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Enhancing Genome-Scale Model by Integrative Exometabolome and Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid Biosynthetic Capability of Cordyceps militaris
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Document Title
Enhancing Genome-Scale Model by Integrative Exometabolome and Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid Biosynthetic Capability of Cordyceps militaris
Author
Cheawchanlertfa P, Chitcharoen S, Raethong N, Liu Q, Chumnanpuen P, Soommat P, Song YD, Koffas M, Laoteng K, Vongsangnak W
Name from Authors Collection
Affiliations
Kasetsart University; Chulalongkorn University; Mahidol University; Shandong University of Technology; Kasetsart University; Rensselaer Polytechnic Institute; National Science & Technology Development Agency - Thailand; National Center Genetic Engineering & Biotechnology (BIOTEC)
Type
Article
Source Title
JOURNAL OF FUNGI
Year
2022
Volume
8
Issue
8
Open Access
Green Published, gold
Publisher
MDPI
DOI
10.3390/jof8080887
Format
Abstract
Cordyceps militaris is an industrially important fungus, which is often used in Asia as traditional medicine. There has been a published genome-scale metabolic model (GSMM) of C. militaris useful for predicting its growth behaviors; however, lipid metabolism, which plays a vital role in cellular functions, remains incomplete in the GSMM of C. militaris. A comprehensive study on C. militaris was thus performed by enhancing GSMM through integrative analysis of metabolic footprint and transcriptome data. Through the enhanced GSMM of C. militaris (called iPC1469), it contained 1469 genes, 1904 metabolic reactions and 1229 metabolites. After model evaluation, in silico growth simulation results agreed well with the experimental data of the fungal growths on different carbon sources. Beyond the model-driven integrative data analysis, interestingly, we found key metabolic responses in alteration of lipid metabolism in C. militaris upon different carbon sources. The sphingoid bases (e.g., sphinganine, sphingosine, and phytosphingosine) and ceramide were statistically significant accumulated in the xylose culture when compared with other cultures; this study suggests that the sphingolipid biosynthetic capability in C. militaris was dependent on the carbon source assimilated for cell growth; this finding provides a comprehensive basis for the sphingolipid biosynthesis in C. militaris that can help to further redesign its metabolic control for medicinal and functional food applications.
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
Funding Sponsor
Thailand Research Fund [RSA6180001]; National Research Council of Thailand (NRCT); Office of the Ministry of Higher Education, Science, Research and Innovation; Thailand Science Research and Innovation through the Kasetsart University Reinventing University Program
License
CC BY
Rights
Authors
Publication Source
WOS