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Jeilu O, Alexandersson E, Johansson E, Simachew A, Gessesse A. A novel GH3-β-glucosidase from soda lake metagenomic libraries with desirable properties for biomass degradation. Sci Rep 2024; 14:10012. [PMID: 38693138 PMCID: PMC11063200 DOI: 10.1038/s41598-024-60645-y] [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: 11/16/2023] [Accepted: 04/25/2024] [Indexed: 05/03/2024] Open
Abstract
Beta-glucosidases catalyze the hydrolysis of the glycosidic bonds of cellobiose, producing glucose, which is a rate-limiting step in cellulose biomass degradation. In industrial processes, β-glucosidases that are tolerant to glucose and stable under harsh industrial reaction conditions are required for efficient cellulose hydrolysis. In this study, we report the molecular cloning, Escherichia coli expression, and functional characterization of a β-glucosidase from the gene, CelGH3_f17, identified from metagenomics libraries of an Ethiopian soda lake. The CelGH3_f17 gene sequence contains a glycoside hydrolase family 3 catalytic domain (GH3). The heterologous expressed and purified enzyme exhibited optimal activity at 50 °C and pH 8.5. In addition, supplementation of 1 M salt and 300 mM glucose enhanced the β-glucosidase activity. Most of the metal ions and organic solvents tested did not affect the β-glucosidase activity. However, Cu2+ and Mn2+ ions, Mercaptoethanol and Triton X-100 reduce the activity of the enzyme. The studied β-glucosidase enzyme has multiple industrially desirable properties including thermostability, and alkaline, salt, and glucose tolerance.
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Affiliation(s)
- Oliyad Jeilu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden.
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia.
| | - Erik Alexandersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
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Zhu Q, Huang Y, Yang Z, Wu X, Zhu Q, Zheng H, Zhu D, Lv Z, Yin Y. A Recombinant Thermophilic and Glucose-Tolerant GH1 β-Glucosidase Derived from Hehua Hot Spring. Molecules 2024; 29:1017. [PMID: 38474529 DOI: 10.3390/molecules29051017] [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: 01/01/2024] [Revised: 02/18/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
As a crucial enzyme for cellulose degradation, β-glucosidase finds extensive applications in food, feed, and bioethanol production; however, its potential is often limited by inadequate thermal stability and glucose tolerance. In this study, a functional gene (lq-bg5) for a GH1 family β-glucosidase was obtained from the metagenomic DNA of a hot spring sediment sample and heterologously expressed in E. coli and the recombinant enzyme was purified and characterized. The optimal temperature and pH of LQ-BG5 were 55 °C and 4.6, respectively. The relative residual activity of LQ-BG5 exceeded 90% at 55 °C for 9 h and 60 °C for 6 h and remained above 100% after incubation at pH 5.0-10.0 for 12 h. More importantly, LQ-BG5 demonstrated exceptional glucose tolerance with more than 40% activity remaining even at high glucose concentrations of 3000 mM. Thus, LQ-BG5 represents a thermophilic β-glucosidase exhibiting excellent thermal stability and remarkable glucose tolerance, making it highly promising for lignocellulose development and utilization.
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Affiliation(s)
- Qian Zhu
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Yuying Huang
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali 671003, China
| | - Zhengfeng Yang
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Xingci Wu
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Qianru Zhu
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Hongzhao Zheng
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Dan Zhu
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Zhihua Lv
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Dali University, Dali 671003, China
| | - Yirui Yin
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali 671003, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Dali University, Dali 671003, China
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Liu S, Zhang M, Hong D, Fang Z, Xiao Y, Fang W, Zhang X. Improving the cellobiose hydrolysis activity of glucose-stimulating β-glucosidase Bgl2A. Enzyme Microb Technol 2023; 169:110289. [PMID: 37473697 DOI: 10.1016/j.enzmictec.2023.110289] [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: 04/07/2023] [Revised: 06/05/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
β-Glucosidases with high catalytic activity and glucose tolerant properties possess promising applications in lignocellulose-based industries. To obtain enzymes possessing these properties, a semi-rational strategy was employed to engineer the glucose-stimulating β-glucosidase Bgl2A for high cellobiose hydrolysis activity. A total of 18 mutants were constructed. A22S, V224D, and A22S/V224D exhibited high specific activities of 272.06, 237.60, and 239.29 U/mg toward cellobiose, which were 2.5- to 2.8-fold of Bgl2A. A22S, V224D, and A22S/V224D exhibited increased kcat values, which were 2.7- to 3.1-fold of Bgl2A. A22S and V224D maintained glucose-stimulating property, whereas A22S/V224D lost it. Using 150 g/L cellobiose as the substrate, the amount of glucose produced by A22S was the highest, yielding 129.70 g/L glucose after 3 h reaction at 35 °C. The synergistic effects of the engineered enzymes with commercial cellulase on hydrolyzing cellulose were investigated. Supplemented with the commercial cellulase and A22S, the highest glucose amount of 23.30 g/L was yielded from cellulose with hydrolysis rate of 21.02 %. Given its high cellobiose hydrolysis activity and glucose-stimulating properties, A22S can be used as a component of enzyme cocktail to match mesophilic cellulases for efficient cellulose hydrolysis.
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Affiliation(s)
- Shuaifeng Liu
- School of Life Sciences, Anhui University; Hefei, Anhui 230601, China; Anhui Key Laboratory of Modern Biomanufacturing; Hefei, Anhui 230601, China; Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis; Hefei, Anhui 230601, China
| | - Meng Zhang
- School of Life Sciences, Anhui University; Hefei, Anhui 230601, China; Anhui Key Laboratory of Modern Biomanufacturing; Hefei, Anhui 230601, China
| | - Dengwang Hong
- School of Life Sciences, Anhui University; Hefei, Anhui 230601, China; Anhui Key Laboratory of Modern Biomanufacturing; Hefei, Anhui 230601, China; Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis; Hefei, Anhui 230601, China
| | - Zemin Fang
- School of Life Sciences, Anhui University; Hefei, Anhui 230601, China; Anhui Key Laboratory of Modern Biomanufacturing; Hefei, Anhui 230601, China; Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis; Hefei, Anhui 230601, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University; Hefei, Anhui 230601, China; Anhui Key Laboratory of Modern Biomanufacturing; Hefei, Anhui 230601, China; Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis; Hefei, Anhui 230601, China
| | - Wei Fang
- School of Life Sciences, Anhui University; Hefei, Anhui 230601, China; Anhui Key Laboratory of Modern Biomanufacturing; Hefei, Anhui 230601, China; Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis; Hefei, Anhui 230601, China.
| | - Xuecheng Zhang
- School of Life Sciences, Anhui University; Hefei, Anhui 230601, China; Anhui Key Laboratory of Modern Biomanufacturing; Hefei, Anhui 230601, China; Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis; Hefei, Anhui 230601, China.
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Characterization of a New Glucose-Tolerant GH1 β-Glycosidase from Aspergillus fumigatus with Transglycosylation Activity. Int J Mol Sci 2023; 24:ijms24054489. [PMID: 36901919 PMCID: PMC10003650 DOI: 10.3390/ijms24054489] [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: 12/23/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
Concern over environmental impacts has spurred many efforts to replace fossil fuels with biofuels such as ethanol. However, for this to be possible, it is necessary to invest in other production technologies, such as second generation (2G) ethanol, in order to raise the levels of this product and meet the growing demand. Currently, this type of production is not yet economically feasible, due to the high costs of the enzyme cocktails used in saccharification stage of lignocellulosic biomass. In order to optimize these cocktails, the search for enzymes with superior activities has been the goal of several research groups. For this end, we have characterized the new β-glycosidase AfBgl1.3 from A. fumigatus after expression and purification in Pichia pastoris X-33. Structural analysis by circular dichroism revealed that increasing temperature destructured the enzyme; the apparent Tm value was 48.5 °C. The percentages of α-helix (36.3%) and β-sheet (12.4%) secondary structures at 25 °C were predicted. Biochemical characterization suggested that the optimal conditions for AfBgl1.3 were pH 6.0 and temperature of 40 °C. At 30 and 40 °C, the enzyme was stable and retained about 90% and 50% of its activity, respectively, after pre-incubation for 24 h. In addition, the enzyme was highly stable at pH between 5 and 8, retaining over 65% of its activity after pre-incubation for 48 h. AfBgl1.3 co-stimulation with 50-250 mM glucose enhanced its specific activity by 1.4-fold and revealed its high tolerance to glucose (IC50 = 2042 mM). The enzyme was active toward the substrates salicin (495.0 ± 49.0 U mg-1), pNPG (340.5 ± 18.6 U mg-1), cellobiose (89.3 ± 5.1 U mg-1), and lactose (45.1 ± 0.5 U mg-1), so it had broad specificity. The Vmax values were 656.0 ± 17.5, 706.5 ± 23.8, and 132.6 ± 7.1 U mg-1 toward p-nitrophenyl-β-D-glucopyranoside (pNPG), D-(-)-salicin, and cellobiose, respectively. AfBgl1.3 displayed transglycosylation activity, forming cellotriose from cellobiose. The addition of AfBgl1.3 as a supplement at 0.9 FPU/g of cocktail Celluclast® 1.5L increased carboxymethyl cellulose (CMC) conversion to reducing sugars (g L-1) by about 26% after 12 h. Moreover, AfBgl1.3 acted synergistically with other Aspergillus fumigatus cellulases already characterized by our research group-CMC and sugarcane delignified bagasse were degraded, releasing more reducing sugars compared to the control. These results are important in the search for new cellulases and in the optimization of enzyme cocktails for saccharification.
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Zhang X, Chen X, Li S, Bello A, Liu J, Gao L, Fan Z, Wang S, Liu L, Ma B, Li H. Mechanism of differential expression of β-glucosidase genes in functional microbial communities in response to carbon catabolite repression. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:3. [PMID: 35418139 PMCID: PMC8756671 DOI: 10.1186/s13068-021-02101-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/29/2021] [Indexed: 11/10/2022]
Abstract
Abstract
Background
β-Glucosidase is the rate-limiting enzyme of cellulose degradation. It has been stipulated and established that β-glucosidase-producing microbial communities differentially regulate the expression of glucose/non-glucose tolerant β-glucosidase genes. However, it is still unknown if this differential expression of functional microbial community happens accidentally or as a general regulatory mechanism, and of what biological significance it has. To investigate the composition and function of microbial communities and how they respond to different carbon metabolism pressures and the transcriptional regulation of functional genes, the different carbon metabolism pressure was constructed by setting up the static chamber during composting.
Results
The composition and function of functional microbial communities demonstrated different behaviors under the carbon metabolism pressure. Functional microbial community up-regulated glucose tolerant β-glucosidase genes expression to maintain the carbon metabolism rate by enhancing the transglycosylation activity of β-glucosidase to compensate for the decrease of hydrolysis activity under carbon catabolite repression (CCR). Micrococcales play a vital role in the resistance of functional microbial community under CCR. The transcription regulation of GH1 family β-glucosidase genes from Proteobacteria showed more obvious inhibition than other phyla under CCR.
