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Wang Q, Lin W, Ni Y, Zhou J, Xu G, Han R. Engineering of Methionine Adenosyltransferase toward Mitigated Product Inhibition for Efficient Production of S-Adenosylmethionine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16900-16910. [PMID: 39016109 DOI: 10.1021/acs.jafc.4c03715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
S-Adenosylmethionine (SAM) is a crucial metabolic intermediate playing irreplaceable roles in organismal activities. However, the synthesis of SAM by methionine adenosyltransferase (MAT) is hindered by low conversion due to severe product inhibition. Herein structure-guided semirational engineering was conducted on MAT from Escherichia coli (EcMAT) to mitigate the product inhibitory effect. Compared with the wild-type EcMAT, the best variant E56Q/Q105R exhibited an 8.13-fold increase in half maximal inhibitory concentration and a 4.46-fold increase in conversion (150 mM ATP and l-methionine), leading to a SAM titer of 47.02 g/L. Another variant, E56N/Q105R, showed superior thermostability with an impressive 85.30-fold increase in half-life (50 °C) value. Furthermore, molecular dynamics (MD) simulation results demonstrate that the alleviation in product inhibitory effect could be attributed to facilitated product release. This study offers molecular insights into the mitigated product inhibition, and provides valuable guidance for engineering MAT toward enhanced catalytic performance.
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Affiliation(s)
- Qiangqiang Wang
- Key laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Weibin Lin
- Key laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Ye Ni
- Key laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jinghui Zhou
- National Engineering Research Center for Enzyme Technology in Medicine and Chemical Industry, Hunan Flag Bio-tech Co., Ltd., Changsha 410100, China
- National Research Center of Engineering and Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha 410128, China
| | - Gang Xu
- National Engineering Research Center for Enzyme Technology in Medicine and Chemical Industry, Hunan Flag Bio-tech Co., Ltd., Changsha 410100, China
| | - Ruizhi Han
- Key laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Tang S, Zhao J, Liu C, Huang D, Tian J, Yang Y. Immobilization of Coprinus comatus with magnetic alginate hydrogel microsphere for improving the antioxidant activity of fermentation products. Prep Biochem Biotechnol 2024:1-10. [PMID: 38648492 DOI: 10.1080/10826068.2024.2345838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Coprinus comatus is an edible mushroom and its fermented product possesses antioxidant activity. In this study, to further enhance the antioxidant activity and improve the reusability of the strain, calcium alginate hydrogel was used as the carrier for embedding and immobilizing Coprinus comatus. The effects of CaCl2 concentration, sodium alginate concentration, microsphere diameter, and the amount of magnetic particle on the antioxidant activity of fermented products were investigated. The results showed that the magnetic immobilized microsphere prepared by 2.50% CaCl2, 2.00% sodium alginate and 0.50% Fe3O4 had the best fermentation antioxidant activity (EC50 was 0.43 ± 0.01 mg/mL) when the diameter was 5 mm, which increased by 24.56% compared to the initial activity. Besides, the microsphere showed strong reusability, the antioxidant activity was still better than the free strain after being used five times. This study not only enhanced the antioxidant activity of Coprinus comatus fermented product through immobilization, but also provided an effective method for microbial fermentation.
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Affiliation(s)
- Shanshan Tang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Jia Zhao
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Chang Liu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Dezhi Huang
- School of Light Industry and Chemical Engineering, Dalian Polytechnic University, Dalian, China
| | - Jing Tian
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Yi Yang
- School of Light Industry and Chemical Engineering, Dalian Polytechnic University, Dalian, China
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Chai H, Gu Q, Robertson DL, Hughes J. Defining the characteristics of interferon-alpha-stimulated human genes: insight from expression data and machine learning. Gigascience 2022; 11:6833046. [PMID: 36399061 PMCID: PMC9673497 DOI: 10.1093/gigascience/giac103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/07/2022] [Accepted: 10/02/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND A virus-infected cell triggers a signalling cascade, resulting in the secretion of interferons (IFNs), which in turn induces the upregulation of the IFN-stimulated genes (ISGs) that play a role in antipathogen host defence. Here, we conducted analyses on large-scale data relating to evolutionary gene expression, sequence composition, and network properties to elucidate factors associated with the stimulation of human genes in response to IFN-α. RESULTS We find that ISGs are less evolutionary conserved than genes that are not significantly stimulated in IFN experiments (non-ISGs). ISGs show obvious depletion of GC content in the coding region. This influences the representation of some compositions following the translation process. IFN-repressed human genes (IRGs), downregulated genes in IFN experiments, can have similar properties to the ISGs. Additionally, we design a machine learning framework integrating the support vector machine and novel feature selection algorithm that achieves an area under the receiver operating characteristic curve (AUC) of 0.7455 for ISG prediction. Its application in other IFN systems suggests the similarity between the ISGs triggered by type I and III IFNs. CONCLUSIONS ISGs have some unique properties that make them different from the non-ISGs. The representation of some properties has a strong correlation with gene expression following IFN-α stimulation, which can be used as a predictive feature in machine learning. Our model predicts several genes as putative ISGs that so far have shown no significant differential expression when stimulated with IFN-α in the cell/tissue types in the available databases. A web server implementing our method is accessible at http://isgpre.cvr.gla.ac.uk/. The docker image at https://hub.docker.com/r/hchai01/isgpre can be downloaded to reproduce the prediction.
