原始小球藻AP2转录因子的生物信息学分析

Bioinformatics analysis of AP2 transcription factor in Auxenochlorella protothecoides

关键词:  原始小球藻, AP2转录因子, 生物信息学

Key words:  Auxenochlorella protothecoides, AP2 transcription factor, bioinformatics

摘要:

为了揭示原始小球藻AP2基因家族编码蛋白的理化特性、分子功能和遗传进化特征,该文对原始小球藻AP2基因家族的蛋白成员进行了详细的生物信息学预测和分析,并利用PrtoParam、Pfam 3.20、Protscale等在线工具分析了原始小球藻AP2家族所包含的8个蛋白成员。结果表明:该家族成员含有的氨基酸数为247(XP_011395646.1)到715(XP_011401904.1),理论等电点最大为9.39(XP_011396011.1)、最小为5.81(XP_011398158.1); 家族中各个成员所含有的保守结构域的位置和数量都各不相同; 所有蛋白成员均无信号肽,均不包含跨膜螺旋,不具有跨膜区域; 蛋白成员中最大亲水性值为-3.222(XP_011398158.1),最大疏水性值为2.333(XP_011401904.1),且所有成员的平均亲疏水性值均小于0; 成员中有多个磷酸化位点值远超标准值0.5,最大磷酸化位点值为0.998; 该基因家族的蛋白成员二级结构的组分含量从大到小排序均为无规则卷曲>α-螺旋>延伸链>β-转角,推测α-螺旋和无规则卷曲是其二级结构的主要方式,延伸链和β-转角则分散在所有蛋白成员的氨基酸链中; 所有成员的三级结构分析中均能观察到α-螺旋、β-折叠、β-转角以及N端和C端; 系统进化分析结果表明,在其余15个物种中,与原始小球藻亲缘关系最远的是金牛介球菌(Ostreococcus tauri),亲缘关系最接近的是小球藻(Chlorella variabilis NC64A)和螺旋孢子虫(Helicosporidium),较接近的是苦参3号(Picochlorum sp. SENEW3)。该研究较系统地分析了原始小球藻AP2蛋白家族的理化特性、保守基序及系统进化关系,为进一步研究原始小球藻AP2转录因子功能和互作关系提供一定参考依据。

Abstract:

In order to reveal the physicochemical properties, molecular functions and genetic evolution characteristics of AP2 gene family encoded proteins in Auxenochlorella protothecoides, in this study, the protein members of AP2 gene family in A. protothecoides are predicted and analyzed in detail by bioinformatics. Eight protein members of the AP2 family of A. protothecoides were analyzed by online tools such as PrtoParam, Pfam 3.20 and Protscale and so on. The results were as follows: Amino acids numbers of the family members were 247(XP_011395646.1)to 715(XP_011401904.1), the maximum theoretical isoelectric point was 9.39(XP_011396011.1), and the minimum was 5.81(XP_011398158.1); The positions and numbers of conserved domains in each member of the family were different; All protein members had no signal peptide, did not contain transmembrane helix, and did not have transmembrane region; The maximum hydrophilicity value of the protein members was -3.222(XP_011398158.1), and the maximum hydrophobicity value was 2.333(XP_011401904.1), and the average hydrophilicity/hydrophobicity values of all members were less than 0; The values of many phosphorylation sites in the members were far beyond the standard value of 0.5, and the maximum value of phosphorylation site was 0.998; The component content of secondary structures of protein members in the gene family was arranged in the order of random coil > alpha-helix > extended strand > β-turn; and it is speculated that alpha-helix and random coil are the main modes of its secondary structure, while extended strand and β-turn are dispersed in the amino acid chain of all protein members; Alpha-helix, β-sheet, β-turn, N-terminal and C-terminal were observed in tertiary structure of all members; Phylogenetic analysis showed that Ostreococcus tauri was the most distant relative to Auxenochlorella protothecoides, the closest relatives were Chlorella variabilis NC64A and Helicosporidium, and the next closest relatives were Picochlorum sp. SENEW3 among the other 15 species. This study systematically analyzed the physicochemical properties, conserved motifs and phylogenetic relationships of AP2 protein family in Auxenochlorella protothecoides. It provides a reference for further study on the function and interaction of AP2 transcription factors in A. protothecoides.