in numerous industrial sectors. Although high thermostability is a prerequisite of industrial applications, enzyme activity is usually sacrificed during thermostability improvement. Therefore, it is vital to select the common and compatible strategies between thermostability and activity improvement to reduce mutants̕ libraries and screening time. Three functional protein engineering approaches, including directed evolution, rational design, and semi-rational design, are employed to manipulate protein structure on a genetic basis. From a structural standpoint, integrative strategies such as increasing substrate affinity; introducing electrostatic interaction; removing steric hindrance; increasing flexibility of the active site; N- and C-terminal engineering; and increasing intramolecular and intermolecular hydrophobic interactions are well-known to improve simultaneous activity and thermostability. The current review aims to analyze relevant strategies to improve thermostability and activity simultaneously to circumvent the thermostability and activity trade-off of industrial enzymes.
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Affiliation(s)
- Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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Monica P, Mutturi S, Kapoor M. Truncation of C-terminal amino acids of GH26 endo-mannanase (ManB-1601) affects biochemical properties and stability against anionic surfactants. Enzyme Microb Technol 2022; 157:110031. [DOI: 10.1016/j.enzmictec.2022.110031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/18/2022] [Accepted: 03/10/2022] [Indexed: 11/16/2022]
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Current Status of Mining, Modification, and Application of Cellulases in Bioactive Substance Extraction. Curr Issues Mol Biol 2021; 43:687-703. [PMID: 34287263 PMCID: PMC8929041 DOI: 10.3390/cimb43020050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 11/24/2022] Open
Abstract
Cellulases have been used to extract bioactive ingredients from medical plants; however, the poor enzymatic properties of current cellulases significantly limit their application. Two strategies are expected to address this concern: (1) new cellulase gene mining strategies have been promoted, optimized, and integrated, thanks to the improvement of gene sequencing, genomic data, and algorithm optimization, and (2) known cellulases are being modified, thanks to the development of protein engineering, crystal structure data, and computing power. Here, we focus on mining strategies and provide a systemic overview of two approaches based on sequencing and function. Strategies based on protein structure modification, such as introducing disulfide bonds, proline, salt bridges, N-glycosylation modification, and truncation of loop structures, have already been summarized. This review discusses four aspects of cellulase-assisted extraction. Initially, cellulase alone was used to extract bioactive substances, and later, mixed enzyme systems were developed. Physical methods such as ultrasound, microwave, and high hydrostatic pressure have assisted in improving extraction efficiency. Cellulase changes the structure of biomolecules during the extraction process to convert them into effective ingredients with better activity and bioavailability. The combination of cellulase with other enzymes and physical technologies is a promising strategy for future extraction applications.
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He L, Zhang R, Shen J, Miao Y, Tang X, Wu Q, Zhou J, Huang Z. Removal of N-terminal tail changes the thermostability of the low-temperature-active exo-inulinase InuAGN25. Bioengineered 2020; 11:921-931. [PMID: 32865156 PMCID: PMC8291819 DOI: 10.1080/21655979.2020.1809921] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Exo-inulinases are members of the glycoside hydrolase family 32 and function by hydrolyzing inulin into fructose with yields up to 90–95%. The N-terminal tail contributes to enzyme thermotolerance, which plays an important role in enzyme applications. However, the role of N-terminal amino acid residues in the thermal performance and structural properties of exo-inulinases remains to be elucidated. In this study, three and six residues of the N-terminus starting from Gln23 of the exo-inulinase InuAGN25 were deleted and expressed in Escherichia coli. After digestion with human rhinovirus 3 C protease to remove the N-terminal amino acid fusion sequence that may affect the thermolability of enzymes, wild-type RfsMInuAGN25 and its mutants RfsMutNGln23Δ3 and RfsMutNGln23Δ6 were produced. Compared with RfsMInuAGN25, thermostability of RfsMutNGln23Δ3 was enhanced while that of RfsMutNGln23Δ6 was slightly reduced. Compared with the N-terminal structures of RfsMInuAGN25 and RfsMutNGln23Δ6, RfsMutNGln23Δ3 had a higher content of (1) the helix structure, (2) salt bridges (three of which were organized in a network), (3) cation–π interactions (one of which anchored the N-terminal tail). These structural properties may account for the improved thermostability of RfsMutNGln23Δ3. The study provides a better understanding of the N-terminus–function relationships that are useful for rational design of thermostability of exo-inulinases.
