Enhancing Genome-Scale Model by Integrative Exometabolome and Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid Biosynthetic Capability of Cordyceps militaris
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Preparation for Dry Weight and Metabolic Footprint Analysis
2.2. Liquid Chromatography-Mass Spectrometry (LC-MS) Analysis
2.3. Metabolite Acquisition and Identification towards Differentially Accumulated Metabolites (DAMs) Analysis
2.4. Improvement of GSMM of C. militaris by Incorporating Metabolic Footprint and Transcriptome Data
3. Results and Discussion
3.1. Quantitative Metabolic Footprinting of C. militaris
3.2. Identification of DAMs across Pairwise Comparisons of the Cultures using Different Carbon Sources
3.3. Identification of Significant Abundant DAMs in the Cultures Using Different Carbon Sources
3.4. Enhancing Genome-Scale Metabolic Model (GSMM) Using Significant Metabolic Footprint Profiles
3.5. Integrative Transcriptome Analysis Using The Enhanced GSMM Revealed Metabolic Response in Lipid Biosynthetic Capability
3.5.1. Glycerolipid Biosynthetic Pathway
3.5.2. Sphingolipid Biosynthetic Capability
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Pairwise Comparison Sets | Number of Significant DAMs | Up-Accumulated Metabolites | Down-Accumulated Metabolites |
---|---|---|---|
C5 vs. C6 cultures | 252 | 212 | 40 |
C12 vs. C6 cultures | 188 | 187 | 1 |
C5 vs. C12 cultures | 30 | 17 | 13 |
Characteristics | iNR1329 * | iPC1469 (This Study) |
---|---|---|
Number of Genes | 1329 | 1469 |
Number of Metabolites | 1171 | 1229 |
Number of Reactions | 1821 | 1904 |
Enzymatic reactions | 1391 | 1404 |
Transport reactions | 271 | 339 |
Exchange reactions | 137 | 140 |
Spontaneous reactions | 21 | 21 |
Biomass synthesis reaction | 1 | 1 |
Biosynthetic capacities of GSMM | Cordycepin | Cordycepin, sphinganine, phytosphingosine, and sphingosine |
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Cheawchanlertfa, P.; Chitcharoen, S.; Raethong, N.; Liu, Q.; Chumnanpuen, P.; Soommat, P.; Song, Y.; Koffas, M.; Laoteng, K.; Vongsangnak, W. Enhancing Genome-Scale Model by Integrative Exometabolome and Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid Biosynthetic Capability of Cordyceps militaris. J. Fungi 2022, 8, 887. https://doi.org/10.3390/jof8080887
Cheawchanlertfa P, Chitcharoen S, Raethong N, Liu Q, Chumnanpuen P, Soommat P, Song Y, Koffas M, Laoteng K, Vongsangnak W. Enhancing Genome-Scale Model by Integrative Exometabolome and Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid Biosynthetic Capability of Cordyceps militaris. Journal of Fungi. 2022; 8(8):887. https://doi.org/10.3390/jof8080887
Chicago/Turabian StyleCheawchanlertfa, Pattsarun, Suwalak Chitcharoen, Nachon Raethong, Qing Liu, Pramote Chumnanpuen, Panyawarin Soommat, Yuanda Song, Mattheos Koffas, Kobkul Laoteng, and Wanwipa Vongsangnak. 2022. "Enhancing Genome-Scale Model by Integrative Exometabolome and Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid Biosynthetic Capability of Cordyceps militaris" Journal of Fungi 8, no. 8: 887. https://doi.org/10.3390/jof8080887