Ethylene receptor gain- and loss-of-function mutants reveal an ETR1-dependent transcriptional network in Arabidopsis roots

In Arabidopsis (Arabidopsis thaliana), a family of 5 receptors mediates ethylene responses in roots, with Ethylene Response 1 (ETR1) controlling increases in root hair proliferation and decreases in lateral root formation. To define the ETR1-dependent gene regulatory network (GRN) controlling root development, we profiled the root transcriptome from Col-0 and the etr1-3 gain-of-function and etr1-7 loss-of-function mutants in the presence and absence of ethylene or the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC). We identified 4,522 differentially expressed (DE) transcripts in Col-0 roots that displayed altered abundance in response to ethylene and/or ACC treatment, with larger-magnitude changes induced by ethylene. These included 553 DE transcripts that were ETR1 dependent, defined by a lack of response to treatment with ethylene and/or ACC in ethylene-insensitive etr1-3 and constitutive alteration response in etr1-7 in the presence or absence of treatment relative to time-0 Col-0. These ETR1-dependent transcripts include transcripts from genes associated with ethylene biosynthesis and those encoding transcription factors (TFs). Reporter fusions driven by promoters from ACC OXIDASE 2 (ACO2) and ACO3, which convert ACC to ethylene, were regulated by ACC in root tissues in appropriate locations to control root development, with pACO5-driven GFP detected in root hairs. We examined the abundance of ETR1-dependent transcripts predicted to encode TFs and ACOs in Col-0 and an ein3 eil1 mutant, with and without ACC treatment. Our results suggested that the ETR1 and Ethylene Insensitive 3 (EIN3)/EIN3-like 1 (EIL1) canonical ethylene signaling pathway regulates some, but not all, of these transcriptional responses. Together, these findings reveal features of an ETR1-dependent GRN that controls both ethylene biosynthesis and root growth and development.