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Li YW, Guo Q, Peng QQ, Shen Q, Nie ZK, Ye C, Shi TQ. Recent Development of Advanced Biotechnology in the Oleaginous Fungi for Arachidonic Acid Production. ACS Synth Biol 2022; 11:3163-3173. [PMID: 36221956 DOI: 10.1021/acssynbio.2c00483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Arachidonic acid is an essential ω-6 polyunsaturated fatty acid, which plays a significant role in cardiovascular health and neurological development, leading to its wide use in the food and pharmaceutical industries. Traditionally, ARA is obtained from deep-sea fish oil. However, this source is limited by season and is depleting the already threatened global fish stocks. With the rapid development of synthetic biology in recent years, oleaginous fungi have gradually attracted increasing attention as promising microbial sources for large-scale ARA production. Numerous advanced technologies including metabolic engineering, dynamic regulation of fermentation conditions, and multiomics analysis were successfully adapted to increase ARA synthesis. This review summarizes recent advances in the bioengineering of oleaginous fungi for ARA production. Finally, perspectives for future engineering approaches are proposed to further improve the titer yield and productivity of ARA.
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Affiliation(s)
- Ya-Wen Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China.,College of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Qian-Qian Peng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Qi Shen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Zhi-Kui Nie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China.,Jiangxi New Reyphon Biochemical Co., Ltd, Salt & Chemical Industry, Xingan, Jiangxi 331399, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China.,College of Food Science and Technology, Nanchang University, No. 999 Xuefu Road, Nanchang 330031, People's Republic of China
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Comparative genome analysis of the oleaginous yeast Trichosporon fermentans reveals its potential applications in lipid accumulation. Microbiol Res 2016; 192:203-210. [PMID: 27664738 DOI: 10.1016/j.micres.2016.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/19/2016] [Accepted: 07/19/2016] [Indexed: 11/22/2022]
Abstract
In this work, Trichosporon fermentans CICC 1368, which has been shown to accumulate cellular lipids efficiently using industry-agricultural wastes, was subjected to preliminary genome analysis, yielding a genome size of 31.3 million bases and 12,702 predicted protein-coding genes. Our analysis also showed a high degree of gene duplications and unique genes compared with those observed in other oleaginous yeasts, with 3-4-fold more genes related to fatty acid elongation and degradation compared with those in Rhodosporidium toruloides NP11 and Yarrowia lipolytica CLIB122. Phylogenetic analysis with other oleaginous microbes suggested that the lipogenic capacity of T. fermentans was obtained during evolution after the divergence of genera. Thus, our study provided the first draft genome and comparative analysis of T. fermentans, laying the foundation for its genetic improvement to facilitate cost-effective lipid production.
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Identification of a critical determinant that enables efficient fatty acid synthesis in oleaginous fungi. Sci Rep 2015; 5:11247. [PMID: 26059272 PMCID: PMC4462047 DOI: 10.1038/srep11247] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/05/2015] [Indexed: 11/30/2022] Open
Abstract
Microorganisms are valuable resources for lipid production. What makes one microbe but not the other able to efficiently synthesize and accumulate lipids is poorly understood. In the present study, global gene expression prior to and after the onset of lipogenesis was determined by transcriptomics using the oleaginous fungus Mortierella alpina as a model system. A core of 23 lipogenesis associated genes was identified and their expression patterns shared a high similarity among oleaginous microbes Chlamydomonas reinhardtii, Mucor circinelloides and Rhizopus oryzae but was dissimilar to the non-oleaginous Aspergillus nidulans. Unexpectedly, Glucose-6-phosphate dehydrogenase (G6PD) and 6-phosphogluconate dehydrogenase (PGD) in the pentose phosphate pathway (PPP) were found to be the NADPH producers responding to lipogenesis in the oleaginous microbes. Their role in lipogenesis was confirmed by a knockdown experiment. Our results demonstrate, for the first time, that the PPP plays a significant role during fungal lipogenesis. Up-regulation of NADPH production by the PPP, especially G6PD, may be one of the critical determinants that enables efficiently fatty acid synthesis in oleaginous microbes.
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Muniraj IK, Uthandi SK, Hu Z, Xiao L, Zhan X. Microbial lipid production from renewable and waste materials for second-generation biodiesel feedstock. ACTA ACUST UNITED AC 2015. [DOI: 10.1080/21622515.2015.1018340] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Iniya Kumar Muniraj
- Civil Engineering, College of Engineering and Informatics, National University of Ireland Galway, Galway, Ireland
| | - Siva Kumar Uthandi
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Zhenhu Hu
- School of Civil Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Liwen Xiao
- Department of Civil, Structural and Environmental Engineering, Trinity College Dublin, Dublin, Ireland
| | - Xinmin Zhan
- Civil Engineering, College of Engineering and Informatics, National University of Ireland Galway, Galway, Ireland
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Liang YJ, Jiang JG. Characterization of malic enzyme and the regulation of its activity and metabolic engineering on lipid production. RSC Adv 2015. [DOI: 10.1039/c5ra04635a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nowadays, microbial lipids are employed as the feedstock for biodiesel production, which has attracted great attention across the whole world.
