葡萄SBP基因家族生物信息学分析

Bioinformatics Analysis of the SBP Gene Family in Grapevine

SBP(squamosa promoter binding protein,SBP)基因家族是植物所特有的一类重要转录因子,广泛参与植物生长、发育以及多种生理生化反应的信号传导。葡萄是继拟南芥、水稻和杨树之后完成全基因组测序的第四种开花植物,因此葡萄逐渐成为分子生物学研究的重点对象,进行葡萄基因组信息挖掘与分析对于葡萄功能基因组学的发展具有重要意义。本文利用生物信息学方法对葡萄家族45条SBP蛋白序列的系统发生和SBP基因组定位进行分析,然后对其氨基酸组成成分、理化性质以及二级和三级结构进行预测和分析,同时还分析了葡萄与拟南芥的SBP基因家族之间的联系。结果显示这45条蛋白序列与拟南芥16个SBP基因蛋白序列一起分成了3个亚族,说明拟南芥与葡萄SBP基因间具有较高的保守性;进一步的基因组定位结果发现其分布在14条染色体上,较拟南芥在染色体上的分布更为分散。研究还发现不同亚家族间氨基酸数目、氨基酸序列间的疏水性存在一定的差异;而二级结构预测结果发现,41条氨基酸序列以随机卷曲为主要组成部分,这与拟南芥相似,且45条氨基酸序列三维结构十分相似。本文实验结果均为葡萄SBP基因家族的进一步功能分析提供了重要研究基础。

SBP gene family （squamosa promoter binding protein,SBP） is a specific kind of important transcriptional factors to plants,which are involved extensively in plant growth,development and signal transduction of many physiological and biochemical responses.After Arabidopsis thaliana,Oryza sativa and Populus trichocarpa,the grape whole genome was sequenced as the fourth flowering plant,so grape has been focused on molecular biology research areas,of which the information mining and analysis of grape genome is very significant for the progress of grape functional genomics.In this article,by utilizing the bioinformatics method,we analyzed the phylogenetic of 45 SBP family protein sequence and SBP genome localization firstly,and then predicted and analyzed their amino acid composition,physical and chemical characteristics,as well as secondary and tertiary structures,meanwhile we still assayed the relation of SBP gene family between grapevine and Arabidopsis thaliana.The result showed that these 45 amino acid sequences could be clustered into three groups together with 16 SBP sequences of Arabidopsis thaliana,which illuminated that SBP genes had highly conservative between grapevine and Arabidopsis thaliana.Further genetic mapping of SBP genome localization found that they could be distributed on 14 chromosomes,which had a more dispersive location comparing with the situation in Arabidopsis thaliana.The research still found that the number of amino acid and hydrophobic of amino acid sequences in different subfamilies presented some differences,however,the results of secondary structure predicted that the main composition of 41 amino acid sequences was random curl,which displayed the same as Arabidopsis thaliana,and the tertiary structure of all the sequences were quite similar.The results of this investigation could definitely provide a significant foundation for further research on function analysis of grapevine SBP gene family.