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Affiliation(s)
- Limei He
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Rui Zhang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Jidong Shen
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Ying Miao
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University , Kunming, People's Republic of China.,College of Life Sciences, Yunnan Normal University , Kunming, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan, Kunming, People's Republic of China
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8
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da Silva ES, Aglas L, Pinheiro CS, de Andrade Belitardo EMM, Silveira EF, Huber S, Torres RT, Wallner M, Briza P, Lackner P, Laimer J, Pacheco LGC, Cruz ÁA, Alcântara-Neves NM, Ferreira F. A hybrid of two major Blomia tropicalis allergens as an allergy vaccine candidate. Clin Exp Allergy 2020; 50:835-847. [PMID: 32314444 PMCID: PMC7384089 DOI: 10.1111/cea.13611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/27/2020] [Accepted: 04/07/2020] [Indexed: 12/21/2022]
Abstract
Introduction Allergen‐specific immunotherapy (AIT) represents a curative approach for treating allergies. In the tropical and subtropical regions of the world, Blomia tropicalis (Blo t 5 and Blo t 21) is the likely dominant source of indoor allergens. Aim To generate a hypoallergenic Blo t 5/Blo t 21 hybrid molecule that can treat allergies caused by B tropicalis. Methods Using in silico design of B tropicalis hybrid proteins, we chose two hybrid proteins for heterologous expression. Wild‐type Blo t 5/Blo t 21 hybrid molecule and a hypoallergenic version, termed BTH1 and BTH2, respectively, were purified by ion exchange and size exclusion chromatography and characterized by physicochemical, as well as in vitro and in vivo immunological, experiments. Results BTH1, BTH2 and the parental allergens were purified to homogeneity and characterized in detail. BTH2 displayed the lowest IgE reactivity that induced basophil degranulation using sera from allergic rhinitis and asthmatic patients. BTH2 essentially presented the same endolysosomal degradation pattern as the shortened rBlo t 5 and showed a higher resistance towards degradation than the full‐length Blo t 5. In vivo immunization of mice with BTH2 led to the production of IgG antibodies that competed with human IgE for allergen binding. Stimulation of splenocytes from BTH2‐immunized mice produced higher levels of IL‐10 and decreased secretion of IL‐4 and IL‐5. In addition, BTH2 stimulated T‐cell proliferation in PBMCs isolated from allergic patients, with secretion of higher levels of IL‐10 and lower levels of IL‐5 and IL‐13, when compared to parental allergens. Conclusions and Clinical Relevance BTH2 is a promising hybrid vaccine candidate for immunotherapy of Blomia allergy. However, further pre‐clinical studies addressing its efficacy and safety are needed.
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Affiliation(s)
- Eduardo Santos da Silva
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil.,Programa de Pós-Graduação em Biotecnologia da Rede Nordeste de Biotecnologia (RENORBIO), Natal, Brazil.,Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Lorenz Aglas
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Carina Silva Pinheiro
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Emília M M de Andrade Belitardo
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil.,Programa de Pós-Graduação em Imunologia da Universidade Federal da Bahia, Salvador, Brazil
| | - Elisânia Fontes Silveira
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Sara Huber
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Rogério Tanan Torres
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Michael Wallner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Peter Briza
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Peter Lackner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Josef Laimer
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Luis Gustavo C Pacheco
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Álvaro A Cruz
- Núcleo de Excelência de Asma da, Universidade Federal da Bahia, Salvador, Brazil
| | - Neuza Maria Alcântara-Neves
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil.,Programa de Pós-Graduação em Biotecnologia da Rede Nordeste de Biotecnologia (RENORBIO), Natal, Brazil.,Programa de Pós-Graduação em Imunologia da Universidade Federal da Bahia, Salvador, Brazil
| | - Fatima Ferreira
- Department of Biosciences, University of Salzburg, Salzburg, Austria
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Gao DY, Sun XB, Liu MQ, Liu YN, Zhang HE, Shi XL, Li YN, Wang JK, Yin SJ, Wang Q. Characterization of Thermostable and Chimeric Enzymes via Isopeptide Bond-Mediated Molecular Cyclization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:6837-6846. [PMID: 31180217 DOI: 10.1021/acs.jafc.9b01459] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mannooligosaccharides are released by mannan-degrading endo-β-1,4-mannanase and are known as functional additives in human and animal diets. To satisfy demands for biocatalysis and bioprocessing in crowed environments, in this study, we employed a recently developed enzyme-engineering system, isopeptide bond-mediated molecular cyclization, to modify a mesophilic mannanase from Bacillus subtilis. The results revealed that the cyclized enzymes showed enhanced thermostability and ion stability and resilience to aggregation and freeze-thaw treatment by maintaining their conformational structures. Additionally, by using the SpyTag/SpyCatcher system, we generated a mannanase-xylanase bifunctional enzyme that exhibited a synergistic activity in substrate deconstruction without compromising substrate affinity. Interestingly, the dual-enzyme ring conformation was observed to be more robust than the linear enzyme but inferior to the single-enzyme ring conformation. Taken together, these findings provided new insights into the mechanisms of molecular cyclization on stability improvement and will be useful in the production of new functional oligosaccharides and feed additives.
