Inferring the transcriptional network of Bacillus subtilis
Inferring the transcriptional network of Bacillus subtilis
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DOI：
10.1039/b907310h
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发表时间：
2009-01-01
影响因子：
--
通讯作者：
Marchal, Kathleen
中科院分区：
文献类型：
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作者：
Fadda, Abeer;Fierro, Ana Carolina;Marchal, Kathleen
细菌对剧烈环境变化的适应对它们的生存至关重要。它们实现这种适应的部分原因是通过对基因转录的复杂调控。在这项研究中，我们推断革兰氏阳性模式生物，枯草芽孢杆菌的转录网络。我们使用数据集成工作流，利用基序和表达数据来生成条件依赖的转录模块。在构建motif数据时，我们既依赖于已知信息，也依赖于预测信息。已知的基序来源于DBTBS，而预测的基序是通过利用比较基因组学的从头基序检测方法生成的。表达数据由不同平台上的微阵列组成。我们的研究结果表明，相当一部分枯草芽孢杆菌网络尚未被发现；我们可以预测已知监管机构的417种新的监管相互作用，以及尚未表征的监管机构的453种相互作用。我们网络中的调节器显示出在特定环境条件下调节模块的偏好。此外，似乎发生了大量依赖于条件的操纵子内调节。全球监管机构似乎需要功能上的灵活性，以通过充当激活者和阻遏者来实现其角色。
The adaptation of bacteria to the vigorous environmental changes they undergo is crucial to their survival. They achieve this adaptation partly via intricate regulation of the transcription of their genes. In this study, we infer the transcriptional network of the Gram-positive model organism, Bacillus subtilis. We use a data integration workflow, exploiting both motif and expression data, towards the generation of condition-dependent transcriptional modules. In building the motif data, we rely on both known and predicted information. Known motifs were derived from DBTBS, while predicted motifs were generated by a de novo motif detection method that utilizes comparative genomics. The expression data consists of a compendium of microarrays across different platforms. Our results indicate that a considerable part of the B. subtilis network is yet undiscovered; we could predict 417 new regulatory interactions for known regulators and 453 interactions for yet uncharacterized regulators. The regulators in our network showed a preference for regulating modules in certain environmental conditions. Also, substantial condition-dependent intra-operonic regulation seems to take place. Global regulators seem to require functional flexibility to attain their roles by acting as both activators and repressors.