title: High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions.
abstract: The time-resolved response of Arabidopsis thaliana towards changing light and/or temperature at the transcriptome and metabolome level is presented. Plants grown at 21°C with a light intensity of 150 μE m⁻² sec⁻¹ were either kept at this condition or transferred into seven different environments (4°C, darkness; 21°C, darkness; 32°C, darkness; 4°C, 85 μE m⁻² sec⁻¹; 21 °C, 75 μE m⁻² sec⁻¹; 21°C, 300 μE m⁻² sec⁻¹ ; 32°C, 150 μE m⁻² sec⁻¹). Samples were taken before (0 min) and at 22 time points after transfer resulting in (8×) 22 time points covering both a linear and a logarithmic time series totaling 177 states. Hierarchical cluster analysis shows that individual conditions (defined by temperature and light) diverge into distinct trajectories at condition-dependent times and that the metabolome follows different kinetics from the transcriptome. The metabolic responses are initially relatively faster when compared with the transcriptional responses. Gene Ontology over-representation analysis identifies a common response for all changed conditions at the transcriptome level during the early response phase (5-60 min). Metabolic networks reconstructed via metabolite-metabolite correlations reveal extensive environment-specific rewiring. Detailed analysis identifies conditional connections between amino acids and intermediates of the tricarboxylic acid cycle. Parallel analysis of transcriptional changes strongly support a model where in the absence of photosynthesis at normal/high temperatures protein degradation occurs rapidly and subsequent amino acid catabolism serves as the main cellular energy supply. These results thus demonstrate the engagement of the electron transfer flavoprotein system under short-term environmental perturbations.
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.
authors.forename: Camila
authors.initials: C
authors.lastname: Caldana
authors.forename: Thomas
authors.initials: T
authors.lastname: Degenkolbe
authors.forename: Alvaro
authors.initials: A
authors.lastname: Cuadros-Inostroza
authors.forename: Sebastian
authors.initials: S
authors.lastname: Klie
authors.forename: Ronan
authors.initials: R
authors.lastname: Sulpice
authors.forename: Andrea
authors.initials: A
authors.lastname: Leisse
authors.forename: Dirk
authors.initials: D
authors.lastname: Steinhauser
authors.forename: Alisdair R
authors.initials: AR
authors.lastname: Fernie
authors.forename: Lothar
authors.initials: L
authors.lastname: Willmitzer
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Hannah
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism / Q000502:physiology* / Q000528:radiation effects; D016000:Cluster Analysis; D003624:Darkness; D005420:Flavoproteins / Q000378:metabolism* / Q000528:radiation effects; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000502:physiology* / Q000528:radiation effects; D007700:Kinetics; D008027:Light; D053858:Metabolic Networks and Pathways / Q000502:physiology / Q000528:radiation effects; D055442:Metabolome / Q000502:physiology* / Q000528:radiation effects; D055432:Metabolomics; D020411:Oligonucleotide Array Sequence Analysis; D010788:Photosynthesis / Q000502:physiology / Q000528:radiation effects; D059748:Proteolysis / Q000528:radiation effects; D013696:Temperature; D013997:Time Factors; D059467:Transcriptome / Q000502:physiology* / Q000528:radiation effects
chemical_list: D005420:Flavoproteins