PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins.

Jiaotong Yang,Tian Tian,Hengyu Yan,Zhen Su,Wenying Xu,Yue Liu,Liwei Zhang,Qi You

doi:10.3389/fgene.2018.00590

Abstract

The Ethylene-responsive element binding factor-associated Amphiphilic Repression (EAR) motifs, which were initially identified in members of the Arabidopsis ethylene response factor (ERF) family, are transcriptional repression motifs in plants and are defined by the consensus sequence patterns of either LxLxL or DLNxxP. EAR motif-containing proteins can function as transcription repressors, thus interacting with co-repressors, such as TOPLESS and AtSAP18, affecting the structure of chromatin by histone modifications and thereby repressing gene transcription. EAR motif-containing proteins are highly conserved across diverse plant species and play important roles in hormone signal transduction, stress responses and development, but they have not been identified in most plants. In this study, we identified 20,542 EAR motif-containing proteins from 71 plant species based on a Hidden Markov Model and orthologous gene search, and then we constructed a functional analysis platform for plant EAR motif-containing proteins (PlantEAR, http://structuralbiology.cau.edu.cn/plantEAR) by integrating a variety of functional annotations and processed data. Several tools were provided as functional support for EAR motif-containing proteins, such as browse, search, co-expression and protein-protein interaction (PPI) network analysis as well as cis-element analysis and gene set enrichment analysis (GSEA). In addition, basing on the identified EAR motif-containing proteins, we also explored their distribution in various species and found that the numbers of EAR motif-containing proteins showed an increasing trend in evolution from algae to angiosperms.

Highlights

element binding factor-associated Amphiphilic Repression (EAR) motifs, which were initially identified in members of the Arabidopsis ethylene response factor (ERF) family, are emerging as transcriptional repression motifs in plants (Ohta et al, 2001)
Following the iTAK (Zheng et al, 2016) rules, we carried out a gene family classification of EAR motif-containing proteins in each plant, and we identified 13,994 transcription factors (TFs) and 3,073 transcription regulators (TRs) (Figure 2B, Supplementary Table 6)
The EAR motif-containing proteins can be browsed by species and family classification, and we provide help information for users using the functional analysis platform

Summary

Introduction

EAR motifs, which were initially identified in members of the Arabidopsis ethylene response factor (ERF) family, are emerging as transcriptional repression motifs in plants (Ohta et al, 2001). EAR motif-containing proteins can recruit a histone deacetylase (HDAC) complex to perform transcriptional repression functions by interacting with co-suppressors, such as SAP18 and TOPLESS, in Arabidopsis thaliana (Song et al, 2005; Song and Galbraith, 2006; Hill et al, 2008; Causier et al, 2012). Obvious examples are JASMONATE ZIM domain (JAZ) proteins with EAR motifs in Arabidopsis thaliana, which can negatively regulate the key transcriptional activators of jasmonate responses, such as MYC2, MYC3, MYC4, MYC5 (Chini et al, 2007; Kagale et al, 2010; Goossens et al, 2015; Thireault et al, 2015; Song et al, 2017)

Methods

Findings

Discussion

Conclusion