Conclusion
Microbial functional communities differentially regulate the expression of glucose/non-glucose tolerant β-glucosidase genes under CCR, which is a general regulatory mechanism, not accidental. Furthermore, the differentially expressed β-glucosidase gene exhibited species characteristics at the phylogenetic level.
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Fernandes CG, Sawant SC, Mule TA, Khadye VS, Lali AM, Odaneth AA. Enhancing cellulases through synergistic β-glucosidases for intensifying cellulose hydrolysis. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Sun N, Liu X, Zhang B, Wang X, Na W, Tan Z, Li X, Guan Q. Characterization of a novel recombinant halophilic β-glucosidase of Trichoderma harzianum derived from Hainan mangrove. BMC Microbiol 2022; 22:185. [PMID: 35902815 PMCID: PMC9331182 DOI: 10.1186/s12866-022-02596-w] [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: 12/26/2021] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND β-glucosidase is an important biomass-degrading enzyme and plays a vital role in generating renewable biofuels through enzymatic saccharification. In this study, we analyzed the transcriptome of Trichoderma harzianum HTASA derived from Hainan mangrove and identified a new gene encoding β-glucosidase Bgl3HB. And the biochemically characterization of β-glucosidase activity was performed. RESULTS Bgl3HB showed substantial catalytic activity in the pH range of 3.0-5.0 and at temperatures of 40 ℃-60 ℃. The enzyme was found quite stable at 50 ℃ with a loss of only 33.4% relative activity after 240 min of heat exposure. In addition, all tested metal ions were found to promote the enzyme activity. The β-glucosidase activity of Bgl3HB was enhanced by 2.12-fold of its original activity in the presence of 5 M NaCl. Surprisingly, Bgl3HB also showed a remarkable ability to hydrolyze laminarin compared to other measured substrates. Enzyme efficiency was examined in the sugarcane bagasse saccharification processes, in which Bgl3HB with 5 M NaCl worked better supplementing Celluclast 1.5L than the commercial Novozyme 188 ascertained it as an admirably suited biocatalyst for the utilization of agricultural waste. In this work, this is the first report of a halophilic β-glucosidase from Trichoderma harzianum, and represents the β-glucosidase with the highest known NaCl activation concentration. And adding 5 M NaCl could enhance saccharification performance even better than commercial cellulase. CONCLUSIONS These results show that Bgl3HB has great promise as a highly stable and highly efficient cellulase with important future applications in the industrial production of biofuels.
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Affiliation(s)
- Nan Sun
- Lab of Animal Nutrition, Reproduction & Breeding, College of Animal Science and Technology, Hainan University, No.58 Renmin Avenue, Meilan, Haikou, 570228, P. R. China
| | - Xiaoxuan Liu
- Lab of Animal Nutrition, Reproduction & Breeding, College of Animal Science and Technology, Hainan University, No.58 Renmin Avenue, Meilan, Haikou, 570228, P. R. China
| | - Bingxi Zhang
- Lab of Animal Nutrition, Reproduction & Breeding, College of Animal Science and Technology, Hainan University, No.58 Renmin Avenue, Meilan, Haikou, 570228, P. R. China
| | - Xuemei Wang
- Lab of Animal Nutrition, Reproduction & Breeding, College of Animal Science and Technology, Hainan University, No.58 Renmin Avenue, Meilan, Haikou, 570228, P. R. China.
| | - Wei Na
- Lab of Animal Genetics, Reproduction & Breeding, College of Animal Science and Technology, Hainan University, No.58 Renmin Avenue, Meilan, Haikou, 570228, P. R. China
| | - Zhen Tan
- Lab of Animal Genetics, Reproduction & Breeding, College of Animal Science and Technology, Hainan University, No.58 Renmin Avenue, Meilan, Haikou, 570228, P. R. China
| | - Xiaochun Li
- Lab of Animal Genetics, Reproduction & Breeding, College of Animal Science and Technology, Hainan University, No.58 Renmin Avenue, Meilan, Haikou, 570228, P. R. China
| | - Qingfeng Guan
- Lab of Microorganism Resource and Utilization Research, School of Life Sciences, Hainan University, No.58 Renmin Avenue, Meilan, Haikou, 570228, P. R. China
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He Y, Wang C, Jiao R, Ni Q, Wang Y, Gao Q, Zhang Y, Xu G. Biochemical characterization of a novel glucose-tolerant GH3 β-glucosidase (Bgl1973) from Leifsonia sp. ZF2019. Appl Microbiol Biotechnol 2022; 106:5063-5079. [PMID: 35833950 DOI: 10.1007/s00253-022-12064-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/27/2022] [Accepted: 07/02/2022] [Indexed: 11/25/2022]
Abstract
Beta-glucosidase (Bgl) is an enzyme with considerable food, beverage, and biofuel processing potential. However, as many Bgls are inhibited by their reaction end product glucose, their industrial applications are greatly limited. In this study, a novel Bgl gene (Bgl1973) was cloned from Leifsonia sp. ZF2019 and heterologously expressed in E. coli. Sequence analysis and structure modeling revealed that Bgl1973 was 748 aa, giving it a molecular weight of 78 kDa, and it showed high similarity with the glycoside hydrolase 3 (GH3) family Bgls with which its active site residues were conserved. By using pNPGlc (p-nitrophenyl-β-D-glucopyranoside) as substrate, the optimum temperature and pH of Bgl1973 were shown to be 50 °C and 7.0, respectively. Bgl1973 was insensitive to most metal ions (12.5 mM), 1% urea, and even 0.1% Tween-80. This enzyme maintained 60% of its original activity in the presence of 20% NaCl, demonstrating its excellent salt tolerance. Furthermore, it still had 83% residual activity in 1 M of glucose, displaying its outstanding glucose tolerance. The Km, Vmax, and kcat of Bgl1973 were 0.22 mM, 44.44 μmol/min mg, and 57.78 s-1, respectively. Bgl1973 had a high specific activity for pNPGlc (19.10 ± 0.59 U/mg) and salicin (20.43 ± 0.92 U/mg). Furthermore, molecular docking indicated that the glucose binding location and the narrow and deep active channel geometry might contribute to the glucose tolerance of Bgl1973. Our results lay a foundation for the studying of this glucose-tolerant β-glucosidase and its applications in many industrial settings. KEY POINTS: • A novel β-glucosidase from GH3 was obtained from Leifsonia sp. ZF2019. • Bgl1973 demonstrated excellent glucose tolerance. • The glucose tolerance of Bgl1973 was explained using molecular docking analysis.
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Affiliation(s)
- Yi He
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Chenxi Wang
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Ronghu Jiao
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Qinxue Ni
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yan Wang
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Qianxin Gao
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Youzuo Zhang
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Guangzhi Xu
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China.
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Crystal structure of metagenomic β-glycosidase MeBglD2 in complex with various saccharides. Appl Microbiol Biotechnol 2022; 106:4539-4551. [PMID: 35723691 DOI: 10.1007/s00253-022-12018-6] [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: 03/08/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 11/02/2022]
Abstract
Metagenomic MeBglD2 is a glycoside hydrolase family 1 (GH1) β-glycosidase that has β-glucosidase, β-fucosidase, and β-galactosidase activities, and is highly activated in the presence of monosaccharides and disaccharides. The β-glucosidase activity of MeBglD2 increases in a cellobiose concentration-dependent manner and is not inhibited by a high concentration of D-glucose or cellobiose. Previously, we solved the crystal structure of MeBglD2 and designed a thermostable mutant; however, the mechanism of substrate recognition of MeBglD2 remains poorly understood. In this paper, we report the X-ray crystal structures of MeBglD2 complexed with various saccharides, such as D-glucose, D-xylose, cellobiose, and maltose. The results showed that subsite - 1 of MeBglD2, which contained two catalytic glutamate residues (a nucleophilic Glu356 and an acid/base Glu170) was common to other GH1 enzymes, but the positive subsites (+ 1 and + 2) had different binding modes depending on the type of sugar. Three residues (Glu183, Asn227, and Asn229), located at the positive subsites of MeBglD2, were involved in substrate specificity toward cellobiose and/or chromogenic substrates in the presence of additive sugars. The docking simulation of MeBglD2-cellobiose indicated that Asn229 and Trp329 play important roles in the recognition of + 1 D-glucose in cellobiose. Our findings provide insights into the unique substrate recognition mechanism of GH1, which can incorporate a variety of saccharides into its positive subsites. KEY POINTS: • Metagenomic glycosidase, MeBglD2, recognizes various saccharides • Structures of metagenomic MeBglD2 complexed with various saccharides are determined • MeBglD2 has a unique substrate recognition mechanism at the positive subsites.
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10
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Pang AP, Luo Y, Hu X, Zhang F, Wang H, Gao Y, Durrani S, Li C, Shi X, Wu FG, Li BZ, Lu Z, Lin F. Transmembrane transport process and endoplasmic reticulum function facilitate the role of gene cel1b in cellulase production of Trichoderma reesei. Microb Cell Fact 2022; 21:90. [PMID: 35590356 PMCID: PMC9118834 DOI: 10.1186/s12934-022-01809-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/30/2022] [Indexed: 11/16/2022] Open
Abstract
Background A total of 11 β-glucosidases are predicted in the genome of Trichoderma reesei, which are of great importance for regulating cellulase biosynthesis. Nevertheless, the relevant function and regulation mechanism of each β-glucosidase remained unknown. Results We evidenced that overexpression of cel1b dramatically decreased cellulase synthesis in T. reesei RUT-C30 both at the protein level and the mRNA level. In contrast, the deletion of cel1b did not noticeably affect cellulase production. Protein CEL1B was identified to be intracellular, being located in vacuole and cell membrane. The overexpression of cel1b reduced the intracellular pNPGase activity and intracellular/extracellular glucose concentration without inducing carbon catabolite repression. On the other hand, RNA-sequencing analysis showed the transmembrane transport process and endoplasmic reticulum function were affected noticeably by overexpressing cel1b. In particular, some important sugar transporters were notably downregulated, leading to a compromised cellular uptake of sugars including glucose and cellobiose. Conclusions Our data suggests that the cellulase inhibition by cel1b overexpression was not due to the β-glucosidase activity, but probably the dysfunction of the cellular transport process (particularly sugar transport) and endoplasmic reticulum (ER). These findings advance the knowledge of regulation mechanism of cellulase synthesis in filamentous fungi, which is the basis for rationally engineering T. reesei strains to improve cellulase production in industry. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01809-1.
