Control of bacterial gene expression by the FinO family of RNA chaperones

背景：小的非编码RNA （sRNAs）在被称为RNA伴侣的蛋白质的帮助下，基本上在所有细菌物种中调控基因表达。RNA伴侣蛋白FinO家族是最重要和广泛存在的伴侣蛋白家族之一，在细菌应激反应和水平基因转移（HGT）的调控中起着重要作用。我们的合作者，Xavier Charpentier（里昂）在军团菌中发现了一种叫做RocC的新的FinO伴侣。他的研究小组发现，RocC结合了一个名为RocR的单一sRNA，从而稳定了RocR，并促进了对控制HGT的特定mRNA靶点的抑制。我们着手了解RocC如何特异性结合RNA以及它如何促进sRNA-mRNA配对。我们发现RocC FinO结构域与RocR的发夹尾转录终止子结合，我们继续确定RocC FinO结构域与RocR终止子复合物的晶体结构。该结构提供了与RNA结合的任何FinO伴侣蛋白的第一个视图，并为我们的关键假设提供了基础，这些假设将指导我们在这个项目的下一个学期的实验。假设：我们提出FinO伴侣以一种读取3' ssRNA尾部长度的方式结合转录终止体结构。此外，我们提出结合机制允许重构sRNA，使sRNA- mrna配对。具体目标完善我们对RocC-RocR相互作用的理解。为了了解RocC-RocR结构的功能含义，我们正在构建大量RocC的定点突变以及RocR发夹尾的修饰，以了解结合亲和性/特异性的关键相互作用。这些突变的影响将通过生化和生物物理实验来探讨，并评估它们对军团菌中RocR稳定、基因表达和能力的影响。具体目标2。探讨RocC结合对RocR结构的影响及其与mRNA靶标的相互作用。在前期工作中，我们发现RocR在终止子发夹和sRNA“种子”序列之间采用假结结构，我们提出这必须展开以促进sRNA- mrna配对。我们将通过足迹、核磁共振研究、伪结结构的结晶以及通过小角度x射线散射分析更大规模的RocC-RocR结构来验证这一想法。这些假设将通过军团菌体内研究得到进一步验证。具体目标3。了解细菌中FinO伴侣蛋白功能的广度。利用一组跨越FinO系统发育树的FinO伴侣，我们将比较它们的结构、RNA结合特异性和RNA配对活性，以了解FinO功能的保守程度，这些作用将在结构域交换实验中进一步验证。这些实验将揭示这些伴侣蛋白之间特异性差异的基础，以及这些蛋白如何促进RNA-RNA配对。

Background: Small non-coding RNAs (sRNAs) regulate gene expression in essentially all bacterial species with the assistance of proteins called RNA chaperones. The FinO family of RNA chaperones is one of the most important and widespread chaperone families with roles in regulation of bacterial stress responses and horizontal gene transfer (HGT). Our collaborator, Xavier Charpentier (Lyon) discovered a new FinO chaperone in Legionella called RocC. His group showed that RocC binds a single sRNA called RocR, thereby stabilizing RocR and facilitating the repression of specific mRNA targets that control HGT. We set out to understand how RocC specifically binds RNA and how it facilitates sRNA-mRNA pairing. We showed that the RocC FinO domain binds the hairpin-tail transcription terminator of RocR and we went on to determine the crystal structure of the RocC FinO domain in complex with a RocR terminator. This structure provides the first view of any FinO chaperone bound to its RNA and provides the basis for our key hypotheses that will guide our experiments in the next term of this program. Hypothesis: We propose that FinO chaperones bind transcriptional terminator structures in a manner that reads the length of the 3' ssRNA tail. In addition, we propose that the mechanism of binding allows the remodeling of the sRNA to enable sRNA-mRNA pairing. Specific Aim 1. Refining our understanding of RocC-RocR interactions. To understand the functional implications of our RocC-RocR structure, we are constructing a large set of site-directed point mutations in RocC as well as modifications in the RocR hairpin-tail to understand critical interactions for binding affinity/specificity. The effects of these mutations will be probed through biochemical and biophysical assays, and their effects on RocR stabilization, gene expression and competence will be assessed in Legionella. Specific Aim 2. Probing the effects of RocC binding on RocR structure and interactions with mRNA targets. In preliminary work, we showed that RocR adopts a pseudoknot structure between the terminator hairpin and the sRNA "seed" sequence, and we propose that this must unfold to facilitate sRNA-mRNA pairing. We will test this idea through footprinting, NMR studies, crystallization of the pseudoknot structure and analysis of larger scale RocC-RocR structures via small angle X-ray scattering. These hypotheses will be further tested through in vivo studies in Legionella. Specific Aim 3. Understanding the breadth of FinO chaperone function in bacteria. Using a set of FinO chaperones that span the FinO phylogenetic tree, we will compare their structures, RNA binding specificities, and RNA pairing activities to understand the degree of conservation of FinO functions, and these roles will be further tested in domain-swap experiments. These experiments should reveal the basis for specificity differences between these chaperones, as well as how these proteins facilitate RNA-RNA pairing.