Genetic dissection of Arabidopsis MAP kinase phosphatase 1-dependent PAMP-induced transcriptional responses

Plant immunity is initiated by extracellular detection of pathogen-associated molecular patterns (PAMPs) through surface-localized pattern recognition receptors (PRRs). PRR activation induces many responses including the activation of mitogen-activated protein kinases (MAPKs) that ultimately limit bacterial growth. Previous work identified Arabidopsis MAP kinase phosphatase 1 (MKP1) as a negative regulator of signaling pathways required for some, but not all, of PAMP-initiated responses. Specifically, loss of MAPK MPK6 in an mkp1 background suppressed a subset of the mkp1-dependent biological phenotypes, indicating the requirement for MPK6 in MKP1-dependent signaling. To further genetically separate the outputs of PAMP-responsive signaling pathways, we performed a transcriptome analysis in Arabidopsis wild type, mkp1 and mkp1 mpk6 seedlings treated with the bacterially derived PAMP elf26 for 0, 30, and 90 min. Using differential genetic and temporal clustering analyses between and within genotypes, we identified and separated 6963 elf26-responsive transcripts based on both genetic requirements of MKP1 (with or without a requirement for MPK6) and temporal transcriptional accumulation patterns, and some of these novel response markers were validated by qRT-PCR over a more extended time course. Taken together, our transcriptome analysis provides novel information for delineating PAMP signaling pathways.