Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli.
Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli.
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DOI：
10.1186/1471-2164-8-48
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发表时间：
2007-02-13
期刊：
影响因子：
4.4
通讯作者：
Goto, Susumu
中科院分区：
文献类型：
--
作者：
Okuda, Shujiro;Kawashima, Shuichi;Kobayashi, Kazuo;Ogasawara, Naotake;Kanehisa, Minoru;Goto, Susumu
操纵子结构在原核生物的转录调控中起着重要作用。然而，关于复杂操纵子结构的研究较少，其中转录单位随着环境条件的变化而变化。有关这些复杂操纵子的信息有助于预测和分析操纵子结构，以及了解基因功能和转录调控。我们系统地分析了从ODB和RegulonDB获得的枯草芽孢杆菌和大肠杆菌中实验验证的转录单位(TU)。为了了解TU和操纵子之间的关系，我们定义了一个新的相邻基因对的分类系统，根据基因协同调节的水平将其分为三组：操纵子对(OP)属于同一TU，亚操纵子对(SOP)位于操纵子内的转录边界，非操纵子对(NOP)属于不同的操纵子。因此，我们发现基因共调控水平与基因间距离和基因表达水平相关。进一步的分析表明，它们还与大约200个原核生物基因组的保守性水平有关。最有趣的是，我们发现SOP中的功能关联更多地出现在环境和遗传信息过程中。复杂的操纵子结构与基因组结构和基因表达谱相关。这种复杂调控的操纵子允许根据环境条件的不同而产生不同的功能。这些调节机制有助于适应细胞周围发生的各种变化。此外，这种差异可能在基因组间基因顺序的进化中发挥重要作用。
Operon structures play an important role in transcriptional regulation in prokaryotes. However, there have been fewer studies on complicated operon structures in which the transcriptional units vary with changing environmental conditions. Information about such complicated operons is helpful for predicting and analyzing operon structures, as well as understanding gene functions and transcriptional regulation. We systematically analyzed the experimentally verified transcriptional units (TUs) in Bacillus subtilis and Escherichia coli obtained from ODB and RegulonDB. To understand the relationships between TUs and operons, we defined a new classification system for adjacent gene pairs, divided into three groups according to the level of gene co-regulation: operon pairs (OP) belong to the same TU, sub-operon pairs (SOP) that are at the transcriptional boundaries within an operon, and non-operon pairs (NOP) belonging to different operons. Consequently, we found that the levels of gene co-regulation was correlated to intergenic distances and gene expression levels. Additional analysis revealed that they were also correlated to the levels of conservation across about 200 prokaryotic genomes. Most interestingly, we found that functional associations in SOPs were more observed in the environmental and genetic information processes. Complicated operon strucutures were correlated with genome organization and gene expression profiles. Such intricately regulated operons allow functional differences depending on environmental conditions. These regulatory mechanisms are helpful in accommodating the variety of changes that happen around the cell. In addition, such differences may play an important role in the evolution of gene order across genomes.