High‐density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions

Abstract

SUMMARYThe 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 lE 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 lE m )2 sec). 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.

Trichoderma gamsii affected herbivore feeding behaviour on Arabidopsis thaliana by modifying the leaf metabolome and phytohormones

“…For example, tryptophan plays a critical role in regulating plant responses to biotic and abiotic stresses (Radwanski and Last, 1995; Zhao and Last, 1996; Sangha et al ., 2011). Transcript profiling data generally show herbivory‐induced changes in the expression of genes related to the production of glutamine, glutamic acid, asparagine and aspartic acid (Thompson and Goggin, 2006; Caldana et al ., 2011; Appel and Cocroft, 2014; Zhou et al ., 2015), which are involved in nitrogen assimilation (Coruzzi and Last, 2000). Amino acids also play a role in signal transduction to induce defence gene expression.…”

Alteration of plant primary metabolism in response to insect herbivory

“…For instance, herbivory on sorghum induced expression of nitrate and nitrite reductases that are required for nitrogen assimilation into Gln and Glu (Zhu-Salzman et al, 2004); expression of Glu synthase (also known as Gln oxoglutarate aminotransferase, or GOGAT) was induced by aphid feeding on N. attenuata (Voelckel et al, 2004); and aphid feeding induced Gln synthetase, which acts together with GOGAT in the Gln synthetase/GOGAT cycle, in celery (Apium graveolens; Divol et al, 2005). However, examination of multiple such data sets shows that either production or degradation amino acids can be preferred, depending on the specific plant-herbivore system being investigated and the type of tissue (local or systemic) being analyzed (Dorschner et al, 1987;Sandström et al, 2000;Arnold et al, 2004;Koyama et al, 2004;Caldana et al, 2011;Appel et al, 2012).…”

“…Or, alternatively, there are other potential energy sources (e.g. protein degradation to release free amino acids, which is observed in response to a variety of plant stress treatments [Caldana et al, 2011]). …”

Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain

“…As a result, we are able to not only ascertain the experimental data but also provide modeling support in confirming the hypotheses concerning the feeding of electrons into the ETC from IVDH and D2HGDH during dark-induced senescence (1). However, it should be noted that, although these pathways are particularly prominent during dark-induced senescence (1,46), recent evidence suggests that they also operate in the dark period of a normal light-dark cycle in the photosynthetic tissue of Arabidopsis (50,51).…”