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Affiliation(s)
- De-Ying Gao
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Xiao-Bao Sun
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Ming-Qi Liu
- National and Local United Engineering Lab of Quality Controlling Technology and Instrumentation for Marine Food, College of Life Science , China Jiliang University , Hangzhou 310018 , Zhejiang , China
| | - Yan-Ni Liu
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Hui-En Zhang
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Xin-Lei Shi
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Yang-Nan Li
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Jia-Kun Wang
- College of Animal Science , Zhejiang University , Hangzhou 310058 , Zhejiang , China
| | - Shang-Jun Yin
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
| | - Qian Wang
- College of Biological and Environmental Sciences , Zhejiang Wanli University , Ningbo 315100 , Zhejiang , China
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10
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Liu L, Yu H, Du K, Wang Z, Gan Y, Huang H. Enhanced trypsin thermostability in Pichia pastoris through truncating the flexible region. Microb Cell Fact 2018; 17:165. [PMID: 30359279 PMCID: PMC6201580 DOI: 10.1186/s12934-018-1012-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/19/2018] [Indexed: 12/03/2022] Open
Abstract
Background High thermostability is required for trypsin to have wider industrial applications. Target mutagenesis at flexible regions has been proved to be an efficient protein engineering method to enhance the protein thermostability. Results The flexible regions in porcine trypsin were predicted using the methods including molecular dynamic simulation, FlexPred, and FoldUnfold. The amino acids 78–90 was predicted to be the highly flexible region simultaneously by the three methods and hence selected to be the mutation target. We constructed five variants (D3, D5, D7, D9, and D11) by truncating the region. And the variant D9 showed higher thermostability, with a 5 °C increase in Topt, 5.8 °C rise in \documentclass[12pt]{minimal}
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\begin{document}$$T_{50}^{10}$$\end{document}T5010, and a 4.5 °C rise in Tm, compared to the wild-type. Moreover, the half-life value of the variant D9 was also found to be dramatically improved by 46 min. Circular dichroism and intrinsic fluorescence indicated that the structures had no significant change between the variant D9 and the wild-type. The surface hydrophobicity of D9 was measured to be lower than that of wild-type, indicating the increased hydrophobic interaction, which could have contributed to the improved thermostability of D9. Conclusions These results showed that the thermostability of variant D9 was increased. The variant D9 could be expected to be a promising tool enzyme for its wider industrial applications. The method of truncating the flexible region used in our study has the potential to be used for enhancing the thermostability of other proteins. Electronic supplementary material The online version of this article (10.1186/s12934-018-1012-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lin Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Haoran Yu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China.,Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK
| | - Kun Du
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Zhiyan Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Yiru Gan
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China. .,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China.
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11
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Zhou H, Yong J, Gao H, Yuan Z, Yang W, Tian Y, Wu Y. Loops Adjacent to Catalytic Region and Molecular Stability of Man1312. Appl Biochem Biotechnol 2016; 180:122-35. [PMID: 27193255 DOI: 10.1007/s12010-016-2087-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/11/2016] [Indexed: 10/21/2022]
Abstract
Hemicelluloses are the second major polysaccharides in nature and can be converted to ethanol product by a variety of enzymes including mannanases. Mannanase is an important enzyme that hydrolyses mannose-containing polysaccharides which are abundant in plants. An optimized mannanase could help to improve conversion process and make the technology efficiently and competitively. In this work, the effects of loops adjacent to active region on enzymic properties of Man1312 were investigated. Loop 6 and 10 are two loops neighboring to Man1312 catalytic region, and deletion mutagenesis and residue substitution were performed on both loops. Deletion on sites S145, Q148, N244, and S255 and substitution on sites N146, S147, S156, and T157 gave significant increased stability to enzyme. The quadruplet mutant ManD4I4 combined all the mutations and had higher optimal temperature and T m value by 5 and 4 °C than Man1312, respectively. From our data, we are able to conclude the loops of enzymes are important to design mutagenesis and obtain improved properties, especially the loops neighboring to catalytic region from tertiary structure. In our experiment, residue deletion and substitution on loops neighboring to catalytic region made significant improvement on enzyme properties.
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Affiliation(s)
- Haiyan Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jie Yong
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Han Gao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Zhihui Yuan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Wenjiao Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Yun Tian
- Key Lab of Agricultural Biochemistry and Biotransformation, Hunan Agricultural University, Changsha, 410128, China
| | - Yongyao Wu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
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