PT  - JOURNAL ARTICLE
AU  - Niaz Bahar Chowdhury
AU  - Wheaton L. Schroeder
AU  - Debolina Sarkar
AU  - Nardjis Amiour
AU  - Isabelle Quilleré
AU  - Bertrand Hirel
AU  - Costas D. Maranas
AU  - Rajib Saha
TI  - Dissecting the Metabolic Reprogramming of Maize Root under Nitrogen Limiting Stress Condition
AID  - 10.1101/2021.04.30.442195
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.04.30.442195
4099  - http://biorxiv.org/content/early/2021/04/30/2021.04.30.442195.short
4100  - http://biorxiv.org/content/early/2021/04/30/2021.04.30.442195.full
AB  - The growth and development of maize (Zea mays L.) largely depends on its nutrient uptake through root. Hence, studying its growth, response, and associated metabolic reprogramming to stress conditions is becoming an important research direction. A genome-scale metabolic model (GSM) for the maize root was developed to study its metabolic reprogramming under nitrogen-stress condition. The model was reconstructed based on the available information from KEGG, UniProt, and MaizeCyc. Transcriptomics data derived from the roots of hydroponically grown maize plants was used to incorporate regulatory constraints in the model and simulate nitrogen-non-limiting (N−) and nitrogen-deficient (N−) conditions. Model-predicted result achieved 70% accuracy comparing to the experimental direction change of metabolite levels. In addition to predicting important metabolic reprogramming in central carbon, fatty acid, amino acid, and other secondary metabolism, maize root GSM predicted several metabolites (e.g., L-methionine, L-asparagine, L-lysine, cholesterol, and L-pipecolate) playing critical regulatory role in the root biomass growth. Furthermore, this study revealed eight phosphatidyl-choline and phosphatidyl-glycerol metabolites which even though not coupled with biomass production played a key role in the increased biomass production under N-. Overall, the omics-integrated-GSM provides a promising tool to facilitate stress-condition analysis for maize root and ultimately engineer better stress-tolerant maize genotypes.SummaryThe growth and development of maize (Zea mays L.) largely depends on its nutrient uptake through root. Hence, studying its growth, response, and associated metabolic reprogramming to stress conditions is becoming an important research direction.A genome-scale metabolic model (GSM) for the maize root was developed to study its metabolic reprogramming under nitrogen-stress condition. The model was reconstructed based on the available information from KEGG, UniProt, and MaizeCyc.Transcriptomics data derived from the roots of hydroponically grown maize plants was used to incorporate regulatory constraints in the model and simulate nitrogen-non-limiting (N+) and nitrogen-deficient (N−) conditions. Model-predicted result achieved 70% accuracy comparing to the experimental direction change of metabolite levels. In addition to predicting important metabolic reprogramming in central carbon, fatty acid, amino acid, and other secondary metabolism, maize root GSM predicted several metabolites (e.g., L-methionine, L-asparagine, L-lysine, cholesterol, and L-pipecolate) playing critical regulatory role in the root biomass growth. Furthermore, this study revealed eight phosphatidyl-choline and phosphatidyl-glycerol metabolites which even though not coupled with biomass production played a key role in the increased biomass production under N−.Overall, the omics-integrated-GSM provides a promising tool to facilitate stress-condition analysis for maize root and ultimately engineer better stress-tolerant maize genotypes.Competing Interest StatementThe authors have declared no competing interest.