PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins
PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins
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DOI：
10.3389/fgene.2018.00590
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发表时间：
2018-11
影响因子：
3.7
通讯作者：
Jiaotong Yang;Yue Liu;Hengyu Yan;Tian Tian-Tian;Qi You;Liwei Zhang;Wenying Xu;Zhen Su
中科院分区：
文献类型：
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作者：
Jiaotong Yang;Yue Liu;Hengyu Yan;Tian Tian-Tian;Qi You;Liwei Zhang;Wenying Xu;Zhen Su
最初在拟南芥乙烯反应因子（ERF）家族成员中鉴定的乙烯反应元件结合因子相关两亲性阻遏（ERF）基序是植物中的转录阻遏基序，并且由LxLxL或DLNxxP的共有序列模式定义。含AtSAP基序的蛋白质可作为转录阻遏物，从而与辅助阻遏物如TOPLESS和AtSAP 18相互作用，通过组蛋白修饰影响染色质的结构，从而抑制基因转录。含植物基序的蛋白质在不同植物物种中高度保守，在激素信号转导、胁迫反应和发育中起重要作用，但在大多数植物中尚未被鉴定。本研究基于隐马尔可夫模型（HiddenMarkovModel）和正向同源基因搜索，从71种植物中鉴定出20,542个含结构域的蛋白质，并通过整合多种功能注释和数据处理，构建了植物含结构域蛋白质功能分析平台（Plantastrophic，http：//structuralbiology.cau.edu.cn/plantastrophic）。一些工具被提供作为功能支持的含p53基序的蛋白质，如浏览，搜索，共表达和蛋白质-蛋白质相互作用（PPI）网络分析，以及顺式元件分析和基因集富集分析（GSEA）。此外，基于已鉴定的含结构域蛋白，我们还探讨了它们在不同物种中的分布，发现从藻类到被子植物，含结构域蛋白的数量呈逐渐增加的趋势。
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.