A Kinetic Analysis of the Auxin Transcriptome Reveals Cell Wall Remodeling Proteins That Modulate Lateral Root Development inArabidopsis   

Abstract

To identify gene products that participate in auxin-dependent lateral root formation, a high temporal resolution, genome-wide transcript abundance analysis was performed with auxin-treated Arabidopsis thaliana roots. Data analysis identified 1246 transcripts that were consistently regulated by indole-3-acetic acid (IAA), partitioning into 60 clusters with distinct response kinetics. We identified rapidly induced clusters containing auxin-response functional annotations and clusters exhibiting delayed induction linked to cell division temporally correlated with lateral root induction. Several clusters were enriched with genes encoding proteins involved in cell wall modification, opening the possibility for understanding mechanistic details of cell structural changes that result in root formation following auxin treatment. Mutants with insertions in 72 genes annotated with a cell wall remodeling function were examined for alterations in IAA-regulated root growth and development. This reverse-genetic screen yielded eight mutants with root phenotypes. Detailed characterization of seedlings with mutations in CELLULASE3/GLYCOSYLHYDROLASE9B3 and LEUCINE RICH EXTENSIN2, genes not normally linked to auxin response, revealed defects in the early and late stages of lateral root development, respectively. The genes identified here using kinetic insight into expression changes lay the foundation for mechanistic understanding of auxin-mediated cell wall remodeling as an essential feature of lateral root development.

Deep Sequencing of the Medicago truncatula Root Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals

“…Additionally, several b-glucanases were induced by 6 hpi. These enzymes are involved in the breakdown of cellulose in the cell wall and have been associated with cell wall loosening, cell growth, and lateral root development (Lewis et al, 2013). Taken together, these data suggest that cell wall degradation begins well in advance of infection and may also mediate the root hair swelling and branching observed during early time points.…”

Functional analysis of molecular interactions in synthetic auxin response circuits

“…Our work ex situ has demonstrated the baseline for auxin response at the molecular level, which can now be used as a breadboard for testing additional layers of regulation and integration with other signaling pathways. In addition, a wealth of transcriptome data (42,43) can now be used to generate hypotheses about the likelihood of binding by a specific ARF through integration of cell type-specific expression maps of auxin signaling components (44) and binding-site preferences from protein binding arrays (16). Yeast auxin response circuits provide a resource to rapidly test these hypotheses and inform experimental designs in planta.…”

AUXIN BINDING PROTEIN1 Links Cell Wall Remodeling, Auxin Signaling, and Cell Expansion in Arabidopsis

“…A simple and unique model of SCF TIR1/AFBdependent gene regulation is clearly not sufficient to account for the complexity of the distinct expression profiles found in the different genetic backgrounds. Previous transcriptomic analyses comparing gene expression in auxin signaling mutants or after auxin treatments have already reported important changes in cell wall related genes (Pufky et al, 2003;Okushima et al, 2005;Overvoorde et al, 2005;Nemhauser et al, 2006;Lewis et al, 2013). The correlation between the auxin-mediated regulation, including cell wall genes, and alteration of their expression in axr3-1 (Overvoorde et al, 2005) or nph4-1 arf19-1 (Okushima et al, 2005) auxin signaling mutants was paradoxically not so well established.…”

“…Apoplastic acidification resulting from auxin-related responses at the plasma membrane is thought to favor the action of expansins on wall loosening (Cosgrove, 2000). Various cell wall-related genes also show differential expression in response to auxin or to alteration of auxin signaling (Lorenzo et al, 2003;Okushima et al, 2005;Overvoorde et al, 2005;Nemhauser et al, 2006;Stepanova et al, 2007;Lewis et al, 2013). However, the effect of such changes in gene expression on the composition or the structure of the cell wall remains unclear.…”