Systematic Discovery of Hidden Dynamics and Regulatory Codes in MAPK Signaling Networks

Biological systems orchestrate complex, dynamic and interconnected signaling networks, which remain challenging to elucidate with static, redundant, deleterious or lethal mutations in multicellular genetic circuits. To uncover hidden regulatory mechanisms and resolve genotype-phenotype discrepancies of mitogen-activated protein kinases (MAPKs) as master signaling integrators, we combined systematic network analyses with quantitative chemical perturbations of genetically engineered MAPKs for signaling interrogation in Arabidopsis thaliana. We demonstrate specific, combinatorial, antagonistic, dynamic and ordered controls of the core MAPKs as the central hub for multi-stress signaling, immune switches, and cell-fate specification. Intertwined MAPK programs with time-based negative-feedbacks control multilayered innate immune responses. Threshold-sensitive MPK4 specifies opposite consequences in triggered-immunity or autoimmunity. MPK3/6 dictate master transcription factors in stem-cell niches to constrain leaf-epidermal and root-meristem reprogramming. Chemical genetic-based systems analyses in time, space, amplitude and developing cell types open new possibilities to reconstruct and discover signaling networks in broad contexts of live organisms. Overall design: Genome-wide survey of 1) Flg22-triggered early response in wild type seedlings, 2) various stimuli (Flg22, Pep3, Mechanical wounding, UVB, H2O2, ABA, MeJA) response in wild type,impk36, and impk4 seedlings, 3) transcriptome network in adult plants of mpk4 and impk4 at various hours after inhibitor treatment