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

Abstract

While the effects of phytohormones on plant gene expression have been well characterized, comparatively little is known about how hormones influence metabolite profiles. This study examined the effects of elevated auxin and ethylene on the metabolome of Arabidopsis roots using a high-resolution 24 h time course, conducted in parallel to time-matched transcriptomic analyses. Mass spectrometry using orthogonal UPLC separation strategies (reversed phase and HILIC) in both positive and negative ionization modes was used to maximize identification of metabolites with altered levels. The findings show that the root metabolome responds rapidly to hormone stimulus and that compounds belonging to the same class of metabolites exhibit similar changes. The responses were dominated by changes in phenylpropanoid, glucosinolate, and fatty acid metabolism, although the nature and timing of the response was unique for each hormone. These alterations in the metabolome were not directly predicted by the corresponding transcriptome data, suggesting that post-transcriptional events such as changes in enzyme activity and/or transport processes drove the observed changes in the metabolome. These findings underscore the need to better understand the biochemical mechanisms underlying the temporal reconfiguration of plant metabolism, especially in relation to the hormone-metabolome interface and its subsequent physiological and morphological effects.

Figure 1

Scores plots derived from sPLS-DA of the reversed phase negative mode metabolomic profiles of ACC- and IAA-treated roots over 24 h. Symbols and colors for each of the eight time points are identified at upper right.

Figure 2

Identification of major patterns associated with time, hormone treatment, and their interactions. The patterns of abundance over time are shown for the two features identified by ASCA, oxIAA hexose (A) and coumaroyl aspartate (B), and one uncovered by targeted analysis, the flavonoid glycoside rutin (C). Note that the x axis is not drawn on a linear scale; this is to allow for better visualization of the data points for early sampling times.