Cloning and bioinformatics analysis of gibberellin insensitive dwarf1 gene DbGID1s in Dioscorea bulbiferas

Abstract

[Objective] The aim of this study was to clone gibberellin insensitive dwarfl (GID1) gene in DbGID1s in Dioscorea bulbifera, conduct bioinformatics analysis, and to provide a theoretical reference for further exploring the mechanism of DbGID1s protein in the growth and development of D. bulbifera.

[Method] DbGID1s were cloned by RT-PCR method; the physical and chemical properties, domains, phosphorylation sites and phylogenetic evolution of these genes were pridicted with bioinformatics softwares.

[Result] Four sequences of gene DbGID1A were obtained, namely DbGID1A (GenBank accession number: MT648372), DbGID1Bl (GenBank accession number: MT648374), DbGID1B2 (GenBank accession number: MT648375) and DbGID1C (GenBank accession number: MT648373). The lengths of four nucleic acid sequences were 862, 1273, 1081 and 1164 bp, respectively, and encoding 292, 340, 289 and 360 amino acids residues, respectively. The molecular weights of the four DbGID1s proteins were 32079.17-40301.83 Da, and their theoretical isoelectric points (pI) varied from 6.05 to 8.62. They were unstable, hydrophilic proteins and located on external membrane. No signal peptide was found in the four DbGID1s proteins. Their phosphorylation sites were mainly serine (Ser, S), and the phosphorylation sites of the four proteins had coincidence sites and mutation sites. The four proteins not only had the hydrolytic activite area of α/α folding hydrolase superfamily carboxylic acid lipase, but also had conserved domains (HGG and GXSXG) and catalytic joint sites (S, D and H) of hormone lipase (HSL). The similarity of proteins between D. bulbifera and other species was high, and the homology between D. bulbifera and yam was over 90%.

[Conclusion] The DbGID1s gene in D. bulbifera has the basic characteristics of GIDl genes in many plants and the encoded proteins have the typical domain of GID1 protein, so it is possible that DbGID1s genes participate in gibberellin signal transduction and regulate the growth and development of organs of D. bulbifera.

Abstract

摘要：【目的】克隆黄独赤霉素受体(GID1)基因 DbGID1s, 并对其进行生物学信息分析, 为深人探究DbGID1s蛋 白在黄独生长发育中的作用机制提供理论参考。 【方法】采用RT-PCR技术克基 DbGID1s因, 利用生物信息学软件对 其理化性质、结构域、磷酸化位点及系统发育进化进行预测分析。 【结果】克隆获得4个 DbGID1s基因序列, 命名为 DbGID1A、 DbGID1B1、 DbGID1B2和 DbGID1C、 GenBank 登录号为 MT648372、MT648374、MT648375 和 MT648373,长度 分别为862、1273、1081和1164 bp, 编码292、340、289和360个氨基酸残基。4个DbGID1s蛋白的分子量为32079.17~40301.83 Da, 理论等电点(pI)为6.05〜8.62,为不稳定的外在膜亲水性蛋白, 不存在信号肽序列, 其磷酸化位点主要以 丝氨酸(Ser, S)为主, 且4个蛋白的磷酸位点均有重合位点和突变位点, 不仅具有α/β折叠水解酶超级家族羧酸脂肪酶 水解活性区域, 还具有激素脂肪酶(HSL)的保守结构域(HGG和GXSXG)和催化联合位点(S、D和H)。DbGID1s蛋白 与其他植物GID1蛋白序列具有较高的氨基酸序列相似性, 其中与山药的相似性达90%以上。 【结论】 DbGID1s基因具 有多种植物 GID1基因的基木特征, 其编码的蛋白具有GID1蛋白典型的结构域, 其可能参与赤霉素(GA)信号转导, 调节黄独的生长发育。