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Affiliation(s)
- Haiting Chai
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Campus, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Campus, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK
| | - David L Robertson
- Correspondence address. David L. Robertson, MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK, E-mail:
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Luo Y, Jiang Y, Chen L, Li C, Wang Y. Applications of protein engineering in the microbial synthesis of plant triterpenoids. Synth Syst Biotechnol 2022; 8:20-32. [PMID: 36381964 PMCID: PMC9634032 DOI: 10.1016/j.synbio.2022.10.001] [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: 07/03/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/26/2022] Open
Abstract
Triterpenoids are a class of natural products widely used in fields related to medicine and health due to their biological activities such as hepatoprotection, anti-inflammation, anti-viral, and anti-tumor. With the advancement in biotechnology, microorganisms have been used as cell factories to produce diverse natural products. Despite the significant progress that has been made in the construction of microbial cell factories for the heterogeneous biosynthesis of triterpenoids, the industrial production of triterpenoids employing microorganisms has been stymied due to the shortage of efficient enzymes as well as the low expression and low catalytic activity of heterologous proteins in microbes. Protein engineering has been demonstrated as an effective way for improving the specificity, catalytic activity, and stability of the enzyme, which can be employed to overcome these challenges. This review summarizes the current progress in the studies of Oxidosqualene cyclases (OSCs), cytochrome P450s (P450s), and UDP-glycosyltransferases (UGTs), the key enzymes in the triterpenoids synthetic pathway. The main obstacles restricting the efficient catalysis of these key enzymes are analyzed, the applications of protein engineering for the three key enzymes in the microbial synthesis of triterpenoids are systematically reviewed, and the challenges and prospects of protein engineering are also discussed.
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Affiliation(s)
- Yan Luo
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Yaozhu Jiang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Linhao Chen
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China,Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Ying Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China,Corresponding author.
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Enhancing the Catalytic Activity of Type II L-Asparaginase from Bacillus licheniformis through Semi-Rational Design. Int J Mol Sci 2022; 23:ijms23179663. [PMID: 36077061 PMCID: PMC9456134 DOI: 10.3390/ijms23179663] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 01/10/2023] Open
Abstract
Low catalytic activity is a key factor limiting the widespread application of type II L-asparaginase (ASNase) in the food and pharmaceutical industries. In this study, smart libraries were constructed by semi-rational design to improve the catalytic activity of type II ASNase from Bacillus licheniformis. Mutants with greatly enhanced catalytic efficiency were screened by saturation mutations and combinatorial mutations. A quintuple mutant ILRAC was ultimately obtained with specific activity of 841.62 IU/mg and kcat/Km of 537.15 min−1·mM−1, which were 4.24-fold and 6.32-fold more than those of wild-type ASNase. The highest specific activity and kcat/Km were firstly reported in type II ASNase from Bacillus licheniformis. Additionally, enhanced pH stability and superior thermostability were both achieved in mutant ILRAC. Meanwhile, structural alignment and molecular dynamic simulation demonstrated that high structure stability and strong substrate binding were beneficial for the improved thermal stability and enzymatic activity of mutant ILRAC. This is the first time that enzymatic activity of type II ASNase from Bacillus licheniformis has been enhanced by the semi-rational approach, and results provide new insights into enzymatic modification of L-asparaginase for industrial applications.
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Preparation of cross-linked cell aggregates (CLCAs) of recombinant E. coli harboring glutamate dehydrogenase and glucose dehydrogenase for efficient asymmetric synthesis of L-phosphinothricin. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Firoozi FR, Raee MJ, Lal N, Ebrahiminezhad A, Teshnizi SH, Berenjian A, Ghasemi Y. Application of magnetic immboilization for ethanol biosynthesis using Saccharomyces cerevisiae. SEP SCI TECHNOL 2021. [DOI: 10.1080/01496395.2021.1939376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Farid Reza Firoozi
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Javad Raee
- Centre for Nanotechnology in Drug Delivery, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences Research Centre, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neha Lal
- School of Engineering, Faculty of Science and Engineering, University of Waikato, Hamilton New Zealand
| | | | - Saeed Hosseini Teshnizi
- Department of Biostatistics, Paramedical School, Hormozgan University of Medical Sciences, Bandar-abbas, Iran
| | - Aydin Berenjian
- School of Engineering, Faculty of Science and Engineering, University of Waikato, Hamilton New Zealand
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences Research Centre, Shiraz University of Medical Sciences, Shiraz, Iran
- Biotechnology Research Centre, Shiraz University of Medical Sciences, Shiraz, Iran
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Fan XM, Shen JJ, Xu YY, Gao J, Zhang YW. Metabolic integration of azide functionalized glycan on Escherichia coli cell surface for specific covalent immobilization onto magnetic nanoparticles with click chemistry. BIORESOURCE TECHNOLOGY 2021; 324:124689. [PMID: 33450627 DOI: 10.1016/j.biortech.2021.124689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
A method for specific immobilization of whole-cell with covalent bonds was developed through a click reaction between alkyne and azide groups. In this approach, magnetic nanoparticle Fe3O4@SiO2-NH2-alkyne was synthesized with Fe3O4 core preparation, SiO2 coating, and alkyne functionalization on the surface. The azides were successfully integrated onto the cell surface of the recombinant E. coli harboring glycerol dehydrogenase, which was employed as the model cell. The highest immobilization yield of 83% and activity recovery of 94% were obtained under the conditions of 0.67 mg mg-1 cell-support ratio, pH 6.0, temperature 45 °C, and 20 mM Cu2+ concentration. The immobilized cell showed good reusability, which remained over 50% of initial activity after 10 cycles of utilization. Its activity was 9.7-fold higher than that of the free cell at the condition of pH 8.0 and each optimal temperature. Furthermore, the immobilized cell showed significantly higher activity, operational stability, and reusability.
