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

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.

Overexpression of tobacco ethylene response factor NtERF3 gene and its homologues from tobacco and rice induces hypersensitive response-like cell death in tobacco

“…The consensus sequence of the EAR motif was at first reported L/FDLNL/FxP in tobacco NtERF3, and in Arabidopsis AtERF3 and AtERF4 (Ohta et al 2001). Recently, Kagale et al (2010) reported two distinct conservation patterns of EAR motif (DLNxxP and LxLxL) and identified 219 EAR motif-containing proteins belonging to 21 different families in Arabidopsis. The LxLxL type of EAR motif was first reported in the SUPERMAN protein of Arabidopsis (Hiratsu et al 2002).…”

Identical Amino Acid Substitutions in the Repression Domain of Auxin/Indole-3-Acetic Acid Proteins Have Contrasting Effects on Auxin Signaling

“…S6). Based upon a bioinformatics approach, the LxLxL motifs located between domains I and II have been predicted to be EAR-like repression domains in IAA7, IAA14, IAA16, and IAA17 proteins (Kagale et al, 2010). This second DLxLxL motif in IAA proteins is generally located at approximately 20 to 25 amino acids C terminal to the TELC/RLGLPG domain I motif.…”

An EAR-Dependent Regulatory Module Promotes Male Germ Cell Division and Sperm Fertility in Arabidopsis

“…Homologous sequences are present in monocots, although these lack the second zinc finger domain and putative NLS (Supplemental Figure 1). In addition to the zinc finger domains, we identified extended conservation around the CLLM motif and the tandem DLNxxP-and LxLxL-type EAR motifs at the C terminus ( Figure 1A) (Kagale et al, 2010).…”