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Affiliation(s)
- Ying-Jie Liang
- School of Biological Science & Engineering
- South China University of Technology
- Guangzhou
- China
| | - Jian-Guo Jiang
- School of Biological Science & Engineering
- South China University of Technology
- Guangzhou
- China
- College of Food Science and Engineering
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Vongsangnak W, Ruenwai R, Tang X, Hu X, Zhang H, Shen B, Song Y, Laoteng K. Genome-scale analysis of the metabolic networks of oleaginous Zygomycete fungi. Gene 2013; 521:180-90. [PMID: 23541380 DOI: 10.1016/j.gene.2013.03.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 03/07/2013] [Indexed: 10/27/2022]
Abstract
Microbial lipids are becoming an attractive option for the industrial production of foods and oleochemicals. To investigate the lipid physiology of the oleaginous microorganisms, at the system level, genome-scale metabolic networks of Mortierella alpina and Mucor circinelloides were constructed using bioinformatics and systems biology. As scaffolds for integrated data analysis focusing on lipid production, consensus metabolic routes governing fatty acid synthesis, and lipid storage and mobilisation were identified by comparative analysis of developed metabolic networks. Unique metabolic features were identified in individual fungi, particularly in NADPH metabolism and sterol biosynthesis, which might be related to differences in fungal lipid phenotypes. The frameworks detailing the metabolic relationship between M. alpina and M. circinelloides generated in this study is useful for further elucidation of the microbial oleaginicity, which might lead to the production improvement of microbial oils as alternative feedstocks for oleochemical industry.
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Li Z, Sun H, Mo X, Li X, Xu B, Tian P. Overexpression of malic enzyme (ME) of Mucor circinelloides improved lipid accumulation in engineered Rhodotorula glutinis. Appl Microbiol Biotechnol 2012. [PMID: 23179623 DOI: 10.1007/s00253-012-4571-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The oleaginous yeast Rhodotorula glutinis has been known to be a potential feedstock for lipid production. In the present study, we investigated the enhancement of expression of malic enzyme (ME; NADP(+) dependent; EC 1.1.1.40) from Mucor circinelloides as a strategy to improve lipid content inside the yeast cells. The 26S rDNA and 5.8S rDNA gene fragments isolated from Rhodotorula glutinis were used for homologous integration of ME gene into R. glutinis chromosome under the control of the constitutively highly expressed gene phosphoglycerate kinase 1 to achieve stable expression. We demonstrated that by increasing the expression of the foreign ME gene in R. glutinis, we successfully improved the lipid content by more than twofold. At the end of lipid accumulation phrase (96 h) in the transformants, activity of ME was increased by twofold and lipid content of the yeast cells was increased from 18.74 % of the biomass to 39.35 %. Simultaneously, there were no significant differences in fatty acid profiles between the wild-type strain and the recombinant strain. Over 94 % of total fatty acids were C16:0, C18:0, C16:1, C18:1, and C18:2. Our results indicated that heterologous expression of NADP(+)-dependent ME involved in fatty acid biosynthesis indeed increased the lipid accumulation in the oleaginous yeast R. glutinis.
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Affiliation(s)
- Zhi Li
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou 510632, China
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Vongsangnak W, Zhang Y, Chen W, Ratledge C, Song Y. Annotation and analysis of malic enzyme genes encoding for multiple isoforms in the fungus Mucor circinelloides CBS 277.49. Biotechnol Lett 2012; 34:941-7. [PMID: 22367279 DOI: 10.1007/s10529-012-0859-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 01/17/2012] [Indexed: 10/14/2022]
Abstract
Based on the newly-released genomic data of Mucor circinelloides CBS 277.49, we have annotated five genes encoding for malic enzyme: all code for proteins that contain conserved domains/motifs for malic acid binding, NAD(+) binding and NAD(P)(+) binding. Phylogenetic analysis for malic enzyme genes showed that genes ID 78524 and 11639 share ~80% amino acid identity and are grouped in cluster 1; genes ID 182779, 186772 and 116127 share ~66% amino acid identity are grouped in cluster 2. Genes ID 78524, 11639 and 166127 produce proteins that are localized in the mitochondrion, while the products from genes 182779 and 186772 are localized in the cytosol. Based on the comparative analysis published previously by Song et al. (Microbiology 147:1507-1515, 2001), we propose that malic enzyme genes ID 78524, 166127, 182779, 186772, 11639, respectively, represent protein isoforms I, II, III/IV, V, and VI.
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Affiliation(s)
- Wanwipa Vongsangnak
- Center for Systems Biology, Soochow University, Suzhou, 215006, People's Republic of China.
