Exploring biogenesis and functions of 3'UTR-derived small regulatory RNAs

大多数对小调控RNA(SRNAs)的研究都集中在细菌染色体基因间区非编码基因的转录本上。然而，越来越多的证据表明，信使核糖核酸基因的3个基序区域构成了一个额外的大型储存库，新的sRNA由此进化而来。到目前为止，很少有人从功能上研究这种3-启动子UTR衍生的sRNA，这类新兴的细菌核转录调节因子的生物发生原理和细胞靶标的调控仍有待阐明。在这个项目中，我们将专注于通过mRNA加工产生的3个基元的非编码区来源的sRNA，并询问这些sRNA是否与来自其亲代mRNAs的蛋白质具有相同的途径。为此，我们选择了两个有希望的候选基因，CpxQ和RbbD，它们分别被预测在包膜压力控制和代谢调节中发挥作用。这两个3-启动子的sRNAs都是保守的，与Hfq蛋白结合，并显示出条件依赖的功能；一个由细菌CPx应激途径中重要的伴侣的单顺反子mRNA组成，另一个由重要代谢酶的长操纵子mRNA组成。这两个sRNAs的吸引力还有其他原因：CpxQ可能是保守的CpxR介导的应激反应中缺失的一环，正在成为一个新的药物靶点；RbbD可能是迄今已知的最短的与HfQ相关的功能最短的sRNA，并有望成为高分辨率结构分析的模型。更广泛地说，了解这些由3个基序UTR衍生的sRNA的细胞作用将提供对为什么在某些情况下细胞更喜欢调控RNA分子而不是调控蛋白质的根本问题的洞察。

Most investigations of small regulatory RNAs (sRNAs) have focused on transcripts from noncoding genes in the intergenic regions of bacterial chromosomes. However, there is growing evidence to suggest that the 3-prime regions of mRNA genes constitute an additional large reservoir from which new sRNAs evolve. To date, very few such 3-prime UTR-derived sRNAs have been investigated with respect to function, and both the biogenesis principles and regulation of the cellular targets of this emerging class of bacterial riboregulators remain to be elucidated. In this project we will focus on 3-prime UTR-derived sRNAs that are generated through mRNA processing and ask if such sRNAs function in the same pathway as the proteins from their parental mRNAs. To this end, we have selected two promising candidates, CpxQ and RybD, with predicted roles in envelope stress control and metabolic regulation, respectively. Both these 3-prime UTR-derived sRNAs are well-conserved, associate with Hfq protein, and show expression indicative of a condition-dependent function; one is made from a monocistronic mRNA of an important chaperone in the bacterial Cpx stress pathway, the other from the long operon mRNA of important metabolic enzymes. Each of these two sRNAs is attractive for additional reasons: CpxQ may be a missing link in the conserved CpxR-mediated stress response that is emerging as a new drug target; RybD may be the shortest functional Hfq-associated sRNA known to date and lends itself as a model for high-resolution structural analysis. More generally, understanding the cellular roles of these 3-prime UTR-derived sRNAs will provide insight into the fundamental question why in some situations cells favour regulatory RNA molecules over regulatory proteins.