Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function.
Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function.
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DOI：
10.1371/journal.pgen.1005613
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发表时间：
2015-10
期刊：
影响因子：
4.5
通讯作者：
Ignatova Z
中科院分区：
文献类型：
--
作者：
Del Campo C;Bartholomäus A;Fedyunin I;Ignatova Z
信使RNA充当DNA和翻译核糖体之间的信息分子。新出现的证据将 mRNA 置于中央细胞过程中，超出了其作为信息实体的主要功能。尽管个别例子表明 mRNA 的特定结构特征调节翻译和转录稳定性，但它们在整个细菌转录组中的作用和功能仍然未知。结合三种测序方法，提供全局 mRNA 二级结构、翻译效率和 mRNA 丰度的高分辨率视图，我们揭示了大肠杆菌 mRNA 的结构特征及其对翻译和 mRNA 降解的影响。编码序列上游结构不良的位点充当核糖体的额外非特异性结合位点，其二级结构倾向的程度与基因表达负相关。编码序列内的二级结构是高度动态的，并且仅影响非常小的位置子集内的翻译。终止密码子上游的二级结构富含由 UAA 密码子终止的基因，可能对翻译终止有影响。整体分析进一步证实了 RNase E 启动核酸内切切割的共同识别特征。这项工作首次确定了大肠杆菌 RNA 结构组，强调了 mRNA 二级结构作为多种过程（包括翻译和 mRNA 降解）的直接效应子的贡献。信使 RNA (mRNA) 本质上易于形成更高级的结构，该结构针对 mRNA 在细胞中的稳定性进行了优化。我们利用高通量测序技术的最新发展，并将其与 RNA 结构探测方法结合起来，在全球转录组范围内提供大肠杆菌 mRNA 二级结构的高分辨率视图。我们的数据强调了 mRNA 二级结构作为多种过程的直接效应器的贡献，包括翻译起始和终止、mRNA 丰度和降解。这超出了 mRNA 作为遗传信息传递中的信息实体的主要功能，并将其置于调节翻译保真度的中心位置。
Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation. Messenger RNA (mRNA) is intrinsically prone to form higher order structures which is optimized for mRNA stability in the cell. We took advantage of recent developments in high throughput sequencing technologies and coupled them with RNA structure-probing approaches to provide a high resolution view of the mRNA secondary structure of Escherichia coli on a global, transcriptome-wide scale. Our data highlight the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation initiation and termination, mRNA abundance and degradation. This goes beyond the primary function of mRNA as an information entity in the transfer of the genetic information and places it more centrally in regulating fidelity of translation.