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Nezhad NG, Rahman RNZRA, Normi YM, Oslan SN, Shariff FM, Leow TC. Thermostability engineering of industrial enzymes through structure modification. Appl Microbiol Biotechnol 2022; 106:4845-4866. [PMID: 35804158 DOI: 10.1007/s00253-022-12067-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/25/2022] [Accepted: 07/02/2022] [Indexed: 01/14/2023]
Abstract
Thermostability is an essential requirement of enzymes in the industrial processes to catalyze the reactions at high temperatures; thus, enzyme engineering through directed evolution, semi-rational design and rational design are commonly employed to construct desired thermostable mutants. Several strategies are implemented to fulfill enzymes' thermostability demand including decreasing the entropy of the unfolded state through substitutions Gly → Xxx or Xxx → Pro, hydrogen bond, salt bridge, introducing two different simultaneous interactions through single mutant, hydrophobic interaction, filling the hydrophobic cavity core, decreasing surface hydrophobicity, truncating loop, aromatic-aromatic interaction and introducing positively charged residues to enzyme surface. In the current review, horizons about compatibility between secondary structures and substitutions at preferable structural positions to generate the most desirable thermostability in industrial enzymes are broadened. KEY POINTS: • Protein engineering is a powerful tool for generating thermostable industrial enzymes. • Directed evolution and rational design are practical approaches in enzyme engineering. • Substitutions in preferable structural positions can increase thermostability.
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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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Li Z, Li L, Huo Y, Chen Z, Zhao Y, Huang J, Jian S, Rong Z, Wu D, Gan J, Hu X, Li J, Xu XW. Structure-guided protein engineering increases enzymatic activities of the SGNH family esterases. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:107. [PMID: 32549911 PMCID: PMC7294632 DOI: 10.1186/s13068-020-01742-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/30/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Esterases and lipases hydrolyze short-chain esters and long-chain triglycerides, respectively, and therefore play essential roles in the synthesis and decomposition of ester bonds in the pharmaceutical and food industries. Many SGNH family esterases share high similarity in sequences. However, they have distinct enzymatic activities toward the same substrates. Due to a lack of structural information, the detailed catalytic mechanisms of these esterases remain barely investigated. RESULTS In this study, we identified two SGNH family esterases, CrmE10 and AlinE4, from marine bacteria with significantly different preferences for pH, temperature, metal ion, and organic solvent tolerance despite high sequence similarity. The crystal structures of these two esterases, including wild type and mutants, were determined to high resolutions ranging from 1.18 Å to 2.24 Å. Both CrmE10 and AlinE4 were composed of five β-strands and nine α-helices, which formed one compact N-terminal α/β globular domain and one extended C-terminal domain. The aspartic residues (D178 in CrmE10/D162 in AlinE4) destabilized the conformations of the catalytic triad (Ser-Asp-His) in both esterases, and the metal ion Cd2+ might reduce enzymatic activity by blocking proton transfer or substrate binding. CrmE10 and AlinE4 showed distinctly different electrostatic surface potentials, despite the similar atomic architectures and a similar swap catalytic mechanism. When five negatively charged residues (Asp or Glu) were mutated to residue Lys, CrmE10 obtained elevated alkaline adaptability and significantly increased the enzymatic activity from 0 to 20% at pH 10.5. Also, CrmE10 mutants exhibited dramatic change for enzymatic properties when compared with the wide-type enzyme. CONCLUSIONS These findings offer a perspective for understanding the catalytic mechanism of different esterases and might facilitate the industrial biocatalytic applications.
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Affiliation(s)
- Zhengyang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Long Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Yingyi Huo
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources, Ministry of Natural Resources & Second Institute of Oceanography, Hangzhou, 310012 China
| | - Zijun Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Yu Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Jing Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Shuling Jian
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources, Ministry of Natural Resources & Second Institute of Oceanography, Hangzhou, 310012 China
| | - Zhen Rong
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources, Ministry of Natural Resources & Second Institute of Oceanography, Hangzhou, 310012 China
| | - Di Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Xiaojian Hu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources, Ministry of Natural Resources & Second Institute of Oceanography, Hangzhou, 310012 China
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Farrokh P, Sheikhpour M, Kasaeian A, Asadi H, Bavandi R. Cyanobacteria as an eco-friendly resource for biofuel production: A critical review. Biotechnol Prog 2019; 35:e2835. [PMID: 31063628 DOI: 10.1002/btpr.2835] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/07/2019] [Accepted: 04/24/2019] [Indexed: 12/26/2022]
Abstract
Cyanobacteria are photosynthetic microorganisms which can be found in various environmental habitats. These photosynthetic bacteria are considered as promising feedstock for the production of the third- and the fourth-generation biofuels. The main subject of this review is highlighting the significant aspects of the biofuel production from cyanobacteria. The most recent investigations about the extraction or separation of the bio-oil from cyanobacteria are also adduced in the present review. Moreover, the genetic engineering of cyanobacteria for improving biofuel production and the impact of bioinformatics studies on the designing better-engineered strains are mentioned. The large-scale biofuel production is challenging, so the economic considerations to provide inexpensive biofuels are also cited. It seems that the future of biofuels is strongly dependent to the following items; understanding the metabolic pathways of the cyanobacterial species, progression in the construction of the engineered cyanobacteria, and inexpensive large-scale cultivation of them.
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Affiliation(s)
- Parisa Farrokh
- Department of cell and molecular biology, School of Biology, Damghan University, Damghan, Iran.,Institute of Biological Sciences, Damghan University, Damghan, Iran
| | - Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Alibakhsh Kasaeian
- Faculty of New Science and Technologies, University of Tehran, Tehran, Iran
| | - Hassan Asadi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Roya Bavandi
- Branch-Marine Science and Technology Faculty, Islamic Azad University North Tehran, Tehran, Iran
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Huang L, Zheng D, Zhao Y, Ma J, Li Y, Xu Z, Shan M, Shao S, Guo Q, Zhang J, Lu F, Liu Y. Improvement of the alkali stability of Penicillium cyclopium lipase by error-prone PCR. ELECTRON J BIOTECHN 2019. [DOI: 10.1016/j.ejbt.2019.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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