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Liu S, Tian L, Cong Y, Shi Q, Wang L, Lu Y, Wang L, Yang G. Recent advances in polygalacturonase: Industrial applications and challenges. Carbohydr Res 2023; 528:108816. [PMID: 37094533 DOI: 10.1016/j.carres.2023.108816] [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: 08/27/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
This review focuses on the applications of polygalacturonase (PG), one of the most commercially produced enzymes on the biocatalyst market, in the food, beverage, feed, textile, and paper industries. Most PGs are acidic mesophilic enzymes, as shown by a summary of their biochemical properties. However, the acidic PGs discovered to date are insufficiently effective for industrial applications. The sequence and structural characteristics of thermophilic PGs are analyzed based on the results of extensive discussions regarding the catalytic mechanism and structural characteristics of PGs with shared right-handed parallel β-helical structures. In addition, the molecular modification methods for obtaining thermostable PGs are systematically presented. Notably, the demand for alkaline heat-resistant PGs has increased significantly concurrent with the biomanufacturing industry development. Therefore, this review also provides a theoretical guideline for mining heat-resistant PG gene resources and modifying PG thermostability.
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Affiliation(s)
- Siyi Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Linfang Tian
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Yuting Cong
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Qianqian Shi
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Lianshun Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Yanan Lu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Li Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China
| | - Guojun Yang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian, 116023, China; Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, 116023, China.
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He L, Zhang R, Shen J, Miao Y, Zeng C, Tang X, Wu Q, Zhou J, Huang Z. Improving the low-temperature properties of an exo-inulinase via the deletion of a loop fragment located in its catalytic pocket. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2021.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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3
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Different-ligand and different-metal xylaratogermanates as effectors of Penicillium restrictum IMV F-100139 α-L-rhamnosidase and α-galactosidase. UKRAINIAN BIOCHEMICAL JOURNAL 2021. [DOI: 10.15407/ubj93.05.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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4
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Wang S, Meng K, Su X, Hakulinen N, Wang Y, Zhang J, Luo H, Yao B, Huang H, Tu T. Cysteine Engineering of an Endo-polygalacturonase from Talaromyces leycettanus JCM 12802 to Improve Its Thermostability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6351-6359. [PMID: 34043362 DOI: 10.1021/acs.jafc.1c01618] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Thermostable enzymes have many advantages for industrial applications. Therefore, in this study, computer-aided design technology was used to improve the thermostability of a highly active endo-polygalacturonase from Talaromyces leycettanus JCM12802 at an optimal temperature of 70 °C. The melting temperature and specific activity of the obtained mutant T316C/G344C were increased by 10 °C and 36.5%, respectively, compared with the wild-type enzyme. The crystal structure of the T316C/G344C mutant showed no formation of a disulfide bond between the introduced cysteines, indicating a different mechanism than the conventional mechanism underlying improved enzyme thermostability. The cysteine substitutions directly formed a new alkyl hydrophobic interaction and caused conformational changes in the side chains of the adjacent residues Asn315 and Thr343, which in turn caused a local reconstruction of hydrogen bonds. This method greatly improved the thermostability of the enzyme without affecting its activity; thus, our findings are of great significance for both theoretical research and practical applications.
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Affiliation(s)
- Sheng Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kun Meng
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, Joensuu 80130, Finland
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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5
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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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Yap PG, Choi SB, Liong MT. Allantoin, a Potential Metabolite That Promotes AMPK Phosphorylation and Suppresses Cholesterol Biosynthesis Via the Mevalonate Pathway and Bloch Pathway. Appl Biochem Biotechnol 2020; 191:226-244. [DOI: 10.1007/s12010-020-03265-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/13/2020] [Indexed: 10/24/2022]
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7
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Hait S, Mallik S, Basu S, Kundu S. Finding the generalized molecular principles of protein thermal stability. Proteins 2019; 88:788-808. [PMID: 31872464 DOI: 10.1002/prot.25866] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/05/2019] [Accepted: 12/14/2019] [Indexed: 11/09/2022]
Abstract
Are there any generalized molecular principles of thermal adaptation? Here, integrating the concepts of structural bioinformatics, sequence analysis, and classical knot theory, we develop a robust computational framework that seeks for mechanisms of thermal adaptation by comparing orthologous mesophilic-thermophilic and mesophilic-hyperthermophilic proteins of remarkable structural and topological similarities, and still leads us to context-independent results. A comprehensive analysis of 4741 high-resolution, non-redundant X-ray crystallographic structures collected from 11 hyperthermophilic, 32 thermophilic and 53 mesophilic prokaryotes unravels at least five "nearly universal" signatures of thermal adaptation, irrespective of the enormous sequence, structure, and functional diversity of the proteins compared. A careful investigation further extracts a set of amino acid changes that can potentially enhance protein thermal stability, and remarkably, these mutations are overrepresented in protein crystallization experiments, in disorder-to-order transitions and in engineered thermostable variants of existing mesophilic proteins. These results could be helpful to find a precise, global picture of thermal adaptation.
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Affiliation(s)
- Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Saurav Mallik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sudipto Basu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
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Tu T, Li Y, Luo Y, Wang Z, Wang Y, Luo H, Yao B. A key residue for the substrate affinity enhancement of a thermophilic endo-polygalacturonase revealed by computational design. Appl Microbiol Biotechnol 2018; 102:4457-4466. [DOI: 10.1007/s00253-018-8948-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/07/2018] [Accepted: 03/14/2018] [Indexed: 12/30/2022]
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9
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Mirchi A, Sizochenko N, Dinadayalane T, Leszczynski J. Binding of Alkali Metal Ions with 1,3,5-Tri(phenyl)benzene and 1,3,5-Tri(naphthyl)benzene: The Effect of Phenyl and Naphthyl Ring Substitution on Cation−π Interactions Revealed by DFT Study. J Phys Chem A 2017; 121:8927-8938. [DOI: 10.1021/acs.jpca.7b08725] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ali Mirchi
- Interdisciplinary
Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric
Sciences, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217, United States
| | - Natalia Sizochenko
- Interdisciplinary
Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric
Sciences, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217, United States
| | - Tandabany Dinadayalane
- Department
of Chemistry, Clark Atlanta University, 223 James P. Brawley Drive, S.W., Atlanta, Georgia 30314, United States
| | - Jerzy Leszczynski
- Interdisciplinary
Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric
Sciences, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217, United States
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