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Wang L, Chen W, Feng Y, Ren Y, Gu Z, Chen H, Wang H, Thomas MJ, Zhang B, Berquin IM, Li Y, Wu J, Zhang H, Song Y, Liu X, Norris JS, Wang S, Du P, Shen J, Wang N, Yang Y, Wang W, Feng L, Ratledge C, Zhang H, Chen YQ. Genome characterization of the oleaginous fungus Mortierella alpina. PLoS One 2011; 6:e28319. [PMID: 22174787 PMCID: PMC3234268 DOI: 10.1371/journal.pone.0028319] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 11/05/2011] [Indexed: 12/15/2022] Open
Abstract
Mortierella alpina is an oleaginous fungus which can produce lipids accounting for up to 50% of its dry weight in the form of triacylglycerols. It is used commercially for the production of arachidonic acid. Using a combination of high throughput sequencing and lipid profiling, we have assembled the M. alpina genome, mapped its lipogenesis pathway and determined its major lipid species. The 38.38 Mb M. alpina genome shows a high degree of gene duplications. Approximately 50% of its 12,796 gene models, and 60% of genes in the predicted lipogenesis pathway, belong to multigene families. Notably, M. alpina has 18 lipase genes, of which 11 contain the class 2 lipase domain and may share a similar function. M. alpina's fatty acid synthase is a single polypeptide containing all of the catalytic domains required for fatty acid synthesis from acetyl-CoA and malonyl-CoA, whereas in many fungi this enzyme is comprised of two polypeptides. Major lipids were profiled to confirm the products predicted in the lipogenesis pathway. M. alpina produces a complex mixture of glycerolipids, glycerophospholipids and sphingolipids. In contrast, only two major sterol lipids, desmosterol and 24(28)-methylene-cholesterol, were detected. Phylogenetic analysis based on genes involved in lipid metabolism suggests that oleaginous fungi may have acquired their lipogenic capacity during evolution after the divergence of Ascomycota, Basidiomycota, Chytridiomycota and Mucoromycota. Our study provides the first draft genome and comprehensive lipid profile for M. alpina, and lays the foundation for possible genetic engineering of M. alpina to produce higher levels and diverse contents of dietary lipids.
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Affiliation(s)
- Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yun Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Yan Ren
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Zhennan Gu
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Hongchao Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Michael J. Thomas
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Baixi Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Isabelle M. Berquin
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Yang Li
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Jiansheng Wu
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Huanxin Zhang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Yuanda Song
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Xiang Liu
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - James S. Norris
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Suriguga Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Peng Du
- Tianjin Biochip Corporation, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Junguo Shen
- Tianjin Biochip Corporation, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Na Wang
- Tianjin Biochip Corporation, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Yanlin Yang
- Tianjin Biochip Corporation, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Wei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Lu Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
- Tianjin Research Center for Functional Genomics and Biochip, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Colin Ratledge
- Department of Biological Sciences, University of Hull, Hull, United Kingdom
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yong Q. Chen
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
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Multiple isoforms of malic enzyme in the oleaginous fungus, Mortierella alpina. ACTA ACUST UNITED AC 2008; 112:725-30. [DOI: 10.1016/j.mycres.2008.01.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Revised: 12/17/2007] [Accepted: 01/10/2008] [Indexed: 11/21/2022]
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Zhang Y, Adams IP, Ratledge C. Malic enzyme: the controlling activity for lipid production? Overexpression of malic enzyme in Mucor circinelloides leads to a 2.5-fold increase in lipid accumulation. MICROBIOLOGY-SGM 2007; 153:2013-2025. [PMID: 17600047 DOI: 10.1099/mic.0.2006/002683-0] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Malic enzyme (ME; NADP(+)-dependent; EC 1 . 1 . 1 . 40) has been postulated to be the rate-limiting step for fatty acid biosynthesis in oleaginous fungi in which the extent of lipid accumulation is below the maximum possible. The genes encoding the isoform of ME involved in fatty acid synthesis were identified in Mucor circinelloides and Mortierella alpina, two commercially useful oil-producing fungi, using degenerate primers. Both showed high similarity with ME genes from other micro-organisms. The whole-length ME gene from each source was cloned into a leucine auxotroph of Mc. circinelloides and placed under the control of the constitutive glyceraldehyde-3-phosphate dehydrogenase gene (gpd1) promoter. After confirming correct expression of the ME genes, the two recombinant strains were grown in fully controlled, submerged-culture bioreactors using a high C : N ratio medium for lipid accumulation. Activities of ME were increased by two- to threefold and the lipid contents of the cells, in both recombinants, were increased from 12 % of the biomass to 30 %. Simultaneously, the degree of fatty acid desaturation increased slightly. Thus, increased expression of the ME gene leads to both increased biosynthesis of fatty acids and formation of unsaturated fatty acids, including gamma-linolenic acid (18 : 3 n-6). At the end of lipid accumulation (96 h), ME activity in the recombinant strains had ceased, as it had done in the parent wild-type cells, indicating that additional, but unknown, controls over its activity must be in place to account for this loss of activity: this may be due to the presence of a specific ME-cleaving enzyme. The hypothesis that the rate-limiting step of fatty acid biosynthesis is therefore the supply of NADPH, as generated specifically and solely by ME, is therefore considerably strengthened by these results.
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Affiliation(s)
- Ying Zhang
- Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
| | - Ian P Adams
- Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
| | - Colin Ratledge
- Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
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