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Affiliation(s)
- Ai-Ping Pang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yongsheng Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xin Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Funing Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yichen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Samran Durrani
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Chengcheng Li
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaotong Shi
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
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11
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Pota G, Sapienza Salerno A, Costantini A, Silvestri B, Passaro J, Califano V. Co-immobilization of Cellulase and β-Glucosidase into Mesoporous Silica Nanoparticles for the Hydrolysis of Cellulose Extracted from Eriobotrya japonica Leaves. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5481-5493. [PMID: 35476419 PMCID: PMC9097537 DOI: 10.1021/acs.langmuir.2c00053] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Fungal cellulases generally contain a reduced amount of β-glucosidase (BG), which does not allow for efficient cellulose hydrolysis. To address this issue, we implemented an easy co-immobilization procedure of β-glucosidase and cellulase by adsorption on wrinkled mesoporous silica nanoparticles with radial and hierarchical open pore structures, exhibiting smaller (WSN) and larger (WSN-p) inter-wrinkle distances. The immobilization was carried out separately on different vectors (WSN for BG and WSN-p for cellulase), simultaneously on the same vector (WSN-p), and sequentially on the same vector (WSN-p) in order to optimize the synergy between cellulase and BG. The obtained results pointed out that the best biocatalyst is that prepared through simultaneous immobilization of BG and cellulase on the same vector (WSN-p). In this case, the adsorption resulted in 20% yield of immobilization, corresponding to an enzyme loading of 100 mg/g of support. 82% yield of reaction and 72 μmol/min·g activity were obtained, evaluated for the hydrolysis of cellulose extracted from Eriobotrya japonica leaves. All reactions were carried out at a standard temperature of 50 °C. The biocatalyst retained 83% of the initial yield of reaction after 9 cycles of reuse. Moreover, it had better stability than the free enzyme mixture in a wide range of temperatures, preserving 72% of the initial yield of reaction up to 90 °C.
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Affiliation(s)
- Giulio Pota
- Department
of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Fuorigrotta, Naples, Italy
| | - Antonio Sapienza Salerno
- Department
of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Fuorigrotta, Naples, Italy
| | - Aniello Costantini
- Department
of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Fuorigrotta, Naples, Italy
| | - Brigida Silvestri
- Department
of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Fuorigrotta, Naples, Italy
| | - Jessica Passaro
- Department
of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Fuorigrotta, Naples, Italy
| | - Valeria Califano
- Institute
of Science and Technology for Sustainable Energy and Mobility (STEMS), National Research Council of Italy (CNR), Viale Marconi 4, 80125 Naples, Italy
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12
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Nhim S, Waeonukul R, Uke A, Baramee S, Ratanakhanokchai K, Tachaapaikoon C, Pason P, Liu YJ, Kosugi A. Biological cellulose saccharification using a coculture of Clostridium thermocellum and Thermobrachium celere strain A9. Appl Microbiol Biotechnol 2022; 106:2133-2145. [PMID: 35157106 PMCID: PMC8930880 DOI: 10.1007/s00253-022-11818-0] [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: 10/13/2021] [Revised: 12/30/2021] [Accepted: 01/30/2022] [Indexed: 11/29/2022]
Abstract
Abstract An anaerobic thermophilic bacterial strain, A9 (NITE P-03545), that secretes β-glucosidase was newly isolated from wastewater sediments by screening using esculin. The 16S rRNA gene sequence of strain A9 had 100% identity with that of Thermobrachium celere type strain JW/YL-NZ35. The complete genome sequence of strain A9 showed 98.4% average nucleotide identity with strain JW/YL-NZ35. However, strain A9 had different physiological properties from strain JW/YL-NZ35, which cannot secrete β-glucosidases or grow on cellobiose as the sole carbon source. The key β-glucosidase gene (TcBG1) of strain A9, which belongs to glycoside hydrolase family 1, was characterized. Recombinant β-glucosidase (rTcBG1) hydrolyzed cellooligosaccharides to glucose effectively. Furthermore, rTcBG1 showed high thermostability (at 60°C for 2 days) and high glucose tolerance (IC50 = 0.75 M glucose), suggesting that rTcBG1 could be used for biological cellulose saccharification in cocultures with Clostridium thermocellum. High cellulose degradation was observed when strain A9 was cocultured with C. thermocellum in a medium containing 50 g/l crystalline cellulose, and glucose accumulation in the culture supernatant reached 35.2 g/l. In contrast, neither a monoculture of C. thermocellum nor coculture of C. thermocellum with strain JW/YL-NZ35 realized efficient cellulose degradation or high glucose accumulation. These results show that the β-glucosidase secreted by strain A9 degrades cellulose effectively in combination with C. thermocellum cellulosomes and has the potential to be used in a new biological cellulose saccharification process that does not require supplementation with β-glucosidases. Key points • Strain A9 can secrete a thermostable β-glucosidase that has high glucose tolerance • A coculture of strain A9 and C. thermocellum showed high cellulose degradation • Strain A9 achieves biological saccharification without addition of β-glucosidase Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11818-0.
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Affiliation(s)
- Sreyneang Nhim
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand
| | - Rattiya Waeonukul
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ayaka Uke
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Sirilak Baramee
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Patthra Pason
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), 10150, Bangkok, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China.,Shandong Energy Institute, Qingdao, 266101, People's Republic of China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, People's Republic of China
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.
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13
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Iram A, Cekmecelioglu D, Demirci A. Salt and nitrogen amendment and optimization for cellulase and xylanase production using dilute acid hydrolysate of distillers' dried grains with solubles (DDGS) as the feedstock. Bioprocess Biosyst Eng 2022; 45:527-540. [PMID: 35013794 DOI: 10.1007/s00449-021-02676-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022]
Abstract
Distillers' dried grains with solubles (DDGS) is a by-product of dry-mill corn ethanol production comprising a high nutritional value due to residual fiber, protein, and lipid contents. The fiber content of DDGS is high enough to be considered a valuable source for the production of hydrolytic enzymes, such as cellulase and xylanases, which can be used for hydrolysis of lignocellulosic feedstock during ethanol production. The DDGS-based medium prepared after acid hydrolysis provides adequate sugars for enzyme production, while additional macronutrients, such as salts and nitrogen sources, can enhance the enzyme production. Therefore, this study was undertaken to evaluate the effect of salts (KH2PO4, CaCl2·2H2O, MgSO4·7H2O, FeSO4·7H2O, CoCl2·6H2O, and MnSO4·H2O), peptone, and yeast extract on enzyme secretion by four different Aspergillus niger strains and to optimize the nitrogen source for maximum enzyme production. Yeast extract improved the cellulase production (0.38 IU/ml) for A. niger (NRRL 1956) as compared to peptone (0.29 IU/ml). However, maximum cellulase productions of 0.42 IU/ml and 0.45 IU/ml were obtained by A. niger (NRRL 330) and A. niger (NRRL 567), respectively, in presence of ammonium sulfate. The optimized nitrogen amounts resulted in a significant increase in the cellulase production from 0.174 to 0.63 IU/ml on day 9 of the fermentation with A. niger (NRRL 330). The composite model improved both cellulase and xylanase production. In conclusion, the optimization of all three nitrogen sources improved both cellulase and xylanase production in the DDGS-based media.
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Affiliation(s)
- Attia Iram
- Department of Agricultural and Biological Engineering, Pennsylvania State University, 221 Agricultural Engineering Building, University Park, PA, 16802, USA
| | - Deniz Cekmecelioglu
- Department of Food Engineering, Middle East Technical University, 06800, Ankara, Turkey
| | - Ali Demirci
- Department of Agricultural and Biological Engineering, Pennsylvania State University, 221 Agricultural Engineering Building, University Park, PA, 16802, USA.
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14
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Xia W, Bai Y, Shi P. Improving the Substrate Affinity and Catalytic Efficiency of β-Glucosidase Bgl3A from Talaromyces leycettanus JCM12802 by Rational Design. Biomolecules 2021; 11:biom11121882. [PMID: 34944526 PMCID: PMC8699594 DOI: 10.3390/biom11121882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/31/2022] Open
Abstract
Improving the substrate affinity and catalytic efficiency of β-glucosidase is necessary for better performance in the enzymatic saccharification of cellulosic biomass because of its ability to prevent cellobiose inhibition on cellulases. Bgl3A from Talaromyces leycettanus JCM12802, identified in our previous work, was considered a suitable candidate enzyme for efficient cellulose saccharification with higher catalytic efficiency on the natural substrate cellobiose compared with other β-glucosidase but showed insufficient substrate affinity. In this work, hydrophobic stacking interaction and hydrogen-bonding networks in the active center of Bgl3A were analyzed and rationally designed to strengthen substrate binding. Three vital residues, Met36, Phe66, and Glu168, which were supposed to influence substrate binding by stabilizing adjacent binding site, were chosen for mutagenesis. The results indicated that strengthening the hydrophobic interaction between stacking aromatic residue and the substrate, and stabilizing the hydrogen-bonding networks in the binding pocket could contribute to the stabilized substrate combination. Four dominant mutants, M36E, M36N, F66Y, and E168Q with significantly lower Km values and 1.4–2.3-fold catalytic efficiencies, were obtained. These findings may provide a valuable reference for the design of other β-glucosidases and even glycoside hydrolases.
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Affiliation(s)
- Wei Xia
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Yingguo Bai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (Y.B.); (P.S.)
| | - Pengjun Shi
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- Correspondence: (Y.B.); (P.S.)
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15
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Fungal cellulases: protein engineering and post-translational modifications. Appl Microbiol Biotechnol 2021; 106:1-24. [PMID: 34889986 DOI: 10.1007/s00253-021-11723-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 12/18/2022]
Abstract
Enzymatic degradation of lignocelluloses into fermentable sugars to produce biofuels and other biomaterials is critical for environmentally sustainable development and energy resource supply. However, there are problems in enzymatic cellulose hydrolysis, such as the complex cellulase composition, low degradation efficiency, high production cost, and post-translational modifications (PTMs), all of which are closely related to specific characteristics of cellulases that remain unclear. These problems hinder the practical application of cellulases. Due to the rapid development of computer technology in recent years, computer-aided protein engineering is being widely used, which also brings new opportunities for the development of cellulases. Especially in recent years, a large number of studies have reported on the application of computer-aided protein engineering in the development of cellulases; however, these articles have not been systematically reviewed. This article focused on the aspect of protein engineering and PTMs of fungal cellulases. In this manuscript, the latest literatures and the distribution of potential sites of cellulases for engineering have been systematically summarized, which provide reference for further improvement of cellulase properties. KEY POINTS: •Rational design based on virtual mutagenesis can improve cellulase properties. •Modifying protein side chains and glycans helps obtain superior cellulases. •N-terminal glutamine-pyroglutamate conversion stabilizes fungal cellulases.
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16
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Pimentel V, Mariano D, Cantão LXS, Bastos LL, Fischer P, de Lima LHF, Fassio AV, de Melo-Minardi RC. VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes. FRONTIERS IN BIOINFORMATICS 2021; 1:730350. [PMID: 36303745 PMCID: PMC9581016 DOI: 10.3389/fbinf.2021.730350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/27/2021] [Indexed: 11/19/2022] Open
Abstract
Evolutionarily related proteins can present similar structures but very dissimilar sequences. Hence, understanding the role of the inter-residues contacts for the protein structure has been the target of many studies. Contacts comprise non-covalent interactions, which are essential to stabilize macromolecular structures such as proteins. Here we show VTR, a new method for the detection of analogous contacts in protein pairs. The VTR web tool performs structural alignment between proteins and detects interactions that occur in similar regions. To evaluate our tool, we proposed three case studies: we 1) compared vertebrate myoglobin and truncated invertebrate hemoglobin; 2) analyzed interactions between the spike protein RBD of SARS-CoV-2 and the cell receptor ACE2; and 3) compared a glucose-tolerant and a non-tolerant β-glucosidase enzyme used for biofuel production. The case studies demonstrate the potential of VTR for the understanding of functional similarities between distantly sequence-related proteins, as well as the exploration of important drug targets and rational design of enzymes for industrial applications. We envision VTR as a promising tool for understanding differences and similarities between homologous proteins with similar 3D structures but different sequences. VTR is available at http://bioinfo.dcc.ufmg.br/vtr.
