Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism with respect to global protein-protein networks. Yet, there has been no global census of RNA/protein complexes in this model species of microbiology. Here, we performed Grad-seq to establish an RNA/protein complexome, reconstructing sedimentation profiles in a glycerol gradient for ∼85% of all E. coli transcripts and ∼49% of the proteins. These include the majority of small noncoding RNAs (sRNAs) detectable in this bacterium as well as the general sRNA-binding proteins, CsrA, Hfq and ProQ. In presenting use cases for utilization of these RNA and protein maps, we show that a stable association of RyeG with 30S ribosomes gives this seemingly noncoding RNA of prophage origin away as an mRNA of a toxic small protein. Similarly, we show that the broadly conserved uncharacterized protein YggL is a 50S subunit factor in assembled 70S ribosomes. Overall, this study crucially extends our knowledge about the cellular interactome of the primary model bacterium E. coli through providing global RNA/protein complexome information and should facilitate functional discovery in this and related species.

中文翻译：

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Grad-seq照亮了模型细菌大肠杆菌中无法识别的RNA和蛋白质复合物。

稳定的蛋白质复合物，包括与RNA形成的复合物，是每个活细胞的主要组成部分。就全球蛋白质-蛋白质网络而言，大肠杆菌一直是领先的细菌生物。但是，在这种微生物学的模型物种中，尚未进行RNA /蛋白质复合物的全球普查。在这里，我们进行了Grad-seq建立RNA /蛋白质复合物组，以甘油梯度重建了约85％的大肠杆菌的沉降曲线。转录本和约49％的蛋白质。这些包括在该细菌中可检测到的大多数小非编码RNA（sRNA），以及一般的sRNA结合蛋白CsrA，Hfq和ProQ。在介绍利用这些RNA和蛋白质图的使用案例时，我们显示RyeG与30S核糖体的稳定结合将这种看似非编码的Prohage来源的RNA作为有毒小蛋白的mRNA送走了。同样，我们显示，广泛保守的未表征蛋白YggL是组装的70S核糖体中的50S亚基因子。总体而言，这项研究通过提供全球RNA /蛋白质复合体信息，从根本上扩展了我们对主要模型细菌大肠杆菌细胞相互作用组的了解，并应促进该物种及相关物种的功能发现。