基于cDNA微阵列数据对乳酸菌生长及应激代谢转录组特征的研究

Study on Growth and Transcriptome Properties of Lactic Acid Bacteria Based on DNA-Microarray Data

应用本实验室编写的perl程序包将GEO数据库中乳酸菌生长、应激代谢相关实验数据和相应的基因组数据整合,构建易于本地查询和访问的MySQL数据库,利用该数据库研究乳酸菌在生长、衰亡及应对不利环境(如胆盐、过氧化氢、碳氮源饥饿)时的转录组特征,并利用MEME软件寻找到了各种情况下部分协同表达基因前导序列的共有motif,即潜在的调控蛋白作用位点。结果表明:除了胆汁和草酸铵对嗜酸乳杆菌细胞代谢特征的影响具有较高的一致性外,面对其他压力环境乳酸菌细胞的应激模式具有较大的差异,有着各自受到特异性诱导表达或抑制的基因群,但在各种情况下翻译(J)、脂类运输和代谢(I)、细胞内运输和分泌(U)相关因的转录水平变化都比较显著,特别是蛋白质翻译相关基因变化最为明显,说明细胞主要通过调控蛋白质翻译相关基因的种类和表达量来对细胞的状态进行调整。

A local MySQL database of lactic acid bacteria （LAB） was built through integrating genome data and chip data from gene expression profile used perl program written by our laboratory. The local database was used to investigate transcriptome properties of LAB in different growth phases or stress environments such as the presence of bile salts, hydrogen peroxide and starvation. Meanwhile, MEME software was also used for searching the common motif located in upstream of transcription starting point in co-expression genes under certain stress environments. Results indicated that no obvious difference was observed in transcriptome properties of LAB under the stress from bile and ammonium oxalate. However, a significant difference was observed in transcriptome properties of LAB under the stress from other factors. These responses to stress exhibited specific induced or inhibition gene expression. In addition, gene expression associated with translation （J）, lipid transport and metabolism （I）, intracellular transport and secretion （U） revealed a high level, especially for translation-related genes, which indicating that modulation of cell metabolism was mainly achieved through regulating the expression of translation-related genes.