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Affiliation(s)
- Vitor Pimentel
- Laboratory of Bioinformatics and Systems, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Diego Mariano
- Laboratory of Bioinformatics and Systems, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Letícia Xavier Silva Cantão
- Laboratory of Bioinformatics and Systems, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luana Luiza Bastos
- Laboratory of Bioinformatics and Systems, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Pedro Fischer
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Universidade Federal de São João Del-Rei, Sete Lagoas, Brazil
| | - Leonardo Henrique Franca de Lima
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Universidade Federal de São João Del-Rei, Sete Lagoas, Brazil
| | - Alexandre Victor Fassio
- Laboratory of Bioinformatics and Systems, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Raquel Cardoso de Melo-Minardi
- Laboratory of Bioinformatics and Systems, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- *Correspondence: Raquel Cardoso de Melo-Minardi,
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17
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Ndata K, Nevondo W, Cekuse B, van Zyl LJ, Trindade M. Characterization of a highly xylose tolerant β-xylosidase isolated from high temperature horse manure compost. BMC Biotechnol 2021; 21:61. [PMID: 34689773 PMCID: PMC8543862 DOI: 10.1186/s12896-021-00722-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a continued need for improved enzymes for industry. β-xylosidases are enzymes employed in a variety of industries and although many wild-type and engineered variants have been described, enzymes that are highly tolerant of the products produced by catalysis are not readily available and the fundamental mechanisms of tolerance are not well understood. RESULTS Screening of a metagenomic library constructed of mDNA isolated from horse manure compost for β-xylosidase activity identified 26 positive hits. The fosmid clones were sequenced and bioinformatic analysis performed to identity putative β-xylosidases. Based on the novelty of its amino acid sequence and potential thermostability one enzyme (XylP81) was selected for expression and further characterization. XylP81 belongs to the family 39 β-xylosidases, a comparatively rarely found and characterized GH family. The enzyme displayed biochemical characteristics (KM-5.3 mM; Vmax-122 U/mg; kcat-107; Topt-50 °C; pHopt-6) comparable to previously characterized glycoside hydrolase family 39 (GH39) β-xylosidases and despite nucleotide identity to thermophilic species, the enzyme displayed only moderate thermostability with a half-life of 32 min at 60 °C. Apart from acting on substrates predicted for β-xylosidase (xylobiose and 4-nitrophenyl-β-D-xylopyranoside) the enzyme also displayed measurable α-L-arabainofuranosidase, β-galactosidase and β-glucosidase activity. A remarkable feature of this enzyme is its ability to tolerate high concentrations of xylose with a Ki of 1.33 M, a feature that is highly desirable for commercial applications. CONCLUSIONS Here we describe a novel β-xylosidase from a poorly studied glycosyl hydrolase family (GH39) which despite having overall kinetic properties similar to other bacterial GH39 β-xylosidases, displays unusually high product tolerance. This trait is shared with only one other member of the GH39 family, the recently described β-xylosidases from Dictyoglomus thermophilum. This feature should allow its use as starting material for engineering of an enzyme that may prove useful to industry and should assist in the fundamental understanding of the mechanism by which glycosyl hydrolases evolve product tolerance.
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Affiliation(s)
- Kanyisa Ndata
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Walter Nevondo
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa.,Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Bongi Cekuse
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa.
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
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18
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Jiang Z, Long L, Liang M, Li H, Chen Y, Zheng M, Ni H, Li Q, Zhu Y. Characterization of a glucose-stimulated β-glucosidase from Microbulbifer sp. ALW1. Microbiol Res 2021; 251:126840. [PMID: 34375805 DOI: 10.1016/j.micres.2021.126840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/18/2021] [Accepted: 08/02/2021] [Indexed: 11/27/2022]
Abstract
Glucose-tolerant and/or glucose-stimulated β-glucosidase is of great interest for its industrial utilization in enzymatic digestion of lignocellulosic biomass for biofuel production. In this study, a new gene of β-glucosidase MaGlu1A was cloned from an alginate-degrading marine bacterium Microbulbifer sp. ALW1. The gene of MaGlu1A encoded a 472-amino acid protein classified into the glycosyl hydrolase family 1 (GH1). The recombinant β-glucosidase was overexpressed and purified from Escherichia coli with a molecular mass of 65.0 kDa. Structure analysis illustrated the catalytic acid/base residue Glu186 and nucleophilic residue Glu370 in the enzyme. MaGlu1A displayed optimal activity at 40 °C and pH 4.5, respectively. It had substrate preference to the aryl-β-glycosidic bonds with glucose, fucose, and galactose moieties, in addition to cellobiose. MaGlu1A demonstrated strong stimulation to the supplemental glucose. Site-directed mutagenesis suggested an essential role of Asn242 in glucose stimulation. The enzymatic characterization of MaGlu1A provides general information about its catalytic properties facilitating its practical applications.
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Affiliation(s)
- Zedong Jiang
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, China
| | - Liufei Long
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Meifang Liang
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Hebin Li
- Xiamen Medical College, Xiamen, 361008, China
| | - Yanhong Chen
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, China
| | - Mingjing Zheng
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, China
| | - Qingbiao Li
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, China
| | - Yanbing Zhu
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, China.
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19
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Lee WH, Jin YS. Observation of Cellodextrin Accumulation Resulted from Non-Conventional Secretion of Intracellular β-Glucosidase by Engineered Saccharomyces cerevisiae Fermenting Cellobiose. J Microbiol Biotechnol 2021; 31:1035-1043. [PMID: 34226403 PMCID: PMC9705985 DOI: 10.4014/jmb.2105.05018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022]
Abstract
Although engineered Saccharomyces cerevisiae fermenting cellobiose is useful for the production of biofuels from cellulosic biomass, cellodextrin accumulation is one of the main problems reducing ethanol yield and productivity in cellobiose fermentation with S. cerevisiae expressing cellodextrin transporter (CDT) and intracellular β-glucosidase (GH1-1). In this study, we investigated the reason for the cellodextrin accumulation and how to alleviate its formation during cellobiose fermentation using engineered S. cerevisiae fermenting cellobiose. From the series of cellobiose fermentation using S. cerevisiae expressing only GH1-1 under several culture conditions, it was discovered that small amounts of GH1-1 were secreted and cellodextrin was generated through trans-glycosylation activity of the secreted GH1-1. As GH1-1 does not have a secretion signal peptide, non-conventional protein secretion might facilitate the secretion of GH1-1. In cellobiose fermentations with S. cerevisiae expressing only GH1-1, knockout of TLG2 gene involved in non-conventional protein secretion pathway significantly delayed cellodextrin formation by reducing the secretion of GH1-1 by more than 50%. However, in cellobiose fermentations with S. cerevisiae expressing both GH1-1 and CDT-1, TLG2 knockout did not show a significant effect on cellodextrin formation, although secretion of GH1-1 was reduced by more than 40%. These results suggest that the development of new intracellular β-glucosidase, not influenced by non-conventional protein secretion, is required for better cellobiose fermentation performances of engineered S. cerevisiae fermenting cellobiose.
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Affiliation(s)
- Won-Heong Lee
- Department of Food Science and Human Nutrition, and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Department of Bioenergy Science and Technology, and Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea,Corresponding author Phone: +82-62-530-2046 Fax: +82-62-530-2047 E-mail:
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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20
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Sukumaran RK, Christopher M, Kooloth-Valappil P, Sreeja-Raju A, Mathew RM, Sankar M, Puthiyamadam A, Adarsh VP, Aswathi A, Rebinro V, Abraham A, Pandey A. Addressing challenges in production of cellulases for biomass hydrolysis: Targeted interventions into the genetics of cellulase producing fungi. BIORESOURCE TECHNOLOGY 2021; 329:124746. [PMID: 33610429 DOI: 10.1016/j.biortech.2021.124746] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Lignocellulosic materials are the favoured feedstock for biorefineries due to their abundant availability and non-completion with food. Biobased technologies for refining these materials are limited mainly by the cost of biomass hydrolyzing enzymes, typically sourced from filamentous fungi. Therefore, considerable efforts have been directed at improving the quantity and quality of secreted lignocellulose degrading enzymes from fungi in order to attain overall economic viability. Process improvements and media engineering probably have reached their thresholds and further production enhancements require modifying the fungal metabolism to improve production and secretion of these enzymes. This review focusses on the types and mechanisms of action of known fungal biomass degrading enzymes, our current understanding of the genetic control exerted on their expression, and possible routes for intervention, especially on modulating catabolite repression, transcriptional regulators, signal transduction, secretion pathways etc., in order to improve enzyme productivity, activity and stability.
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Affiliation(s)
- Rajeev K Sukumaran
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Meera Christopher
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Prajeesh Kooloth-Valappil
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - AthiraRaj Sreeja-Raju
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Reshma M Mathew
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Meena Sankar
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Anoop Puthiyamadam
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Velayudhanpillai-Prasannakumari Adarsh
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Aswathi Aswathi
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Valan Rebinro
- Centre for Biofuels, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Amith Abraham
- Department of Chemical Engineering, Hanyang University, Seoul, Republic of Korea
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
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21
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Lin MC, Kuo HW, Kao MR, Lin WD, Li CW, Hung KS, Yang SC, Yu SM, Ho THD. From simple and specific zymographic detections to the annotation of a fungus Daldinia caldariorum D263 that encodes a wide range of highly bioactive cellulolytic enzymes. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:120. [PMID: 34020690 PMCID: PMC8140500 DOI: 10.1186/s13068-021-01959-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Lignocellulolytic enzymes are essential for agricultural waste disposal and production of renewable bioenergy. Many commercialized cellulase mixtures have been developed, mostly from saprophytic or endophytic fungal species. The cost of complete cellulose digestion is considerable because a wide range of cellulolytic enzymes is needed. However, most fungi can only produce limited range of highly bioactive cellulolytic enzymes. We aimed to investigate a simple yet specific method for discovering unique enzymes so that fungal species producing a diverse group of cellulolytic enzymes can be identified. RESULTS The culture medium of an endophytic fungus, Daldinia caldariorum D263, contained a complete set of cellulolytic enzymes capable of effectively digesting cellulose residues into glucose. By taking advantage of the unique product inhibition property of β-glucosidases, we have established an improved zymography method that can easily distinguish β-glucosidase and exoglucanase activity. Our zymography method revealed that D263 can secrete a wide range of highly bioactive cellulases. Analyzing the assembled genome of D263, we found over 100 potential genes for cellulolytic enzymes that are distinct from those of the commercially used fungal species Trichoderma reesei and Aspergillus niger. We further identified several of these cellulolytic enzymes by mass spectrometry. CONCLUSIONS The genome of Daldinia caldariorum D263 has been sequenced and annotated taking advantage of a simple yet specific zymography method followed by mass spectrometry analysis, and it appears to encode and secrete a wide range of bioactive cellulolytic enzymes. The genome and cellulolytic enzyme secretion of this unique endophytic fungus should be of value for identifying active cellulolytic enzymes that can facilitate conversion of agricultural wastes to fermentable sugars for the industrial production of biofuels.
