毛果杨 RAV/PLC 基因生物信息学分析

    Bioinformatics Analysis of RAV/PLCGene in Populus trichocarpa

    • 摘要: 【目的】利用生物信息学手段,对毛果杨(Populus trichocarpa)RAV/PLC 基因编码蛋白质结构和特征进行预测。【方法】以 PLC(Phospholipases C)为关键字在 Phytozome 数据库搜索毛果杨磷脂酶 C 基因序列,以 RAV/PLC 基因及其蛋白质序列为研究对象,利用多种生物信息学分析工具对其基因结构及蛋白功能进行分析。【结果】在毛果杨 PLC 编码基因中发现了一个可编码 RAV 和 PLC 结构域的特殊基因,该基因在Phytozome 数据库中编号为 Potri.018G109200,ORF 区域长度为 1 650 bp,编码 549 个氨基酸,预测分子量为62.72338 ku,理论等电点为 9.16;该基因在茎中表达量最高 , 芽中表达量其次之根和叶中表达量较低。其编码蛋白包含 1 个 AP2 结构域、1 个 B3 结构域和 1 个 PLC-X 结构域,AP2/B3 结构域和 PLC-X 结构域之间可能存在一个跨膜区;启动子元件分析表明,RAV/PLC 基因可能与光应答及激素应答相关;String 软件预测 RAV/PLC基因可能与 MYB103、WRKY49、ABI5、DXS2 存在功能关联;KEGG 分析表明,该基因主要与 RAV 转录因子信号通路有关;同时利用同源建模方法获得了 RAV/PLC 的完整三维模型。【结论】通过对 RAV/PLC 基因结构和蛋白功能预测,为该基因克隆及参与信号通路分析提供参考。

       

      Abstract: 【Objective】The study was conducted to predict protein structure and features of RAV/PLC in Populus trichocarpa based on bioinformatics analysis.【Method】RAV/PLC gene sequence was obtained from Phytozome database with PLC (Phospholipases C) as the key word and multiple bioinformatics tools were used to analyze RAV/PLC gene and protein sequence.【Results】A 1 650 bp open reading frame (Potri. 018G109200) was identified from Phytozome in P. trichocarpa, encoding 549 amino acids and a special peptide with a RAV domain and a PLC domain. The predicted molecular weight for RAV/PLC was 62.72338 ku and the theoretical pI was 9.16. A higher expression of RAV/PLC was observed in stem compared to leaf, bud and root. An AP2 domain, a B3 domain and a PLC-X domain were contained in RAV/PLC, and there might be a transmembrane helices structure between the AP2/B3 domain and the PLC-X domain. Promoter analysis showed that RAV/PLC might mainly be linked to light and hormone response. String delineated the function network between RAV/PLC and MYB103, WRKY49, ABI5, DXS2; KEGG analysis showed that this gene was mainly related to the RAV transcription factor signaling pathway. And the complete 3D structure was generated via homology modeling.【Conclusion】The information obtained for RAV/ PLC will provide a foundation for the cloning and signal pathway analysis of RAV/PLC.

       

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