利用比较基因组学方法预测短小芽孢杆菌转录调控网络

A transcriptional regulatory network of Bacillus pumilus predicted by comparative genomcis methods

为探讨短小芽孢杆菌(Bacillus pumilus)的基因调控关系,通过在其亲缘关系最近的模式菌——枯草芽孢杆菌(Bacillus subtilis)中寻找同源转录因子及其调控基因的方式,预测出B.pumilus的候选转录调控网络;并利用转录因子绑定位点的位置权重矩阵(PositionalWeight Matrix)在B.pumilus全基因组的基因上游区域扫描rnotif的方式来验证候选转录调控网络;最后再整合其他B.pumilus专属的调控数据,最终形成一个较完备的B.pumilus基因转录调控网络(包含1 95个转录因子和1201个受控基因).上述结果表明,在细菌中,利用比较基因组学的方法,以一个被广泛研究的模式生物所积累的基因转录调控关系数据为基础,推测出亲缘关系较近的其他物种的基因调控网络,其结果是可靠的,为探索一些尚不具备大规模基因表达芯片数据的物种的基因调控网络提供了一种可行的方法.

To explore the gene transcriptional regulatory relations of Bacillus pumilus, a candidate transcriptional regulatory network of B. purnilus has been predicted by searching the homologous transcription factors（TFs） and the homologous regulated genes from Bacillus subtilis genome. The positional weight matrix（PWM） of transcription factor binding sites（TFBSs） was used to scan the whole B. pumilus genome in order to verify the candidate transcriptional regulatory networks. Finally, a more complete transcriptional regulatory networks had been constructed by integrating with other B. pumilus TFs and regulated genes. The network consist of 195 TFs and 1201 regulated genes. The result showed that, in bacteria, with the data set of the closely related model species which has a long history of experimental research, it is feasible to predict the transcriptional regulatory network by using comparative genomics methods. The study provided a feasible approach for exploring gene regulatory networks of the organism which lacks large-scale gene expression microarray data.