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Affiliation(s)
- Meng-Chun Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Hsion-Wen Kuo
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan, ROC
| | - Mu-Rong Kao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Chen-Wei Li
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Kuo-Sheng Hung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Sheng-Chih Yang
- Institute of Tropical Plant Science, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
- Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC.
- Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan, ROC.
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22
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Abstract
Trichoderma reesei has 11 putative β-glucosidases in its genome, playing key parts in the induction and production of cellulase. Nevertheless, the reason why the T. reesei genome encodes so many β-glucosidases and the distinct role each β-glucosidase plays in cellulase production remain unknown. In the present study, the cellular function and distribution of 10 known β-glucosidases (CEL3B, CEL3E, CEL3F, CEL3H, CEL3J, CEL1A, CEL3C, CEL1B, CEL3G, and CEL3D) were explored in T. reesei, leaving out BGL1 (CEL3A), which has been well investigated. We found that the overexpression of cel3b or cel3g significantly enhanced extracellular β-glucosidase production, whereas the overexpression of cel1b severely inhibited cellulase production by cellulose, resulting in nearly no growth of T. reesei. Four types of cellular distribution patterns were observed for β-glucosidases in T. reesei: (i) CEL3B, CEL3E, CEL3F, and CEL3G forming clearly separated protein secretion vesicles in the cytoplasm; (ii) CEL3H and CEL3J diffusing the whole endomembrane as well as the cell membrane with protein aggregation, like a reticular network; (iii) CEL1A and CEL3D in vacuoles; (iv) and CEL3C in the nucleus. β-glucosidases CEL1A, CEL3B, CEL3E, CEL3F, CEL3G, CEL3H, and CEL3J were identified as extracellular, CEL3C and CEL3D as intracellular, and CEL1B as unknown. The extracellular β-glucosidases CEL3B, CEL3E, CEL3F, CEL3H, and CEL3G were secreted through a tip-directed conventional secretion pathway, and CEL1A, via a vacuole-mediated pathway that was achieved without any signal peptide, while CEL3J was secreted via an unconventional protein pathway bypassing the endoplasmic reticulum (ER) and Golgi.
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23
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Zhang X, Su E, Li S, Chen X, Fan Z, Liu M, Ma B, Li H. Molecular analyses of the diversity and function of the family 1 β-glucosidase-producing microbial community in compost. Can J Microbiol 2021; 67:713-723. [PMID: 33905664 DOI: 10.1139/cjm-2020-0576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The diversity and transcription efficiency of GH1 family β-glucosidase genes were investigated in natural and inoculated composts using a DNA clone library and real-time qPCR. Compositional differences were observed in the functional community between both composting processes. Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi were the dominant phyla. Twenty representative β-glucosidase genes were quantitatively analyzed from DNA and RNA pools. Principal component analysis and Pearson's correlation analysis showed that cellulose degradation is correlated with the composition and succession of functional microbial communities, and this correlation was mainly observed in Proteobacteria and Actinobacteria. Compared with inoculated compost, the functional microbial communities in natural compost with a low diversity index exhibited weak buffering capacity for function in response to environmental changes. This may explain the consistency and dysfunction of cellulose degradation and transcriptional regulation by dominant β-glucosidase genes. Except for the β-glucosidase genes encoding constitutive enzymes, individual β-glucosidase genes responded to environmental changes more drastically than the group β-glucosidase genes. Correlation results suggested that β-glucosidase genes belonging to Micrococcales played an important role in the regulation of intracellular β-glucosidase. These results indicated that the responses of functional microorganisms were different during both composting processes, and were reflected at both the individual and group levels.
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Affiliation(s)
- Xinyue Zhang
- Northeast Agricultural University, 12430, Harbin, China;
| | - Erlie Su
- Northeast Agricultural University, 12430, Harbin, China;
| | - Shanshan Li
- Northeast Agricultural University, 12430, Harbin, China;
| | - Xiehui Chen
- Northeast Agricultural University, 12430, Harbin, China;
| | - Zhihua Fan
- Northeast Agricultural University, 12430, Harbin, China;
| | - Meiting Liu
- Northeast Agricultural University, 12430, Harbin, Harbin, China;
| | - Bo Ma
- Northeast Agricultural University, 12430, Harbin, China, 150030;
| | - Hongtao Li
- Northeast Agricultural University, 12430, Harbin, China, 150030;
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24
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Saleh Zada N, Belduz AO, Güler HI, Khan A, Sahinkaya M, Kaçıran A, Ay H, Badshah M, Shah AA, Khan S. Cloning, expression, biochemical characterization, and molecular docking studies of a novel glucose tolerant β-glucosidase from Saccharomonospora sp. NB11. Enzyme Microb Technol 2021; 148:109799. [PMID: 34116753 DOI: 10.1016/j.enzmictec.2021.109799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/10/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
Most of the presently known β-glucosidases are sensitive to end-product inhibition by glucose, restricting their potential use in many industrial applications. Identification of novel glucose tolerant β-glucosidase can prove a pivotal solution to eliminate end-product inhibition and enhance the overall lignocellulosic saccharification process. In this study, a novel gene encoding β-glucosidase BglNB11 of 1405bp was identified in the genome of Saccharomonospora sp. NB11 and was successfully cloned and heterologously expressed in E. coli BL21 (DE3).The presence of conserved amino acids; NEPW and TENG indicated that BglNB11 belonged to GH1 β-glucosidases. The recombinant enzyme was purified using a Ni-NTA column, with the molecular mass of 51 kDa, using SDS-PAGE analysis. BglNB11 showed optimum activity at 40 °C and pH 7 and did not require any tested co-factors for activation. The kinetic values, Km, Vmax, kcat, and kcat/Km of purified enzyme were 0.4037 mM, 5735.8 μmol/min/mg, 5042.16 s-1 and 12487.71 s-1 mM-1, respectively. The enzyme was not inhibited by glucose to a concentration of 4 M but was slightly stimulated in the presence of glucose. Molecular docking of BglNB11 with glucose suggested that the relative binding position of glucose in the active site channel might be responsible for modulating end product tolerance and stimulation. β-glucosidase from BglNB11 is an excellent enzyme with high catalytic efficiency and enhanced glucose tolerance compared to many known glucose tolerant β-glucosidases. These unique properties of BglNB11 make it a prime candidate to be utilized in many biotechnological applications.
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Affiliation(s)
- Numan Saleh Zada
- Department of Microbiology, Quaid-i-Azam University, Islamabad, 45320, Pakistan; Department of Molecular Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Ali Osman Belduz
- Department of Molecular Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Halil Ibrahim Güler
- Department of Molecular Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Anum Khan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Miray Sahinkaya
- Department of Molecular Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Arife Kaçıran
- Department of Molecular Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Sciences and Arts, Ondokuz Mayis University, Samsun, Turkey
| | - Malik Badshah
- Department of Microbiology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Aamer Ali Shah
- Department of Microbiology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Samiullah Khan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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Dadwal A, Singh V, Sharma S, Satyanarayana T. Structural aspects of β-glucosidase of Myceliophthora thermophila (MtBgl3c) by homology modelling and molecular docking. J Biomol Struct Dyn 2021; 40:5211-5228. [PMID: 33413029 DOI: 10.1080/07391102.2020.1869095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cellulases are the enzymes with diverse range of industrial applications. Cellulases degrade cellulose into monomeric glucose units by hydrolysing β-1,4-glycosidic bonds. There are three components of cellulases: a) endoglucanase, b) exoglucanase and c) β-glucosidase which act synergistically in cellulose bioconversion. The cellulases are the third largest industrial enzymes with a great potential in bioethanol production. In this investigation, a β-glucosidase of a thermophilic fungus Myceliophthora thermophila (MtBgl3c) was analysed for its structural characterization using in silico approaches. The protein structure of MtBgl3c is unknown, therefore an attempt has been made to model 3D structure using Modeller 9.23 software. The MtBgl3c protein model generated was validated from Verify 3D and ERRAT scores of 89.37% and 71.25%, respectively derived from SAVES. Using RAMPAGE the Ramachandran plot was generated, which predicted the accuracy of the 3D model with 91.5% amino acid residues in the favored region. The ion binding and N-glycosylation sites were also predicted. The generated model was docked with cellobiose to predict the most favorable binding sites of MtBgl3c. The key amino acid residues involved in cellobiose bonding are Val88, Asp106, Asp287, Tyr255, Arg170, Glu514. The catalytic conserved amino residues of MtBgl3c were identified. The dock score of cellobiose with MtBgl3c is much lower (-6.46 kcal/mol) than that of glucose (-5.61 kcal/mol), suggesting its high affinity for cellobiose. The docking data of MtBgl3c with glucose illustrate its tolerance to glucose. The present study provides insight into structural characteristics of the MtBgl3c which can be further validated by experimental data. Highlights3D structure of β-glucosidase (MtBgl3c) of Myceliophthora thermophila is being proposed based on computational analysesThe amino acid residues Asp106, Asp287, Tyr255, Arg170 and Glu514 have been identified to play catalytically important role in substrate bindingDocking and interaction of MtBgl3c with cellobiose and glucose has been confirmedDocking analysis of MtBgl3c with glucose suggested its glucose toleranceThe data would be useful in engineering enzymes for attaining higher catalytic efficiencyCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anica Dadwal
- Department of Biological Sciences and Engineering, Netaji Subhas Institute of Technology (University of Delhi), New Delhi, India
| | - Vishal Singh
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, Uttar Pradesh, India
| | - Shilpa Sharma
- Department of Biological Sciences and Engineering, Netaji Subhas Institute of Technology (University of Delhi), New Delhi, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas Institute of Technology (University of Delhi), New Delhi, India
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26
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Almeida PZD, Oliveira TBD, Lucas RCD, Salgado JCS, Pérez MM, Gálan B, García JL, Polizeli MDLTDM. Heterologous production and biochemical characterization of a new highly glucose tolerant GH1 β-glucosidase from Anoxybacillus thermarum. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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27
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Qu X, Ding B, Li J, Liang M, Du L, Wei Y, Huang R, Pang H. Characterization of a GH3 halophilic β-glucosidase from Pseudoalteromonas and its NaCl-induced activity toward isoflavones. Int J Biol Macromol 2020; 164:1392-1398. [PMID: 32763400 DOI: 10.1016/j.ijbiomac.2020.07.300] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/23/2020] [Accepted: 07/29/2020] [Indexed: 02/06/2023]
Abstract
A novel β-glucosidase gene was isolated from Pseudoalteromonas sp. GXQ-1 and heterologously expressed in Escherichia coli. The activity of the encoded enzyme, PABGL, toward p-nitrophenyl-β-D-glucopyranoside was increased 8.74-fold by the presence of 3 M NaCl relative to the absence of added NaCl. PABGL hydrolyzed a variety of soy isoflavone substrates. For the conversion of daidzin to daidzein, the production rate was 1.44 mM/h. The addition of NaCl enhanced the hydrolytic activity of PABGL toward daidzin and genistein; the maximum activation by NaCl was 3.48- and 6.79-fold, respectively. This is the first report of a halophilic β-glucosidase from Pseudoalteromonas spp., and represents the β-glucosidase with the highest multiple of activation by NaCl. PABGL exhibits strong potential for applications in food processing and industrial production.
