Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production
In this study, we reconstructed for the first time a genome-scale metabolic model (GSMM) of Ganoderma lucidum strain CGMCC5.26, termed model iZBM1060, containing 1060 genes, 1202 metabolites, and 1404 reactions. Important findings based on model iZBM1060 and its predictions are as follows: (i) The e...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-12-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2018.03076/full |
| _version_ | 1819085431271063552 |
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| author | Zhongbao Ma Zhongbao Ma Chao Ye Chao Ye Weiwei Deng Mengmeng Xu Mengmeng Xu Qiong Wang Qiong Wang Gaoqiang Liu Feng Wang Liming Liu Liming Liu Zhenghong Xu Zhenghong Xu Guiyang Shi Guiyang Shi Zhongyang Ding Zhongyang Ding |
| author_facet | Zhongbao Ma Zhongbao Ma Chao Ye Chao Ye Weiwei Deng Mengmeng Xu Mengmeng Xu Qiong Wang Qiong Wang Gaoqiang Liu Feng Wang Liming Liu Liming Liu Zhenghong Xu Zhenghong Xu Guiyang Shi Guiyang Shi Zhongyang Ding Zhongyang Ding |
| author_sort | Zhongbao Ma |
| collection | DOAJ |
| description | In this study, we reconstructed for the first time a genome-scale metabolic model (GSMM) of Ganoderma lucidum strain CGMCC5.26, termed model iZBM1060, containing 1060 genes, 1202 metabolites, and 1404 reactions. Important findings based on model iZBM1060 and its predictions are as follows: (i) The extracellular polysaccharide (EPS) biosynthetic pathway was elucidated completely. (ii) A new fermentation strategy is proposed: addition of phenylalanine increased EPS production by 32.80% in simulations and by 38.00% in experiments. (iii) Eight genes for key enzymes were proposed for EPS overproduction. Model iZBM1060 provides a useful platform for regulating EPS production in terms of system metabolic engineering for G. lucidum, as well as a guide for future metabolic pathway construction of other high value-added edible/ medicinal mushroom species. |
| first_indexed | 2024-12-21T21:04:15Z |
| format | Article |
| id | doaj.art-a05c93bd6fdc471f8dc1e893803423f9 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-21T21:04:15Z |
| publishDate | 2018-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-a05c93bd6fdc471f8dc1e893803423f92022-12-21T18:50:20ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-12-01910.3389/fmicb.2018.03076419823Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide ProductionZhongbao Ma0Zhongbao Ma1Chao Ye2Chao Ye3Weiwei Deng4Mengmeng Xu5Mengmeng Xu6Qiong Wang7Qiong Wang8Gaoqiang Liu9Feng Wang10Liming Liu11Liming Liu12Zhenghong Xu13Zhenghong Xu14Guiyang Shi15Guiyang Shi16Zhongyang Ding17Zhongyang Ding18Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, ChinaNational Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, ChinaKey Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, ChinaNational Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, ChinaNational Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, ChinaKey Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, ChinaNational Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, ChinaKey Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, ChinaNational Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, ChinaKey Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, ChinaSchool of Food and Biological Engineering, Jiangsu University, Zhenjiang, ChinaKey Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, ChinaNational Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, ChinaKey Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, ChinaNational Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, ChinaKey Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, ChinaNational Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, ChinaKey Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, ChinaNational Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, ChinaIn this study, we reconstructed for the first time a genome-scale metabolic model (GSMM) of Ganoderma lucidum strain CGMCC5.26, termed model iZBM1060, containing 1060 genes, 1202 metabolites, and 1404 reactions. Important findings based on model iZBM1060 and its predictions are as follows: (i) The extracellular polysaccharide (EPS) biosynthetic pathway was elucidated completely. (ii) A new fermentation strategy is proposed: addition of phenylalanine increased EPS production by 32.80% in simulations and by 38.00% in experiments. (iii) Eight genes for key enzymes were proposed for EPS overproduction. Model iZBM1060 provides a useful platform for regulating EPS production in terms of system metabolic engineering for G. lucidum, as well as a guide for future metabolic pathway construction of other high value-added edible/ medicinal mushroom species.https://www.frontiersin.org/article/10.3389/fmicb.2018.03076/fullGanoderma lucidumextracellular polysaccharidegenome-scale metabolic modelbiosynthetic pathwayphenylalaninesimulation |
| spellingShingle | Zhongbao Ma Zhongbao Ma Chao Ye Chao Ye Weiwei Deng Mengmeng Xu Mengmeng Xu Qiong Wang Qiong Wang Gaoqiang Liu Feng Wang Liming Liu Liming Liu Zhenghong Xu Zhenghong Xu Guiyang Shi Guiyang Shi Zhongyang Ding Zhongyang Ding Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production Frontiers in Microbiology Ganoderma lucidum extracellular polysaccharide genome-scale metabolic model biosynthetic pathway phenylalanine simulation |
| title | Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production |
| title_full | Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production |
| title_fullStr | Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production |
| title_full_unstemmed | Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production |
| title_short | Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production |
| title_sort | reconstruction and analysis of a genome scale metabolic model of ganoderma lucidum for improved extracellular polysaccharide production |
| topic | Ganoderma lucidum extracellular polysaccharide genome-scale metabolic model biosynthetic pathway phenylalanine simulation |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2018.03076/full |
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