Genome-Wide Analysis of Ethylene-Responsive Element Binding Factor-Associated Amphiphilic Repression Motif-Containing Transcriptional Regulators in Arabidopsis
Open Access
- 22 January 2010
- journal article
- Published by Oxford University Press (OUP) in Plant Physiology
- Vol. 152 (3), 1109-1134
- https://doi.org/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.Keywords
This publication has 113 references indexed in Scilit:
- Jasmonate signaling: a conserved mechanism of hormone sensingCurrent Opinion in Plant Biology, 2008
- PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictorNucleic Acids Research, 2007
- Phosphate Homeostasis and Root Development in Arabidopsis Are Synchronized by the Zinc Finger Transcription Factor ZAT6Plant Physiology, 2007
- Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlingsProceedings of the National Academy of Sciences of the United States of America, 2007
- Gain‐ and loss‐of‐function mutations in Zat10 enhance the tolerance of plants to abiotic stressFEBS Letters, 2006
- WUSCHEL controls meristem function by direct regulation of cytokinin-inducible response regulatorsNature, 2005
- A gene expression map of Arabidopsis thaliana developmentNature Genetics, 2005
- WebLogo: A Sequence Logo Generator: Figure 1Genome Research, 2004
- OrthoMCL: Identification of Ortholog Groups for Eukaryotic GenomesGenome Research, 2003
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994