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Affiliation(s)
- Xiaoyi Qu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Bo Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Meng Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Liqin Du
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
| | - Yutuo Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ribo Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Hao Pang
- Guangxi Key Laboratory of Bio-refinery, National Engineering Research Center for Non-Food Bio-refinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China.
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28
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Karatas M, Dogan S, Spahiu E, Ašić A, Bešić L, Turan Y. Enzyme kinetics and inhibition parameters of human leukocyte glucosylceramidase. Heliyon 2020; 6:e05191. [PMID: 33163670 PMCID: PMC7609449 DOI: 10.1016/j.heliyon.2020.e05191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/29/2020] [Accepted: 10/05/2020] [Indexed: 11/26/2022] Open
Abstract
Glucosylceramidase (GCase) is a lysosomal enzyme that catalyzes the cleavage of β-glucosidic linkage of glucocerebroside (GC) into glucose and ceramide; thereby, plays an essential function in the degradation of complex lipids and the turnover of cellular membranes. The growing list of 460 mutations in the gene coding for it-glucosylceramidase beta acid 1 (GBA1)-is reported to abolish its catalytic activity and decrease its enzyme stability, associating it with severe health conditions such as Gaucher disease (GD), Parkinson Disease (PD) and Dementia with Lewy bodies (DLB). Although the three-dimensional structure of wild type glucosylceramidase is elucidated, little is known about its features in human cells. Moreover, alternative sources of GCase that prove to be effective in the treatment of diseases with enzyme treatment therapies, impose the need for a simple and cost-effective procedure to study the enzyme behavior. This work, for the first time, shows a well-established, yet simple, cost- and time-efficient protocol for the study of GCase enzyme in human leukocytes by the artificial substrate p-Nitrophenyl-β-D-glucopyranoside (PNPG). Characterization of the enzyme in human leukocytes for activation parameters (optimal pH, Km, and Vmax) and enzyme inhibition was done. The results indicate that the optimum pH of GCase enzyme with PNPG is 5.0. The Km and Vmax values are 12.6mM and 333 U/mg, respectively. Gluconolactone competitively inhibits GCase, with a Ki value of 0.023 mM and IC50 of 0.047 mM. Glucose inhibition is uncompetitive with a Ki of 1.94 mM and IC50 of 55.3 mM. This is the first report for the inhibitory effect of glucose, δ-gluconolactone on human leukocyte GCase activity.
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Affiliation(s)
- Mesut Karatas
- International Burch University, Faculty of Engineering and Natural Sciences, Department of Genetics and Bioengineering, Francuske revolucije bb, 71000 Sarajevo, Bosnia and Herzegovina
| | - Senol Dogan
- Leipzig University, Faculty for Physics and Earth Sciences, Peter Debye Institute, Linnéstraße 5, 04103, Leipzig, Germany
| | - Emrulla Spahiu
- Institute of Molecular and Cell Physiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Adna Ašić
- International Burch University, Faculty of Engineering and Natural Sciences, Department of Genetics and Bioengineering, Francuske revolucije bb, 71000 Sarajevo, Bosnia and Herzegovina
| | - Larisa Bešić
- International Burch University, Faculty of Engineering and Natural Sciences, Department of Genetics and Bioengineering, Francuske revolucije bb, 71000 Sarajevo, Bosnia and Herzegovina
| | - Yusuf Turan
- International Burch University, Faculty of Engineering and Natural Sciences, Department of Genetics and Bioengineering, Francuske revolucije bb, 71000 Sarajevo, Bosnia and Herzegovina
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Vishnu Prasad J, Sahoo TK, Naveen S, Jayaraman G. Evolutionary engineering of Lactobacillus bulgaricus reduces enzyme usage and enhances conversion of lignocellulosics to D-lactic acid by simultaneous saccharification and fermentation. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:171. [PMID: 33088341 PMCID: PMC7566127 DOI: 10.1186/s13068-020-01812-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/06/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Simultaneous saccharification and fermentation (SSF) of pre-treated lignocellulosics to biofuels and other platform chemicals has long been a promising alternative to separate hydrolysis and fermentation processes. However, the disparity between the optimum conditions (temperature, pH) for fermentation and enzyme hydrolysis leads to execution of the SSF process at sub-optimal conditions, which can affect the rate of hydrolysis and cellulose conversion. The fermentation conditions could be synchronized with hydrolysis optima by carrying out the SSF at a higher temperature, but this would require a thermo-tolerant organism. Economically viable production of platform chemicals from lignocellulosic biomass (LCB) has long been stymied because of the significantly higher cost of hydrolytic enzymes. The major objective of this work is to develop an SSF strategy for D-lactic acid (D-LA) production by a thermo-tolerant organism, in which the enzyme loading could significantly be reduced without compromising on the overall conversion. RESULTS A thermo-tolerant strain of Lactobacillus bulgaricus was developed by adaptive laboratory evolution (ALE) which enabled the SSF to be performed at 45 °C with reduced enzyme usage. Despite the reduction of enzyme loading from 15 Filter Paper Unit/gLCB (FPU/gLCB) to 5 FPU/gLCB, we could still achieve ~ 8% higher cellulose to D-LA conversion in batch SSF, in comparison to the conversion by separate enzymatic hydrolysis and fermentation processes at 45 °C and pH 5.5. Extending the batch SSF to SSF with pulse-feeding of 5% pre-treated biomass and 5 FPU/gLCB, at 12-h intervals (36th-96th h), resulted in a titer of 108 g/L D-LA and 60% conversion of cellulose to D-LA. This is one among the highest reported D-LA titers achieved from LCB. CONCLUSIONS We have demonstrated that the SSF strategy, in conjunction with evolutionary engineering, could drastically reduce enzyme requirement and be the way forward for economical production of platform chemicals from lignocellulosics. We have shown that fed-batch SSF processes, designed with multiple pulse-feedings of the pre-treated biomass and enzyme, can be an effective way of enhancing the product concentrations.
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Affiliation(s)
- J. Vishnu Prasad
- Bioprocess and Metabolic Engineering Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036 India
| | - Tridweep K. Sahoo
- Bioprocess and Metabolic Engineering Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036 India
| | - S. Naveen
- Present Address: Indian Institute of Technology, BHU, Varanasi, India
| | - Guhan Jayaraman
- Bioprocess and Metabolic Engineering Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036 India
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30
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Qin Y, Li Q, Luo F, Fu Y, He H. One-step purification of two novel thermotolerant β-1,4-glucosidases from a newly isolated strain of Fusarium chlamydosporum HML278 and their characterization. AMB Express 2020; 10:182. [PMID: 33030626 PMCID: PMC7544787 DOI: 10.1186/s13568-020-01116-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/24/2020] [Indexed: 01/07/2023] Open
Abstract
A newly identified cellulase-producing Fusarium chlamydosporum HML278 was cultivated under solid-state fermentation of sugarcane bagasse, and two new β-glucosides enzymes (BG FH1, BG FH2) were recovered from fermentation solution by modified non-denaturing active gel electrophoresis and gel filtration chromatography. SDS-PAGE analysis showed that the molecular weight of BG FH1 and BG FH2 was 93 kDa and 52 kDa, respectively, and the enzyme activity was 5.6 U/mg and 11.5 U/mg, respectively. The optimal reaction temperature of the enzymes was 60 ℃, and the enzymes were stable with a temperature lower than 70 ℃. The optimal pH of the purified enzymes was 6.0, and the enzymes were stable between pH 4–10. Km and Vmax values were 2.76 mg/mL and 20.6 U/mg for pNPG, respectively. Thin-layer chromatography and high-performance liquid chromatography analysis showed that BG FH1and BG FH2 had hydrolysis activity toward cellobiose and could hydrolyze cellobiose into glucose. In addition, both enzymes exhibited transglycoside activity, which could use glucose to synthesize cellobiose and cellotriose, and preferentially synthesize alcohol. In conclusion, our study demonstrated that F. chlamydosporum HML278 produces heat-resistant β-glucosidases with both hydrolytic activity and transglycosidic activity, and these β-glucosidases have potential application in bioethanol and papermaking industries.
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Yin YR, Sang P, Yang FL, Li T, Yang RF, Liu HY, Luo ZL, Li WJ, Yang LQ. Characterization of a Cu 2+, SDS, alcohol and glucose tolerant GH1 β-glucosidase from Bacillus sp. CGMCC 1.16541. Antonie Van Leeuwenhoek 2020; 113:1467-1477. [PMID: 32748077 DOI: 10.1007/s10482-020-01455-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
A β-glucosidase gene (bsbgl1a) from Bacillus sp. CGMCC 1.16541 was expressed in Escherichia coli BL21 and subsequently characterized. The amino acid sequence shared 83.64% identity with β-glucosidase (WP_066390903.1) from Fictibacillus phosphorivorans. The recombinant β-glucosidase (BsBgl1A) had a molecular weight of 52.2 kDa and could hydrolyze cellobiose, cellotriose, cellotetrose, p-nitrophenyl-β-D-glucopyranoside (pNPG), and p-nitrophenyl-β-D-xylopyranoside (pNPX). Optimal activity for BsBgl1A was recorded at 45 °C with a pH between 5.6 and 7.6, and 100% of its activity was maintained after a 24 h incubation between pH 4 and 9. Kinetic characterization revealed an enzymatic turnover (Kcat) of 616 ± 2 s-1 (with cellobiose) and 3.5 ± 0.1 s-1 (with p-nitrophenyl-β-D-glucopyranoside). Interestingly, the recombinant enzyme showed cupric ion (Cu2+), sodium dodecyl sulfate (SDS) and alcohol tolerance at 10 mM for Cu2+ and 10% for both SDS and alcohol. Additionally, BsBgl1A had high tolerance for glucose (Ki = 2095 mM), which is an extremely desirable feature for industrial applications. Following the addition of BsBgl1A (0.05 mg/ml) to a commercial cellulase reaction system, glucose yields from sugarcane bagasse increased 100% after 1 day at 45 °C. This work identifies a Cu2+, SDS, alcohol, and glucose tolerant GH1 β-glucosidase with potential applications in the hydrolysis of cellulose for the bioenergy industry.
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Affiliation(s)
- Yi-Rui Yin
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
| | - Peng Sang
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
| | - Feng-Li Yang
- Xiaguan No. 1 Middle School, Dali, 671000, People's Republic of China
| | - Tao Li
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
| | - Run-Feng Yang
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
| | - Hong-Yan Liu
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
| | - Zong-Long Luo
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Li-Quan Yang
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China.