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Affiliation(s)
- Xiao-Man Fan
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Jia-Jia Shen
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Yuan-Yuan Xu
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Jian Gao
- College of Petroleum and Chemical Engineering, Beibu Gulf University, 535100 Qinzhou, People's Republic of China
| | - Ye-Wang Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, People's Republic of China; College of Petroleum and Chemical Engineering, Beibu Gulf University, 535100 Qinzhou, People's Republic of China.
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Liu T, Liu B, Zhou H, Zhang J. Knockout of the DAS gene increases S-adenosylmethionine production in Komagataella phaffii. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2020.1837012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Taiyu Liu
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Baolin Liu
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Hualan Zhou
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Jianguo Zhang
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
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Gupta K, Daroch P, Harjai K, Chhibber S. Parallels among natural and synthetically modified quorum-quenching strategies as convoy to future therapy. Microbiology (Reading) 2019; 165:1265-1281. [DOI: 10.1099/mic.0.000826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Kshitiz Gupta
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Priya Daroch
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Kusum Harjai
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sanjay Chhibber
- Department of Microbiology, Panjab University, Chandigarh, India
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Semi-rationally engineered variants of S-adenosylmethionine synthetase from Escherichia coli with reduced product inhibition and improved catalytic activity. Enzyme Microb Technol 2019; 129:109355. [PMID: 31307578 DOI: 10.1016/j.enzmictec.2019.05.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/29/2019] [Accepted: 05/26/2019] [Indexed: 11/20/2022]
Abstract
S-adenosylmethionine synthetase (MAT) catalyzes the synthesis of S-adenosylmethionine (SAM) from ATP and L-methionine. SAM is the major methyl donor for more than 100 transmethylation reactions. It is also a common cosubstrate involved in transsulfuration and aminopropylation. However, product inhibition largely restrains the activity of MAT and limits the enzymatic synthesis of SAM. In this research, the product inhibition of MAT from Escherichia coli was reduced via semi-rational modification. A triple variant (Variant III, I303 V/I65 V/L186 V) showed a 42-fold increase in Ki,ATP and a 2.08-fold increase in specific activity when compared to wild-type MAT. Its Ki,ATP was 0.42 mM and specific acitivity was 3.78 ±0.19 U/mg. Increased Ki,ATP means reduced product inhibition which enhances SAM accumulation. The SAM produced by Variant III could reach to 3.27 mM while SAM produced by wild-type MAT was 1.62 mM in the presence of 10 mM substrates. When the residue in 104th of Variant III was further optimized by site-saturated mutagenesis, the specific activity of Variant IV (I303 V/I65 V/L186 V/N104 K) reached to 6.02 ±0.22 U/mg at 37 °C, though the SAM concentration decreased to 2.68 mM with 10 mM substrates. Analysis of protein 3D structure suggests that changes in hydrogen bonds or other ligand interactions around active site may account for the variety of product inhibition and enzyme activity. The Variant III and Variant IV with reduced inhibition and improved enzyme activity in the study would be more suitable candidates for SAM production in the future.
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He J, Sun S, Zhou Z, Yuan Q, Liu Y, Liang H. Thermostable enzyme-immobilized magnetic responsive Ni-based metal–organic framework nanorods as recyclable biocatalysts for efficient biosynthesis of S-adenosylmethionine. Dalton Trans 2019; 48:2077-2085. [DOI: 10.1039/c8dt04857f] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A novel magnetic responsive Ni-based metal–organic framework material was developed to efficiently separate and immobilize thermal enzymes with high catalytic performance.
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Affiliation(s)
- Jie He
- State Key laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P.R. China
| | - Shanshan Sun
- State Key laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P.R. China
| | - Zhao Zhou
- State Key laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P.R. China
| | - Qipeng Yuan
- State Key laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P.R. China
| | - Yanhui Liu
- State Key laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P.R. China
| | - Hao Liang
- State Key laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing
- P.R. China
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