Genome-Wide Analysis of Ethylene-Responsive Element Binding Factor-Associated Amphiphilic Repression Motif-Containing Transcriptional Regulators in Arabidopsis

Sateesh Kagale,Matthew G Links,Kevin Rozwadowski

doi:10.1104/pp.109.151704

Abstract

The ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif is a transcriptional regulatory motif identified in members of the ethylene-responsive element binding factor, C2H2, and auxin/indole-3-acetic acid families of transcriptional regulators. Sequence comparison of the core EAR motif sites from these proteins revealed two distinct conservation patterns: LxLxL and DLNxxP. Proteins containing these motifs play key roles in diverse biological functions by negatively regulating genes involved in developmental, hormonal, and stress signaling pathways. Through a genome-wide bioinformatics analysis, we have identified the complete repertoire of the EAR repressome in Arabidopsis (Arabidopsis thaliana) comprising 219 proteins belonging to 21 different transcriptional regulator families. Approximately 72% of these proteins contain a LxLxL type of EAR motif, 22% contain a DLNxxP type of EAR motif, and the remaining 6% have a motif where LxLxL and DLNxxP are overlapping. Published in vitro and in planta investigations support approximately 40% of these proteins functioning as negative regulators of gene expression. Comparative sequence analysis of EAR motif sites and adjoining regions has identified additional preferred residues and potential posttranslational modification sites that may influence the functionality of the EAR motif. Homology searches against protein databases of poplar (Populus trichocarpa), grapevine (Vitis vinifera), rice (Oryza sativa), and sorghum (Sorghum bicolor) revealed that the EAR motif is conserved across these diverse plant species. This genome-wide analysis represents the most extensive survey of EAR motif-containing proteins in Arabidopsis to date and provides a resource enabling investigations into their biological roles and the mechanism of EAR motif-mediated transcriptional regulation.

Highlights

The ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif is a transcriptional regulatory motif identified in members of the ethylene-responsive element binding factor, C2H2, and auxin/indole-3-acetic acid families of transcriptional regulators
The protein sequence comparison of these proteins in the conserved EAR motif region (Fig. 1) revealed two distinct degenerate consensus sequence patterns: DLNxxP, consisting of a conserved DLN box and a Pro residue at the fifth or sixth position, wherein the Asp and Leu residues are implicated in repression activity (Ohta et al, 2001; Tsukagoshi et al, 2005); and LxLxL, consisting of three conserved Leu residues in alternate positions, which have been shown to be critical for both repressor activity and interaction with corepressors (Hiratsu et al, 2004; Tiwari et al, 2004; Szemenyei et al, 2008)
73 out of the 187 group of proteins and 352 out of the 5,471 group of proteins were found to be potential transcriptional regulators based on The Arabidopsis Information Resource (TAIR) Gene Ontology (GO)

Summary

Introduction

The ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif is a transcriptional regulatory motif identified in members of the ethylene-responsive element binding factor, C2H2, and auxin/indole-3-acetic acid families of transcriptional regulators. Sequence comparison of the core EAR motif sites from these proteins revealed two distinct conservation patterns: LxLxL and DLNxxP Proteins containing these motifs play key roles in diverse biological functions by negatively regulating genes involved in developmental, hormonal, and stress signaling pathways. Homology searches against protein databases of poplar (Populus trichocarpa), grapevine (Vitis vinifera), rice (Oryza sativa), and sorghum (Sorghum bicolor) revealed that the EAR motif is conserved across these diverse plant species This genome-wide analysis represents the most extensive survey of EAR motif-containing proteins in Arabidopsis to date and provides a resource enabling investigations into their biological roles and the mechanism of EAR motif-mediated transcriptional regulation. Several other ERFs and ZFPs containing an EAR motif function as transcriptional repressors and are known to play roles in hormone signaling, disease resistance, and abiotic stress resistance (Fujimoto et al, 2000; Sakamoto et al, 2004; McGrath et al, 2005; Song et al, 2005; Yang et al, 2005; Kazan, 2006; Jiang et al, 2008)

Methods

Results

Conclusion