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Sinha SK, Das S, Konar S, Ghorai PK, Das R, Datta S. Elucidating the regulation of glucose tolerance in a β-glucosidase from Halothermothrix orenii by active site pocket engineering and computational analysis. Int J Biol Macromol 2020; 156:621-632. [DOI: 10.1016/j.ijbiomac.2020.04.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 03/16/2020] [Accepted: 04/04/2020] [Indexed: 12/18/2022]
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Ariaeenejad S, Nooshi-Nedamani S, Rahban M, Kavousi K, Pirbalooti AG, Mirghaderi S, Mohammadi M, Mirzaei M, Salekdeh GH. A Novel High Glucose-Tolerant β-Glucosidase: Targeted Computational Approach for Metagenomic Screening. Front Bioeng Biotechnol 2020; 8:813. [PMID: 32850705 PMCID: PMC7406677 DOI: 10.3389/fbioe.2020.00813] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/24/2020] [Indexed: 11/24/2022] Open
Abstract
The rate-limiting component of cellulase for efficient degradation of lignocellulosic biomass through the enzymatic route depends on glucosidase’s sensitivity to the end product (glucose). Therefore, there is still a keen interest in finding glucose-tolerant β-glucosidase (BGL) that is active at high glucose concentrations. The main objective of this study was to identify, isolate, and characterize novel highly glucose-tolerant and halotolerant β-glucosidase gene (PersiBGL1) from the mixed genome DNA of sheep rumen metagenome as a suitable environment for efficient cellulase by computationally guided experiments instead of costly functional screening. At first, an in silico screening approach was utilized to find primary candidate enzymes with superior properties. The structure-dependent mechanism of glucose tolerance was investigated for candidate enzymes. Among the computationally selected candidates, PersiBGL1 was cloned, isolated, and structurally characterized, which achieved very high activity in relatively high temperatures and alkaline pH and was successfully used for the hydrolysis of cellobiose. This enzyme exhibits a very high glucose tolerance, with the highest inhibition constant Ki (8.8 M) among BGLs reported so far and retained 75% of its initial activity in the presence of 10 M glucose. Furthermore, a group of multivalent metal, including Mg2+, Mn2+, and Ca2+, as a cofactor, could improve the catalytic efficiency of PersiBGL1. Our results demonstrated the power of computational selected candidates to discover novel glucose tolerance BGL, effective for the bioconversion of lignocellulosic biomass.
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Affiliation(s)
- Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Safura Nooshi-Nedamani
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Mahdie Rahban
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Atefeh Ghasemi Pirbalooti
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - SeyedSoheil Mirghaderi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Mahsa Mohammadi
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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Mariano D, Pantuza N, Santos LH, Rocha REO, de Lima LHF, Bleicher L, de Melo-Minardi RC. Glutantβase: a database for improving the rational design of glucose-tolerant β-glucosidases. BMC Mol Cell Biol 2020; 21:50. [PMID: 32611314 PMCID: PMC7329481 DOI: 10.1186/s12860-020-00293-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/22/2020] [Indexed: 11/22/2022] Open
Abstract
Β-glucosidases are key enzymes used in second-generation biofuel production. They act in the last step of the lignocellulose saccharification, converting cellobiose in glucose. However, most of the β-glucosidases are inhibited by high glucose concentrations, which turns it a limiting step for industrial production. Thus, β-glucosidases have been targeted by several studies aiming to understand the mechanism of glucose tolerance, pH and thermal resistance for constructing more efficient enzymes. In this paper, we present a database of β-glucosidase structures, called Glutantβase. Our database includes 3842 GH1 β-glucosidase sequences collected from UniProt. We modeled the sequences by comparison and predicted important features in the 3D-structure of each enzyme. Glutantβase provides information about catalytic and conserved amino acids, residues of the coevolution network, protein secondary structure, and residues located in the channel that guides to the active site. We also analyzed the impact of beneficial mutations reported in the literature, predicted in analogous positions, for similar enzymes. We suggested these mutations based on six previously described mutants that showed high catalytic activity, glucose tolerance, or thermostability (A404V, E96K, H184F, H228T, L441F, and V174C). Then, we used molecular docking to verify the impact of the suggested mutations in the affinity of protein and ligands (substrate and product). Our results suggest that only mutations based on the H228T mutant can reduce the affinity for glucose (product) and increase affinity for cellobiose (substrate), which indicates an increment in the resistance to product inhibition and agrees with computational and experimental results previously reported in the literature. More resistant β-glucosidases are essential to saccharification in industrial applications. However, thermostable and glucose-tolerant β-glucosidases are rare, and their glucose tolerance mechanisms appear to be related to multiple and complex factors. We gather here, a set of information, and made predictions aiming to provide a tool for supporting the rational design of more efficient β-glucosidases. We hope that Glutantβase can help improve second-generation biofuel production. Glutantβase is available at http://bioinfo.dcc.ufmg.br/glutantbase .
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Affiliation(s)
- Diego Mariano
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
| | - Naiara Pantuza
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Lucianna H Santos
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Rafael E O Rocha
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Leonardo H F de Lima
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Universidade Federal de São João Del-Rei, Campus Sete Lagoas, Sete Lagoas, 35701-970, Brazil
| | - Lucas Bleicher
- Protein Computational Biology Laboratory, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Raquel Cardoso de Melo-Minardi
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
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Facile Construction of Synergistic β-Glucosidase and Cellulase Sequential Co-immobilization System for Enhanced Biomass Conversion. CHINESE JOURNAL OF POLYMER SCIENCE 2020. [DOI: 10.1007/s10118-020-2437-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Cao L, Chen R, Huang X, Li S, Zhang S, Yang X, Qin Z, Kong W, Xie W, Liu Y. Engineering of β-Glucosidase Bgl15 with Simultaneously Enhanced Glucose Tolerance and Thermostability To Improve Its Performance in High-Solid Cellulose Hydrolysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5391-5401. [PMID: 32338906 DOI: 10.1021/acs.jafc.0c01817] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, a Petri-dish-based double-layer high-throughput screening method was established to improve glucose tolerance of β-glucosidase Bgl15. Two beneficial mutations were identified, and the joint mutant 2R1 improved the half-maximal inhibitory concentration of glucose from 0.04 to 2.1 M. The crystal structure of 2R1 was subsequently determined at 2.7 Å. Structure analysis revealed that enhancement of glucose tolerance may be due to improved transglycosylation activity made possible by a hydrophobic binding site for glucose as an acceptor and more stringent control of a putative water channel. To further ameliorate the application potential of the enzyme, it was engineered to increase the half-life at 50 °C from 0.8 h (Bgl15) to 180 h (mutant 5R1). Furthermore, supplementation of 5R1 to the cellulase cocktail significantly improved glucose production from pretreated sugar cane bagasse by 38%. Consequently, this study provided an efficient approach to enhance glucose tolerance and generated a promising catalyst for cellulose saccharification.
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Ashoor S, Sukumaran RK. Mild alkaline pretreatment can achieve high hydrolytic and fermentation efficiencies for rice straw conversion to bioethanol. Prep Biochem Biotechnol 2020; 50:814-819. [PMID: 32204649 DOI: 10.1080/10826068.2020.1744007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Mild alkaline pretreatment was evaluated as a strategy for effective lignin removal and hydrolysis of rice straw. The pretreatment efficiency of different NaOH concentrations (0.5, 1.0, 1.5 or 2.0% w/w) was assessed. Rice straw (RS) pretreated with 1.5% NaOH achieved better sugar yield compared to other concentrations used. A cellulose conversion efficiency of 91% (45.84 mg/ml glucose release) was attained from 1.5% NaOH pretreated rice straw (PRS), whereas 1% NaOH pretreated rice straw yielded 35.10 mg/ml of glucose corresponding to a cellulose conversion efficiency of 73.81%. The ethanol production from 1% and 1.5% NaOH pretreated RS hydrolysates was similar at ∼3.3% (w/v), corresponding to a fermentation efficiency of 86%. The non-detoxified hydrolysate was fermented using the novel yeast strain Saccharomyces cerevisiae RPP-03O without any additional supplementation of nutrients.
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Affiliation(s)
- Selim Ashoor
- Department of Agricultural Microbiology, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Rajeev K Sukumaran
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
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Utilization of Bacillus subtilis cells displaying a glucose-tolerant β-glucosidase for whole-cell biocatalysis. Enzyme Microb Technol 2020; 132:109444. [DOI: 10.1016/j.enzmictec.2019.109444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 11/22/2022]
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Cloning, purification and study of recombinant GH3 family β-glucosidase from Penicillium verruculosum. Biochimie 2020; 168:231-240. [DOI: 10.1016/j.biochi.2019.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022]
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Zhang X, Ma B, Liu J, Chen X, Li S, Su E, Gao L, Li H. β-Glucosidase genes differentially expressed during composting. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:174. [PMID: 33088344 PMCID: PMC7570026 DOI: 10.1186/s13068-020-01813-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Cellulose degradation by cellulase is brought about by complex communities of interacting microorganisms, which significantly contribute to the cycling of carbon on a global scale. β-Glucosidase (BGL) is the rate-limiting enzyme in the cellulose degradation process. Thus, analyzing the expression of genes involved in cellulose degradation and regulation of BGL gene expression during composting will improve the understanding of the cellulose degradation mechanism. Based on our previous research, we hypothesized that BGL-producing microbial communities differentially regulate the expression of glucose-tolerant BGL and non-glucose-tolerant BGL to adapt to the changes in cellulose degradation conditions. RESULTS To confirm this hypothesis, the structure and function of functional microbial communities involved in cellulose degradation were investigated by metatranscriptomics and a DNA library search of the GH1 family of BGLs involved in natural and inoculated composting. Under normal conditions, the group of non-glucose-tolerant BGL genes exhibited higher sensitivity to regulation than the glucose-tolerant BGL genes, which was suppressed during the composting process. Compared with the expression of endoglucanase and exoglucanase, the functional microbial communities exhibited a different transcriptional regulation of BGL genes during the cooling phase of natural composting. BGL-producing microbial communities upregulated the expression of glucose-tolerant BGL under carbon catabolite repression due to the increased glucose concentration, whereas the expression of non-glucose-tolerant BGL was suppressed. CONCLUSION Our results support the hypothesis that the functional microbial communities use multiple strategies of varying effectiveness to regulate the expression of BGL genes to facilitate adaptation to environmental changes.
