Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function. Escherichia coli

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. Overall design: Structural probing of the total RNA of E.coli under normal conditions

信使RNA（mRNA）是DNA与进行翻译的核糖体之间的信息传递分子。越来越多的研究证据表明，mRNA的功能远不止作为信息传递载体这一核心作用，而是广泛参与诸多关键细胞过程。尽管已有个别研究揭示mRNA的特定结构特征可调控翻译过程与转录本稳定性，但目前针对整个细菌转录组中mRNA结构的整体功能与作用机制仍不明晰。本研究结合三种测序技术，实现了对大肠杆菌（E. coli）全基因组范围内mRNA二级结构、翻译效率与mRNA表达丰度的高分辨率解析，进而揭示了大肠杆菌mRNA中与翻译及mRNA降解相关的结构特征：编码序列上游的低结构化区域可作为核糖体的额外非特异性结合位点，且该区域的二级结构形成倾向与基因表达水平呈负相关；编码序列内部的二级结构具有高度动态性，仅在极少数位点上对翻译过程产生影响；终止密码子上游的二级结构在以UAA作为终止密码子的基因中显著富集，这可能与翻译终止过程相关。本次全基因组分析进一步证实了核糖核酸酶E（RNase E）介导内切核酸切割的通用识别特征。本研究首次构建了大肠杆菌的RNA结构组（RNA structurome），阐明了mRNA二级结构作为直接效应分子在翻译、mRNA降解等多种细胞过程中的重要贡献。整体实验设计：在正常培养条件下对大肠杆菌的总RNA进行结构探测。