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Peptide-based Identification of Functional Motifs and their Binding Partners
Published on: June 30, 2013
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PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins
Jiaotong Yang1, Yue Liu1, Hengyu Yan1
1State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China.
Frontiers in Genetics
|December 18, 2018
Summary
Ethylene-responsive element binding factor-associated Amphiphilic Repression (EAR) motifs are crucial for plant gene transcription repression. This study identified over 20,000 EAR proteins across 71 species, revealing their evolutionary trends and providing a new analysis platform.
Area of Science:
- Plant molecular biology
- Transcriptional regulation
- Evolutionary genomics
Background:
- Ethylene-responsive element binding factor-associated Amphiphilic Repression (EAR) motifs are plant transcriptional repression domains.
- These motifs, characterized by LxLxL or DLNxxP sequences, interact with co-repressors to modify chromatin structure and repress gene transcription.
- EAR proteins are vital for plant hormone signaling, stress responses, and development, but their comprehensive identification across species has been limited.
Purpose of the Study:
- To identify and characterize Ethylene-responsive element binding factor-associated Amphiphilic Repression (EAR) motif-containing proteins across a wide range of plant species.
- To develop a functional analysis platform, PlantEAR, for exploring the roles and interactions of these proteins.
- To investigate the evolutionary distribution and trends of EAR proteins from algae to angiosperms.
Main Methods:
- Utilized Hidden Markov Model (HMM) and orthologous gene searches to identify EAR motif-containing proteins.
- Developed the PlantEAR platform (http://structuralbiology.cau.edu.cn/plantEAR) integrating functional annotations and data.
- Employed tools for browsing, searching, co-expression analysis, protein-protein interaction (PPI) network analysis, cis-element analysis, and gene set enrichment analysis (GSEA).
Main Results:
- Identified 20,542 EAR motif-containing proteins from 71 diverse plant species.
- The PlantEAR platform provides comprehensive functional analysis tools for these proteins.
- Observed an evolutionary trend of increasing EAR protein numbers from algae to angiosperms.
Conclusions:
- This study provides a large-scale identification and functional analysis resource for plant EAR proteins.
- The PlantEAR platform facilitates in-depth research into the roles of EAR proteins in plant biology.
- The evolutionary analysis highlights the increasing importance of EAR proteins in the development of higher plants.
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