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Affiliation(s)
- Xinyue Zhang
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Bo Ma
- School of Animal Medicine, Northeast Agricultural University, Harbin, 150030 China
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, 150030 China
| | - Jiawen Liu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Xiehui Chen
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Shanshan Li
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Erlie Su
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Liyuan Gao
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Hongtao Li
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
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Characterization of an extremely thermo-active archaeal β-glucosidase and its activity towards glucan and mannan in concert with an endoglucanase. Appl Microbiol Biotechnol 2019; 103:9505-9514. [PMID: 31713674 DOI: 10.1007/s00253-019-10218-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/17/2019] [Accepted: 10/22/2019] [Indexed: 10/25/2022]
Abstract
A metagenome from an enrichment culture of a hydrothermal vent sample taken at Vulcano Island (Italy) was sequenced and an endoglucanase-encoding gene (vul_cel5A) was identified in a previous work. Vul_Cel5A with maximal activity at 115 °C was characterized as the most heat-active endoglucanase to date. Based on metagenome sequences, genomes were binned and bin4 included vul_cel5A as well as a putative GH1 β-glycosidase-encoding gene (vul_bgl1A) with highest identities to sequences from the archaeal genus Thermococcus. The recombinant β-glucosidase Vul_Bgl1A produced in E. coli BL21 pQE-80L exhibited highest activity at 105 °C and pH 7.0 (76.12 ± 5.4 U/mg, 100%) using 4NP β-D-glucopyranoside as substrate and 61% relative activity at 120 °C. Accordingly, Vul_Bgl1A represents one of the most heat-active β-glucosidases to date. The enzyme has a broad substrate specificity with 155% activity towards 4NP β-D-mannopyranoside in comparison with 4NP β-D-glucopyranoside. Moreover, nearly complete hydrolysis of cellobiose was demonstrated. The enzyme exhibited a high glucose tolerance with 26% residual activity in presence of 2 M glucose and was furthermore activated at glucose concentrations of up to 0.5 M. When the endoglucanase Vul_Cel5A and the β-glucosidase Vul_Bgl1A were applied simultaneously at 99 °C, 158% activity towards barley β-glucan and 215% towards mannan were achieved compared with the activity of Vul_Cel5A alone (100%). Consequently, a significant increase in glucose formation was observed when both enzymes were incubated with β-glucan and mannan suggesting a synergistic effect. Hence, the two archaeal extremozymes are ideal candidates for complete glucan and mannan saccharification at temperatures above the boiling point of water.
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Molecular Dynamics Gives New Insights into the Glucose Tolerance and Inhibition Mechanisms on β-Glucosidases. Molecules 2019; 24:molecules24183215. [PMID: 31487855 PMCID: PMC6766793 DOI: 10.3390/molecules24183215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/15/2019] [Accepted: 08/23/2019] [Indexed: 12/23/2022] Open
Abstract
β-Glucosidases are enzymes with high importance for many industrial processes, catalyzing the last and limiting step of the conversion of lignocellulosic material into fermentable sugars for biofuel production. However, β-glucosidases are inhibited by high concentrations of the product (glucose), which limits the biofuel production on an industrial scale. For this reason, the structural mechanisms of tolerance to product inhibition have been the target of several studies. In this study, we performed in silico experiments, such as molecular dynamics (MD) simulations, free energy landscape (FEL) estimate, Poisson-Boltzmann surface area (PBSA), and grid inhomogeneous solvation theory (GIST) seeking a better understanding of the glucose tolerance and inhibition mechanisms of a representative GH1 β-glucosidase and a GH3 one. Our results suggest that the hydrophobic residues Y180, W350, and F349, as well the polar one D238 act in a mechanism for glucose releasing, herein called "slingshot mechanism", dependent also on an allosteric channel (AC). In addition, water activity modulation and the protein loop motions suggest that GH1 β-Glucosidases present an active site more adapted to glucose withdrawal than GH3, in consonance with the GH1s lower product inhibition. The results presented here provide directions on the understanding of the molecular mechanisms governing inhibition and tolerance to the product in β-glucosidases and can be useful for the rational design of optimized enzymes for industrial interests.
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Liu X, Cao L, Zeng J, Liu Y, Xie W. Improving the cellobiose-hydrolysis activity and glucose-tolerance of a thermostable β-glucosidase through rational design. Int J Biol Macromol 2019; 136:1052-1059. [DOI: 10.1016/j.ijbiomac.2019.06.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/01/2019] [Accepted: 06/05/2019] [Indexed: 12/20/2022]
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44
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Carli S, Carneiro LABDC, Ward RJ, Meleiro LP. Immobilization of a β-glucosidase and an endoglucanase in ferromagnetic nanoparticles: A study of synergistic effects. Protein Expr Purif 2019; 160:28-35. [DOI: 10.1016/j.pep.2019.03.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 01/11/2019] [Accepted: 03/29/2019] [Indexed: 12/14/2022]
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45
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Barruetabeña N, Alonso-Lerma B, Galera-Prat A, Joudeh N, Barandiaran L, Aldazabal L, Arbulu M, Alcalde M, De Sancho D, Gavira JA, Carrion-Vazquez M, Perez-Jimenez R. Resurrection of efficient Precambrian endoglucanases for lignocellulosic biomass hydrolysis. Commun Chem 2019. [DOI: 10.1038/s42004-019-0176-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Srivastava N, Rathour R, Jha S, Pandey K, Srivastava M, Thakur VK, Sengar RS, Gupta VK, Mazumder PB, Khan AF, Mishra PK. Microbial Beta Glucosidase Enzymes: Recent Advances in Biomass Conversation for Biofuels Application. Biomolecules 2019; 9:E220. [PMID: 31174354 PMCID: PMC6627771 DOI: 10.3390/biom9060220] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 01/10/2023] Open
Abstract
The biomass to biofuels production process is green, sustainable, and an advanced technique to resolve the current environmental issues generated from fossil fuels. The production of biofuels from biomass is an enzyme mediated process, wherein β-glucosidase (BGL) enzymes play a key role in biomass hydrolysis by producing monomeric sugars from cellulose-based oligosaccharides. However, the production and availability of these enzymes realize their major role to increase the overall production cost of biomass to biofuels production technology. Therefore, the present review is focused on evaluating the production and efficiency of β-glucosidase enzymes in the bioconversion of cellulosic biomass for biofuel production at an industrial scale, providing its mechanism and classification. The application of BGL enzymes in the biomass conversion process has been discussed along with the recent developments and existing issues. Moreover, the production and development of microbial BGL enzymes have been explained in detail, along with the recent advancements made in the field. Finally, current hurdles and future suggestions have been provided for the future developments. This review is likely to set a benchmark in the area of cost effective BGL enzyme production, specifically in the biorefinery area.
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Affiliation(s)
- Neha Srivastava
- Department of Chemical Engineering and Technology, IIT (BHU), Varanasi 221005, India.
| | - Rishabh Rathour
- Department of Bioengineering, Integral University, Lucknow 226026, India.
| | - Sonam Jha
- Department of Botany, Banaras Hindu University, Varanasi 221005, India.
| | - Karan Pandey
- Department of Chemical Engineering and Technology, IIT (BHU), Varanasi 221005, India.
| | - Manish Srivastava
- Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India.
| | - Vijay Kumar Thakur
- Enhanced Composites and Structures Center, School of Aerospace, Transport and Manufacturing, Cranfield University, Bedfordshire MK43 0AL, UK.
| | - Rakesh Singh Sengar
- Department of Agriculture Biotechnology, College of Agriculture, Sardar Vallabhbhai Patel, University of Agriculture and Technology, Meerut 250110, U.P., India.
| | - Vijai K Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia.
| | | | - Ahamad Faiz Khan
- Department of Bioengineering, Integral University, Lucknow 226026, India.
| | - Pradeep Kumar Mishra
- Department of Chemical Engineering and Technology, IIT (BHU), Varanasi 221005, India.
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Andrades DD, Graebin NG, Ayub MA, Fernandez-Lafuente R, Rodrigues RC. Physico-chemical properties, kinetic parameters, and glucose inhibition of several beta-glucosidases for industrial applications. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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49
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A Computational Method to Propose Mutations in Enzymes Based on Structural Signature Variation (SSV). Int J Mol Sci 2019; 20:ijms20020333. [PMID: 30650542 PMCID: PMC6359350 DOI: 10.3390/ijms20020333] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/29/2018] [Accepted: 01/06/2019] [Indexed: 11/26/2022] Open
Abstract
With the use of genetic engineering, modified and sometimes more efficient enzymes can be created for different purposes, including industrial applications. However, building modified enzymes depends on several in vitro experiments, which may result in the process being expensive and time-consuming. Therefore, computational approaches could reduce costs and accelerate the discovery of new technological products. In this study, we present a method, called structural signature variation (SSV), to propose mutations for improving enzymes’ activity. SSV uses the structural signature variation between target enzymes and template enzymes (obtained from the literature) to determine if randomly suggested mutations may provide some benefit for an enzyme, such as improvement of catalytic activity, half-life, and thermostability, or resistance to inhibition. To evaluate SSV, we carried out a case study that suggested mutations in β-glucosidases: Essential enzymes used in biofuel production that suffer inhibition by their product. We collected 27 mutations described in the literature, and manually classified them as beneficial or not. SSV was able to classify the mutations with values of 0.89 and 0.92 for precision and specificity, respectively. Then, we used SSV to propose mutations for Bgl1B, a low-performance β-glucosidase. We detected 15 mutations that could be beneficial. Three of these mutations (H228C, H228T, and H228V) have been related in the literature to the mechanism of glucose tolerance and stimulation in GH1 β-glucosidase. Hence, SSV was capable of detecting promising mutations, already validated by in vitro experiments, that improved the inhibition resistance of a β-glucosidase and, consequently, its catalytic activity. SSV might be useful for the engineering of enzymes used in biofuel production or other industrial applications.
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Geronimo I, Ntarima P, Piens K, Gudmundsson M, Hansson H, Sandgren M, Payne CM. Kinetic and molecular dynamics study of inhibition and transglycosylation in Hypocrea jecorina family 3 β-glucosidases. J Biol Chem 2019; 294:3169-3180. [PMID: 30602567 DOI: 10.1074/jbc.ra118.007027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Indexed: 01/09/2023] Open
Abstract
β-Glucosidases enhance enzymatic biomass conversion by relieving cellobiose inhibition of endoglucanases and cellobiohydrolases. However, the susceptibility of these enzymes to inhibition and transglycosylation at high glucose or cellobiose concentrations severely limits their activity and, consequently, the overall efficiency of enzyme mixtures. We determined the impact of these two processes on the hydrolytic activity of the industrially relevant family 3 β-glucosidases from Hypocrea jecorina, HjCel3A and HjCel3B, and investigated the underlying molecular mechanisms through kinetic studies, binding free energy calculations, and molecular dynamics (MD) simulations. HjCel3B had a 7-fold higher specificity for cellobiose than HjCel3A but greater tendency for glucose inhibition. Energy decomposition analysis indicated that cellobiose has relatively weak electrostatic interactions with binding site residues, allowing it to be easily displaced by glucose and free to inhibit other hydrolytic enzymes. HjCel3A is, thus, preferable as an industrial β-glucosidase despite its lower activity caused by transglycosylation. This competing pathway to hydrolysis arises from binding of glucose or cellobiose at the product site after formation of the glycosyl-enzyme intermediate. MD simulations revealed that binding is facilitated by hydrophobic interactions with Trp-37, Phe-260, and Tyr-443. Targeting these aromatic residues for mutation to reduce substrate affinity at the product site would therefore potentially mitigate transglycosidic activity. Engineering improved variants of HjCel3A and other structurally similar β-glucosidases would have a significant economic effect on enzymatic biomass conversion in terms of yield and production cost as the process can be consequently conducted at higher substrate loadings.
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Affiliation(s)
- Inacrist Geronimo
- From the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046
| | - Patricia Ntarima
- the Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium, and
| | - Kathleen Piens
- the Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium, and
| | - Mikael Gudmundsson
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Henrik Hansson
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Mats Sandgren
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Christina M Payne
- From the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046, .,the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
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