Identifying modules of coexpressed transcript units and their organization of Saccharopolyspora erythraea from time series gene expression profiles.
Identifying modules of coexpressed transcript units and their organization of Saccharopolyspora erythraea from time series gene expression profiles.
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从时间序列基因表达谱中识别红糖多孢菌的共表达转录单元模块及其组织
DOI：
10.1371/journal.pone.0012126
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发表时间：
2010-08-12
期刊：
影响因子：
3.7
通讯作者：
Li YY
中科院分区：
文献类型：
--
作者：
Chang X;Liu S;Yu YT;Li YX;Li YY
研究背景2007年公布了红多孢菌的基因组序列。为了在全转录组水平上研究基因调控，我们设计了一个表达芯片。拟南芥菌株NRRL 2338基因组序列。基于这些数据，我们着手研究潜在的转录调控网络及其组织。方法/主要发现鉴于细菌转录调控的层次结构，我们在整个转录组水平上构建了一个层次共表达网络。从1255个差异表达的转录单位（TU）中鉴定出27个模块，并将其进一步分为4组。功能富集分析表明，我们的层次网络的生物学意义。结果表明，在第一个快速生长期（A期），初级代谢被激活，当生长减慢时（B期），次级代谢被诱导。在27个模块中，有两个与红霉素生产高度相关。一个包含红霉素生物合成（ery）基因簇中的所有基因，另一个似乎通过共享共同的中间代谢产物与红霉素生产相关。观察到生产和表达调节之间的非伴随相关性。特别是，通过计算偏相关系数和基于高斯图模型构建网络，发现了模块间的内在关联，并包含了与红霉素生产相关的两个模块间的关联。结论这项工作创建了一个分层模型，将转录组数据聚集到协调的模块中，并在整个时间过程中将模块分组，从而深入了解协调的转录调节，特别是对应于S.红霉素产生的调节。菜这一策略可以推广到其他原核微生物的研究。
Background The Saccharopolyspora erythraea genome sequence was released in 2007. In order to look at the gene regulations at whole transcriptome level, an expression microarray was specifically designed on the S. erythraea strain NRRL 2338 genome sequence. Based on these data, we set out to investigate the potential transcriptional regulatory networks and their organization. Methodology/Principal Findings In view of the hierarchical structure of bacterial transcriptional regulation, we constructed a hierarchical coexpression network at whole transcriptome level. A total of 27 modules were identified from 1255 differentially expressed transcript units (TUs) across time course, which were further classified in to four groups. Functional enrichment analysis indicated the biological significance of our hierarchical network. It was indicated that primary metabolism is activated in the first rapid growth phase (phase A), and secondary metabolism is induced when the growth is slowed down (phase B). Among the 27 modules, two are highly correlated to erythromycin production. One contains all genes in the erythromycin-biosynthetic (ery) gene cluster and the other seems to be associated with erythromycin production by sharing common intermediate metabolites. Non-concomitant correlation between production and expression regulation was observed. Especially, by calculating the partial correlation coefficients and building the network based on Gaussian graphical model, intrinsic associations between modules were found, and the association between those two erythromycin production-correlated modules was included as expected. Conclusions This work created a hierarchical model clustering transcriptome data into coordinated modules, and modules into groups across the time course, giving insight into the concerted transcriptional regulations especially the regulation corresponding to erythromycin production of S. erythraea. This strategy may be extendable to studies on other prokaryotic microorganisms.