马铃薯LINC4206及其靶基因StDFR的克隆与StDFR的生物信息学分析

Cloning of LINC4206 and Its Target Gene StDFR and Bioinformatics Analysis of StDFR in Potato

为了研究lncRNA对马铃薯块茎花青素生物合成的调控机制,通过分析紫心马铃薯(希森8号)和黄心马铃薯(晋16)块茎的lncRNA转录组数据,筛选到参与马铃薯块茎花青素生物合成的lncRNA及其靶基因,并进一步从希森8号中克隆得到1个与马铃薯块茎花青素合成相关的lncRNA-LINC4206及其靶基因StDFR,其序列长度分别为816、1 149 bp,并对StDFR基因编码的蛋白进行了生物信息学分析。结果表明,该基因编码383个氨基酸,分子量为42 469.78,是一个亲水性稳定蛋白,没有跨膜结构,也没有信号肽;亚细胞定位预测显示,St DFR蛋白定位于细胞质和细胞质膜上,St DFR蛋白的二级结构主要由无规则卷曲、α-螺旋组成,所占比例分别为43.98%和36.65%;保守结构域分析表明,该蛋白具有典型的差相异构化结构域(epimerase),该基因编码的NAD(P)结合的折叠超家族蛋白属于短链脱氢酶/还原酶家族。系统进化树分析表明,马铃薯St DFR蛋白与茄子Sm DFR具有较近的亲缘关系。RT-q RCR分析结果显示,LINC4206与StDFR基因在希森8号和晋16中的表达趋势一致,这进一步从m RNA水平证明了StDFR是LINC4206的靶基因,推测LINC4206可能靶向作用于StDFR正调控马铃薯块茎花青素的生物合成。研究结果可为解析lncRNA调控马铃薯块茎花青素的分子机制提供一定的理论参考。

To study the regulation mechanism of lncRNA on potato(Solanum tuberosum L.)tuber anthocyanin biosynthesis,the paper analyzed the lncRNA transcriptome data of the tubers of purple-fleshed potato(Xisen 8)and yellow-fleshed potato(Jin 16),and screened the lncRNAs and their target genes involved in the biosynthesis of potato tuber anthocyanin,and one lncRNA-LINC4206 and its target gene StDFR related to potato tuber anthocyanin biosynthesis were cloned from Xisen 8.Their sequence lengths were 816 bp and 1149 bp,respectively.Bisides,the protein encoded by the StDFR gene was analyzed by bioinformatics.The results showed that the StDFR gene encodes 383 amino acids with a molecular quality of 42469.78.It was a hydrophilic stable protein with neither a transmembrane structure nor a signal peptide.Subcellular location prediction showed that it was located in the cytoplasm and plasma membrane.The secondary structure of StDFR protein was mainly composed of random coils and alpha-helix,which accounted for 43.98%and 36.65%,respectively.The conserved domain analysis showed that this protein had a typical differential isomerization domain(epimerase),and the NAD(P)-binding Rossmann folding superfamily protein encoded by StDFR belonged to the short-chain dehydrogenase/reductase family.Phylogenetic tree analysis found that potato StDFR protein had a close relationship with eggplant SmDFR protein.The results of RT-qRCR analysis showed that the expression trend of LINC4206 was consistent with that of StDFR gene in Xisen 8 and Jin 16,which further proved that StDFR was the target gene of LINC4206 from mRNA level,inferring that LINC4206 might target StDFR to positively regulate the biosynthesis of anthocyanins in potato tubers.The results will provide a reference for elucidating the molecular mechanism of lncRNA regulating potato tuber anthocyanins.