Time course RNA-seq analysis of expression changes upon MLACC expression in Arabidopsis using a dexamethasone-inducible system which mirrors NLR activation

Innate immune responses of plant cells confer the first line of defence against pathogens. Signals generated by activated receptors are integrated inside the cell and converge on transcriptional programmes in the nucleus. The barley NLR intracellular receptor MLA is fully functionnal in Arabidopsis and the MLA N-terminal coiled-coil domain (MLACC) is sufficient for initiating the MLA-dependent immune signalling. Using RNA-seq, we analyzed the early MLACC-mediated transcriptional changes over time in a dexamethasone-inducible and pathogen-independent system. Overall design: We used transgenic Arabidopsis plants expressing MLACC-mYFP under a dexamethasone-inducible promoter (DEXp), a genetic background in which an immune-like response can be turned on rapidly and synchronously in leaf cells after dexamethasone treatment. We used transgenic lines in WT and in the phytohormone-depleted and partially immunocompromised pen2 pad4 sag101 dde2 ein2 sid2 (ppsdes) sextuple mutant backgrounds to assess the contribution of the three main defense phytohormones (jasmonate, ethylene, salycilic acid) in the MLACC-mediated immune signalling. In order to substract defense-unrelated artifacts due to the dexamethasone treatment, we used plants expressing the mYFP under the dexamethasone-inducible promoter in WT background and non-transgenic sextuple mutant plants in parallel as negative control. Samples were collected at 0, 2, 4, 6, and 8 hours after dexamethasone infiltration into leaves. For each condition, three biological replicates were obtained.