1Laboratory of Molecular Genetics, University of Groningen, 9747 AG Groningen, The Netherlands.
2Top Institute Food and Nutrition (TIFN), Nieuwe Kanaal 9A, 6709 PA Wageningen, The Netherlands.
Microb Genom. 2018 Feb;4(2). doi: 10.1099/mgen.0.000157. Epub 2018 Feb 9.
Sporulation is a survival strategy, adapted by bacterial cells in response to harsh environmental adversities. The adaptation potential differs between strains and the variations may arise from differences in gene regulation. Gene networks are a valuable way of studying such regulation processes and establishing associations between genes. We reconstructed and compared sporulation gene co-expression networks (GCNs) of the model laboratory strain Bacillus subtilis 168 and the food-borne industrial isolate Bacillus amyloliquefaciens. Transcriptome data obtained from samples of six stages during the sporulation process were used for network inference. Subsequently, a gene set enrichment analysis was performed to compare the reconstructed GCNs of B. subtilis 168 and B. amyloliquefaciens with respect to biological functions, which showed the enriched modules with coherent functional groups associated with sporulation. On basis of the GCNs and time-evolution of differentially expressed genes, we could identify novel candidate genes strongly associated with sporulation in B. subtilis 168 and B. amyloliquefaciens. The GCNs offer a framework for exploring transcription factors, their targets, and co-expressed genes during sporulation. Furthermore, the methodology described here can conveniently be applied to other species or biological processes.
孢子形成是一种生存策略，细菌细胞通过这种策略来适应恶劣的环境逆境。适应潜力因菌株而异，这种差异可能源于基因调控的差异。基因网络是研究这种调控过程并建立基因之间关联的一种有价值的方法。我们重建并比较了模式实验室菌株枯草芽孢杆菌 168 和食源性工业分离株解淀粉芽孢杆菌的孢子形成基因共表达网络（GCN）。使用来自孢子形成过程六个阶段的样本中的转录组数据进行网络推断。随后，进行了基因集富集分析，以比较枯草芽孢杆菌 168 和解淀粉芽孢杆菌的重建 GCN 在生物学功能方面的差异，结果显示了与孢子形成相关的具有一致功能群的富集模块。基于 GCN 和差异表达基因的时间演变，我们可以鉴定出与枯草芽孢杆菌 168 和解淀粉芽孢杆菌的孢子形成强烈相关的新候选基因。GCN 为探索转录因子、它们的靶标和孢子形成过程中的共表达基因提供了一个框架。此外，这里描述的方法可以方便地应用于其他物种或生物过程。
