Bioinformatics of Growth-interacting Factor Genes in Foxtail Millet
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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。 -
关键词:
- 谷子 /
- 生长调节因子互作因子 /
- 基因家族 /
- 进化分析
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. -
Key words:
- Setaria italica /
- GIF /
- gene family /
- phylogeny analysis
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图 2 拟南芥、水稻和谷子的GIFs蛋白保守基序分布
Figure 2. Distribution of conserved motifs in
GIFs of Arabidopsis, rice, and millet 
图 3 拟南芥、水稻和谷子的GIFs蛋白系统进化树
Figure 3. Phylogenetic tree on
GIFs of Arabidopsis, rice, and millet 表 1 谷子GIF基因家族的基本特征
Table 1. Characteristics of GIF genes in S. italica
基因名称
Gene name基因座
Locus name转录本
Transcript name别名
Alias染色体定位
Chromosome location开放阅读框
ORF/bp编码蛋白
Protein/aa外显子个数
Extron numberSiGIF1 Seita.3G360000 Seita.3G360000.1 Si023367m.g scaffold_3:46155062..46160910 + 561 186 4 SiGIF2 Seita.8G193300 Seita.8G193300.1 Si026850m.g scaffold_8:34062291..34066801− 639 212 4 SiGIF3 Seita.9G104500 Seita.9G104500.1 Si037326m.g scaffold_9:6299035..6302512− 696 231 4 
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表 2 谷子SiGIFs蛋白的二级结构分析
Table 2. Secondary structure of SiGIFs
蛋白名称
Protein nameα-螺旋
Alpha
helix/%β-折叠
Extended
strand/%β-转角
Beta
turn/%无规则卷曲
Random
coil/%SiGIF1 34.95 3.23 5.91 55.91 SiGIF2 34.43 3.77 5.19 56.60 SiGIF3 35.50 11.26 11.69 41.56 平均 Average 34.96 6.09 7.60 51.36
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表 3 谷子SiGIFs蛋白潜在磷酸化位点分析
Table 3. Potential phosphorylation sites in
SiGIFs 谷子GIF 家族
SiGIF gene family位点数量 Site number 丝氨酸
Serine苏氨酸
Threoine酪氨酸
TyrosineSiGIF1 8 7 0 SiGIF2 5 7 0 SiGIF3 17 1 2
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