Amino acid pathways are central for defense in Arabidopsis revealed by time-resolved, integrated multi-omics analysis

Plants respond to biotic stress by altering transcription and metabolism. While the temporal dynamic of transcriptional changes in immune-stimulated plants is established, little is known about spatio-temporal metabolic changes. Here, we investigate immune-stimulated Arabidopsis thaliana shoot, root, and root exudate metabolite profiles in a time-resolved manner. Roots and shoots exhibited comparable metabolite changes upon immune stimulation, with various metabolites increasing. First metabolite changes occurred after 1.5 hours and persisted for 3 days. Exudate responses occurred within 4 hours and diminished for pulse-treated but persisted for continuously treated plants. Many chemical classes responded to immune-stimulation: defense compounds (phenylpropanoids) increased within hours, and amino acids preceded this increase at 1.5 h in shoots, roots, and exudates. Transcriptome analysis at 4 h and 1 d and integrated, multi-omic analysis of transcription and metabolome supported the role of aromatic and aliphatic amino acids as central players preceding defense responses.