Dataset Information

Arabidopsis thaliana Col-0 pgm1 spsa1 highlight and chilling temperatures proteins LC-MS/MS

ABSTRACT: Abiotic stress exposure of plants induces metabolic reprogramming which is tightly regulated by signalling cascades connecting transcriptional with translational and metabolic regulation. Complexity of such interconnected metabolic networks impedes the functional understanding of molecular plant stress response compromising the design of breeding strategies and biotechnological processes. Thus, defining a molecular network to enable the prediction of a plant’s stress mode promises to promote the understanding of stress responsive biochemical regulation and its technological application. Arabidopsis wild type plants and two mutant lines with deficiency in sucrose or starch metabolism were grown under ambient and cold/high light stress conditions. Stress-induced dynamics of the primary metabolome and the proteome were quantified in a mass spectrometry-based high-throughput experiment. Wild type data were used to train a machine learning algorithm to classify mutant lines under control and stress conditions. Multivariate analysis and classification identified a module consisting of 23 proteins enabling the reliable prediction of coupled temperature and light stress conditions. 18 of these 23 proteins displayed putative protein-protein interactions connecting transcriptional regulation with regulation of primary and secondary metabolism under stress. The identified stress-responsive core module provides evidence for predictability of complex biochemical regulation during environmental fluctuation.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Photosynthetic Cell, Leaf

SUBMITTER: Lisa Fürtauer

LAB HEAD: Thomas Nägele

PROVIDER: PXD010580 | Pride | 2018-11-06

REPOSITORIES: Pride

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Publications

Combined multivariate analysis and machine learning reveals a predictive module of metabolic stress response in Arabidopsis thaliana.

Fürtauer Lisa L Pschenitschnigg Alice A Scharkosi Helene H Weckwerth Wolfram W Nägele Thomas T

Molecular omics 20181201 6

Abiotic stress exposure of plants induces metabolic reprogramming which is tightly regulated by signalling cascades connecting transcriptional with translational and metabolic regulation. Complexity of such interconnected metabolic networks impedes the functional understanding of molecular plant stress response compromising the design of breeding strategies and biotechnological processes. Thus, defining a molecular network to enable the prediction of a plant's stress mode will improve the unders ...[more]

PMID: 30387490

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Project description:Exposure of Saccharomyces cerevisiae to alkaline pH represents a stress condition that generates a compensatory reaction. Here we examine a possible role of the protein kinase-A (PKA) pathway in this response. The phenotypic analysis reveals that mutations that activate the PKA pathway (ira1 ira2, bcy1) tend to cause sensitivity to alkaline pH, whereas its deactivation develops tolerance to this stress. We observe that alkalinization causes a transient decrease in cAMP, the main regulator of the pathway. Alkaline pH causes rapid nuclear localization of the PKA-regulated Msn2 transcription factor which, together with Msn4, mediates a general stress response by binding to STRE sequences in many promoters. Consequently, a synthetic STRE-LacZ reporter shows a rapid induction in response to alkaline stress. An msn2 msn4 mutant is sensitive to alkaline pH, and transcriptomic analysis reveals that after 10 minutes of alkaline stress, the expression of many induced genes (47%) depends, at least in part, on the presence of Msn2 and Msn4. Taken together, these results demonstrate that inhibition of the PKA pathway by alkaline pH represents a substantial part of the adaptive response to this kind of stress and that this response involves Msn2/Msn4-mediated gene remodeling. However, the relevance of attenuation of PKA in high pH tolerance is not restricted to regulation of Msn2 function. Eight samples were analyzed: WT and the MCY5278 mutant strain, lacking both Msn2 and Msn4, in the presence of 20 mM KOH (pH 8) and in the presence of 20 mM KCl (non-induced conditions) for 10 and 30 min of stress. 2 biological replicates were analyzed for each condition, and dye-swapping was carried out for each comparison of samples. We compared the expression profiles of: 1) WT +KOH vs. WT +KCl after 10 min 2) msn2 msn4 mutant +KOH vs. msn2 msn4 +KCl after 10 min 3)WT +KOH vs. WT +KCl after 30 min 4) msn2 msn4 mutant +KOH vs. msn2 msn4 +KCl after 30 min Total number of chips analyzed: 16.

			Action	DRS
	10_spsa1_s1.raw	Raw
	11_spsa1_s2.raw	Raw
	12_spsa1_s3.raw	Raw
	13_pgm1_c1.raw	Raw
	14_pgm1_c2.raw	Raw