TY  - JOUR
A1  - Töpfer, Nadine
A1  - Caldana, Camila
A1  - Grimbs, Sergio
A1  - Willmitzer, Lothar
A1  - Fernie, Alisdair R.
A1  - Nikoloski, Zoran
T1  - Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in arabidopsis
T2  - The plant cell
N2  - Understanding metabolic acclimation of plants to challenging environmental conditions is essential for dissecting the role of metabolic pathways in growth and survival. As stresses involve simultaneous physiological alterations across all levels of cellular organization, a comprehensive characterization of the role of metabolic pathways in acclimation necessitates integration of genome-scale models with high-throughput data. Here, we present an integrative optimization-based approach, which, by coupling a plant metabolic network model and transcriptomics data, can predict the metabolic pathways affected in a single, carefully controlled experiment. Moreover, we propose three optimization-based indices that characterize different aspects of metabolic pathway behavior in the context of the entire metabolic network. We demonstrate that the proposed approach and indices facilitate quantitative comparisons and characterization of the plant metabolic response under eight different light and/or temperature conditions. The predictions of the metabolic functions involved in metabolic acclimation of Arabidopsis thaliana to the changing conditions are in line with experimental evidence and result in a hypothesis about the role of homocysteine-to-Cys interconversion and Asn biosynthesis. The approach can also be used to reveal the role of particular metabolic pathways in other scenarios, while taking into consideration the entirety of characterized plant metabolism.
Y1  - 2013
UR  - https://publishup.uni-potsdam.de/frontdoor/index/index/docId/35097
SN  - 1040-4651
VL  - 25
IS  - 4
SP  - 1197
EP  - 1211
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  -