• 中文核心期刊
  • CSCD来源期刊
  • 中国科技核心期刊
  • CA、CABI、ZR收录期刊

谷子生长调节因子互作因子基因家族生物信息学分析

Bioinformatics of Growth-interacting Factor Genes in Foxtail Millet

  • 摘要:
      目的  生长调节因子互作因子(GRF-interacting factor,GIF)是植物体内一类转录共激活因子,在植物生长发育和逆境胁迫中起重要作用。通过系统分析谷子GIF基因家族的组成、各成员的结构以及进化关系,为GIF基因调节机制研究提供参考。
      方法  利用谷子基因组数据库,采用生物信息学的方法,鉴定谷子GIF 基因家族的基因结构、染色体定位,编码蛋白相似性、二级结构、跨膜区和磷酸化位点预测,通过序列比对进行进化和分类分析。
      结果  谷子含有3个GIF 基因,均含有4个外显子,分布于第3、8和9号染色体上。编码SiGIF1蛋白和SiGIF2蛋白相似性最高,为72.04%,SiGIF1蛋白和SiGIF3蛋白相似性最低,为37.08%。二级结构分析显示,谷子GIF蛋白无规则卷曲占比最高(41.56%~56.60%),其次为α-螺旋(34.43%~35.50%),再次为β-转角(5.19%~11.69%),β-折叠最低(3.23%~11.26%)。TMHMM 跨膜区进行分析显示,谷子GIF蛋白均不含有跨膜区。MEME保守基序分析显示,谷子GIF 蛋白均含有保守的SSXT (PF05030)结构域。磷酸化位点预测分析表明谷子GIF 蛋白均含有潜在磷酸化位点。
      结论  谷子GIF基因家族的基因结构、磷酸化位点预测等生物信息学分析结果将为揭示谷子GIF基因家族在谷子生长发育过程中的功能提供重要的线索。

     

    Abstract:
      Objective  The composition, structure, and evolution of each member of the growth-interacting factors (GIF) of the growth-regulating factors (GRF) and the transcription cofactors that closely associate with the growth, development, and stress response of plants in Setaria italica were analyzed.
      Method  Based on the S. italica genome database and bioinformatics, the structure, characteristics, position on the chromosome, proteins similarity, secondary structure, transmembrane domain, and phosphorylation sites of the GIF genes were obtained.
      Result  The 3 SiGIFs in S. italica genome contained 4 exons locating on the 3, 8, and 9 chromosomes. The greatest similarity between SiGIF1 and SiGIF2 was 72.04%, while the lowest was 37.08% between SiGIF1 and SiGIF3. The secondary structure consisted of 41.56%~56.60% random coils, 34.43%~35.50% alpha helix, 5.19%~11.69% beta turns and 3.23%~11.26% extended strands. The TMHMM transmembrane domain analysis showed no transmembrane domain in SiGIFs. MEME indicated that all SiGIFs contained conserved SSXT (PF05030) domain. And potential phosphorylation sites in the GIFs were predicted by analysis.
      Conclusion   The bioinformatics revealed information on the structure, phosphorylation sites of SiGIF gene family provided crucial insights for the studies on the growth and development of plants.

     

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