Journal
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
Volume 58, Issue 1, Pages 2-11Publisher
WILEY
DOI: 10.1111/jipb.12370
Keywords
Metabolic model; gene expression; multi-scale analysis; low; elevated CO2; post-transcriptional regulation
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Funding
- SMC-SJTU Chen Xing Program for Excellent Young Scholars [AF0800012]
- Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry [15Z102050028]
- open project from Key Laboratory of Computational Biology and Key Laboratory of Synthetic Biology, Chinese Academy of Sciences
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Multi-scale investigation from gene transcript level to metabolic activity is important to uncover plant response to environment perturbation. Here we integrated a genome-scale constraint-based metabolic model with transcriptome data to explore Arabidopsis thaliana response to both elevated and low CO2 conditions. The four condition-specific models from low to high CO2 concentrations show differences in active reaction sets, enriched pathways for increased/decreased fluxes, and putative post-transcriptional regulation, which indicates that condition-specific models are necessary to reflect physiological metabolic states. The simulated CO2 fixation flux at different CO2 concentrations is consistent with the measured Assimilation-CO2intercellular curve. Interestingly, we found that reactions in primary metabolism are affected most significantly by CO2 perturbation, whereas secondary metabolic reactions are not influenced a lot. The changes predicted in key pathways are consistent with existing knowledge. Another interesting point is that Arabidopsis is required to make stronger adjustment on metabolism to adapt to the more severe low CO2 stress than elevated CO2. The challenges of identifying post-transcriptional regulation could also be addressed by the integrative model. In conclusion, this innovative application of multi-scale modeling in plants demonstrates potential to uncover the mechanisms of metabolic response to different conditions.
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