title: Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis.
abstract: 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.
authors.affiliation: Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
authors.forename: Nadine
authors.initials: N
authors.lastname: Töpfer
authors.forename: Camila
authors.initials: C
authors.lastname: Caldana
authors.forename: Sergio
authors.initials: S
authors.lastname: Grimbs
authors.forename: Lothar
authors.initials: L
authors.lastname: Willmitzer
authors.forename: Alisdair R
authors.initials: AR
authors.lastname: Fernie
authors.forename: Zoran
authors.initials: Z
authors.lastname: Nikoloski
mesh_terms: D000064:Acclimatization / Q000235:genetics*; D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects; D053263:Gene Regulatory Networks / Q000528:radiation effects; D018745:Genome, Plant / Q000235:genetics*; D008027:Light; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008957:Models, Genetic; D013696:Temperature