Identification of Transcriptional and Receptor Networks That Control Root Responses to Ethylene

Abstract

Transcriptomic analyses with high temporal resolution provide substantial new insight into hormonal response networks. This study identified the kinetics of genome-wide transcript abundance changes in response to elevated levels of the plant hormone ethylene in roots from light-grown Arabidopsis () seedlings, which were overlaid on time-matched developmental changes. Functional annotation of clusters of transcripts with similar temporal patterns revealed rapidly induced clusters with known ethylene function and more slowly regulated clusters with novel predicted functions linked to root development. In contrast to studies with dark-grown seedlings, where the canonical ethylene response transcription factor, EIN3, is central to ethylene-mediated development, the roots of and single and double mutants still respond to ethylene in light-grown seedlings. Additionally, a subset of these clusters of ethylene-responsive transcripts were enriched in targets of EIN3 and ERFs. These results are consistent with EIN3-independent developmental and transcriptional changes in light-grown roots. Examination of single and multiple gain-of-function and loss-of-function receptor mutants revealed that, of the five ethylene receptors, ETR1 controls lateral root and root hair initiation and elongation and the synthesis of other receptors. These results provide new insight into the transcriptional and developmental responses to ethylene in light-grown seedlings.

The dynamic response of the Arabidopsis root metabolome to auxin and ethylene is not predicted by changes in the transcriptome

“…Another consistent finding is that changes in the metabolome were not well correlated with previously-published transcriptomics and proteomics datasets for matching tissues. Although the majority of changes at the transcript level were also transient, rapidly returning to the levels present in time-matched controls 11,12 , there was little evidence that these were responsible for the observed changes in the metabolome except possibly in the case of auxin-mediate changes in phosphatidylcholine metabolism and ethylene-induced changes in lignin biosynthesis. For both hormones, the largest differentially-expressed clusters were comprised of known auxin-and ethylene-responsive genes, genes related to RNA and DNA processes, and cell wall biogenesis and organization, among a few others; none were related to specialized metabolism.…”

“…The goal of this study was to examine the root metabolome in the first 24 h following exposure to the endogenous auxin, IAA, or the ethylene precursor, ACC. Experiments were carried out under conditions that paralleled earlier transcriptome studies so as to also enable exploration of cause and effect relationships at these two levels of cellular phenotyping 11,12 . Seedlings were grown for 5d on nylon filters overlaid on MS-sucrose-agar.…”

“…Plant growth and hormone treatment. Arabidopsis tissue preparation and hormone treatment were performed as described previously 11,12 . Briefly, Arabidopsis Col-0 seedlings were grown on nylon filters (03-100/32; Sefar Filtration) overlaid on solid MS medium supplemented with 1.0% sucrose.…”

“…To identify downstream targets of the auxin and ethylene signaling machinery that drive changes in growth and development, transcriptome analyses of the immediate response of Arabidopsis seedling roots to auxin and ethylene application were previously undertaken at high temporal resolution 11,12 . These time courses comprised eight time points over a 24 h period, which were overlaid on time-matched developmental controls.…”

“…Transcripts associated with auxin-responsive metabolic processes. Shown are genes having average log two-fold values relative to time-matched controls of ≥ 0.5 or ≤ −0.5 (~1.4 or −1.4-fold differences) in all three biological replicates at one or more sampling times (data from11,12), with values meeting these criteria shown in bold and are underlined.Positive numbers indicate elevated levels and negative numbers indicate reduced levels relative to the untreated controls. The full list of genes examined for each class with values for each biological replicate are provided in Datafile S5.…”