DELLA-Induced Early Transcriptional Changes during Etiolated Development in Arabidopsis thaliana

Javier Gallego-Bartolomé,David Alabadí,Miguel A Blázquez,Mohammed Bendahmane

doi:10.1371/journal.pone.0023918

Javier Gallego-Bartolomé, David Alabadí + Show 2 more

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https://doi.org/10.1371/journal.pone.0023918

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Abstract

The hormones gibberellins (GAs) control a wide variety of processes in plants, including stress and developmental responses. This task largely relies on the activity of the DELLA proteins, nuclear-localized transcriptional regulators that do not seem to have DNA binding capacity. The identification of early target genes of DELLA action is key not only to understand how GAs regulate physiological responses, but also to get clues about the molecular mechanisms by which DELLAs regulate gene expression. Here, we have investigated the global, early transcriptional response triggered by the Arabidopsis DELLA protein GAI during skotomorphogenesis, a developmental program tightly regulated by GAs. Our results show that the induction of GAI activity has an almost immediate effect on gene expression. Although this transcriptional regulation is largely mediated by the PIFs and HY5 transcription factors based on target meta-analysis, additional evidence points to other transcription factors that would be directly involved in DELLA regulation of gene expression. First, we have identified cis elements recognized by Dofs and type-B ARRs among the sequences enriched in the promoters of GAI targets; and second, an enrichment in additional cis elements appeared when this analysis was extended to a dataset of early targets of the DELLA protein RGA: CArG boxes, bound by MADS-box proteins, and the E-box CACATG that links the activity of DELLAs to circadian transcriptional regulation. Finally, Gene Ontology analysis highlights the impact of DELLA regulation upon the homeostasis of the GA, auxin, and ethylene pathways, as well as upon pre-existing transcriptional networks.

Highlights

Plants are sessile organisms that cannot change their location as a strategy to optimize their access to energy sources or in response to the environment
To confirm that the inductive treatment resulted in an increase of GAI activity, we checked the expression of the GA20ox2 and GA3ox1 genes, that encode key enzymes in the GA biosynthetic pathway subject to feedback regulation by DELLA proteins [6,24,25,26]
To get hints regarding the identity of the additional transcription factors mediating DELLA regulation, we investigated the enrichment of particular cis elements among the promoters of genes up- and downregulated in HS::gai-1 using ELEMENT [33]

Summary

Introduction

Plants are sessile organisms that cannot change their location as a strategy to optimize their access to energy sources or in response to the environment Adjusting their growth and choosing the correct developmental program has to be precise and robust otherwise chances of survival could be reduced. Gibberellins (GAs) are one of the classical plant hormones They regulate several processes during the plant life cycle such as germination, vegetative growth or flowering [3] through gene transcriptional regulation [4,5,6,7]. When GA levels increase, the binding of the hormone to its receptor, GID1, promotes the formation of a GA-GID1-DELLA complex [9,10] that favors the recognition of the DELLA protein by the SCFSLY ubiquitin ligase [11] and the subsequent ubiquitination This modification leads to DELLA degradation by the 26S proteosome [12,13] and transcriptional changes to the hormone take place

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