RNA-protein interactions are the crucial basis for many steps of bacterial gene expression, including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast to recent progress in the analysis of Gram-negative bacteria, knowledge about RNA-protein complexes in Gram-positive species remains scarce. Here, we used the Grad-seq approach to draft a comprehensive landscape of such complexes in Streptococcus pneumoniae, in total determining the sedimentation profiles of ~ 88% of the transcripts and ~ 62% of the proteins of this important human pathogen. Analysis of in-gradient distributions and subsequent tag-based protein capture identified interactions of the exoribonuclease Cbf1/YhaM with sRNAs that control bacterial competence for DNA uptake. Unexpectedly, the nucleolytic activity of Cbf1 stabilizes these sRNAs, thereby promoting their function as repressors of competence. Overall, these results provide the first RNA/protein complexome resource of a Gram-positive species and illustrate how this can be utilized to identify new molecular factors with functions in RNA-based regulation of virulence-relevant pathways.

中文翻译：

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革兰氏阳性细菌中的Grad-seq显示了能力控制中的核酸外切sRNA激活。

RNA-蛋白质相互作用是细菌基因表达许多步骤的关键基础，包括通过小调节RNA（sRNA）进行转录后控制。与革兰氏阴性菌分析的最新进展形成鲜明对比的是，关于革兰氏阳性菌种中RNA-蛋白质复合物的知识仍然匮乏。在这里，我们使用Grad-seq方法绘制了肺炎链球菌中此类复合物的综合图，总共确定了该重要人类病原体的〜88％的转录本和〜62％的蛋白质的沉降曲线。梯度分布和随后基于标签的蛋白质捕获的分析确定了外切核糖核酸酶Cbf1 / YhaM与控制细菌DNA吸收能力的sRNA的相互作用。出乎意料的是，Cbf1的溶核活性稳定了这些sRNA，从而提升他们作为能力抑制者的功能。总体而言，这些结果提供了革兰氏阳性菌种的首个RNA /蛋白质复合体资源，并说明了如何利用它来鉴定在基于RNA的毒力相关途径调控中具有功能的新分子因子。