结核分枝杆菌CarD蛋白结构与功能的生物信息学分析

Bioinformatic analysis of the structure and function of CarD from Mycobacterium tuberculosis

目的应用生物学信息分析软件预测结核分枝杆菌CarD蛋白的结构和功能。方法运用NCBI中Blast工具,将结核分枝杆菌H37Rv carD基因序列与GenBank中相似序列进行核苷酸比对;利用MEGA 6.06软件,采用邻位相连法构建N-J进化树;运用ClustalX 2.1软件,将结核分枝杆菌H37Rv CarD及与其同源性较高的分枝杆菌CarD氨基酸序列进行多重比对分析;登录ExPASy网站,运用ProtParam工具分析CarD蛋白的理化性质,运用ProtScale进行蛋白质疏水性分析,运用SignalP 4.1Server预测蛋白质信号肽,运用TMHMM Server v.2.0以及TMPred预测蛋白质跨膜螺旋区,运用SOPMA预测蛋白质二级结构,运用SWISS-MODEL进行蛋白质三级结构同源建模;运用NetPhos 3.1Server预测蛋白质磷酸化位点;运用NCBI中CDD工具预测CarD蛋白保守结构域。结果分枝杆菌carD基因序列相似度为100%,进化关系较近。H37Rv与田鼠分枝杆菌起源于同一物种,同源性较高。CarD分子在进化过程中高度保守,为稳定、亲水性蛋白,无跨膜区、无信号肽,蛋白序列中存在4个丝氨酸磷酸化位点,二级结构中以α-螺旋为主,三级结构同源建模成功。CarD蛋白是一种结合RNA聚合酶的转录调控因子,属于CarD/CdnL/TRCF家族。结论 CarD蛋白为RNA聚合酶结合蛋白,调控转录和控制结核分枝杆菌的生长。该蛋白序列保守稳定,是治疗结核病潜在的新靶标。

Objective To use bioinformatic software to predict the structure and function of the CarD protein of Mycobacterium tuberculosis. Methods The sequence of the carD gene of the H37Rv strain of M. tuberculosis and similar sequences from GenBank were blasted using the Nucleotide BLAST tool, and the software MEGA 6.06 was then used to construct a neighbor-joining tree. The software ClustalX 2. 1 was used to perform multiple sequence alignment of CarD from the H37Rv strain of M. tuberculosis and highly homologous amino acid sequences. Tools from the ExPASy website such as ProtParam were used to analyze the physical and chemical properties of CarD protein, ProtScale was used to ana- lyze its hydrophobicity, SignalP 4.1 Server was used to predict its signal peptides, TMHMM Server v. 2.0 and TMPred were used to predict its transmembrane helical segments, SOPMA was used to predict its secondary structure, SWISS MODEL was used to model its tertiary structure. NetPhos 3.1 Server was used to predict its phosphorylation sites and the tool CDD was used to predict conserved domains in CarD. Results CarD of M. tuberculosis has been highly con- served over its evolution. CarD is a stable hydrophilic protein with no transmembrane helical segments and no signal pep- tides. The CarD protein sequence contains four serine phosphorylation sites. The secondary structure of the protein pri- marily consists of alpha helices, and a homology-based model of its tertiary structure was successfully constructed. CarD is a type of RNA polymerase binding protein. A transcription regulator, CarD belongs to the CarD/CdnL/TRCF family. Conclusion Bioinformatic analysis of the CarD protein revealed that the protein is an RNA polymerase binding protein that can regulate transcription and control the growth of M. tuberculosis. A conserved and stable protein, CarD is a new potential target for the treatment of tuberculosis.