Abstract:

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-CO_{2intercellular} 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.

Liu L, Shen F, Xin C, Wang Z (2016) Multi-scale modeling of Arabidopsis thaliana response to different CO₂ conditions: From gene expression to metabolic flux. J Integr Plant Biol 58: 2–11 doi: 10.1111/jipb.12370

Key words: Metabolic model, gene expression, multi-scale analysis, low/elevated CO₂, post-transcriptional regulation