Department of Molecular Biology, Princeton University, Lewis Thomas Laboratories, Princeton, NJ 08544, USA.
Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, D-82152 Martinsried, Germany.
Nucleic Acids Res. 2018 Nov 16;46(20):10969-10982. doi: 10.1093/nar/gky765.
Bacterial small RNAs (sRNAs) are a heterogeneous group of post-transcriptional regulators that often act at the heart of large networks. Hundreds of sRNAs have been discovered by genome-wide screens and most of these sRNAs exert their functions by base-pairing with target mRNAs. However, studies addressing the molecular roles of sRNAs have been largely confined to gamma-proteobacteria, such as Escherichia coli. Here we identify and characterize a novel sRNA, ChvR, from the alpha-proteobacterium Caulobacter crescentus. Transcription of chvR is controlled by the conserved two-component system ChvI-ChvG and it is expressed in response to DNA damage, low pH, and growth in minimal medium. Transient over-expression of ChvR in combination with genome-wide transcriptome profiling identified the mRNA of the TonB-dependent receptor ChvT as the sole target of ChvR. Genetic and biochemical analyses showed that ChvR represses ChvT at the post-transcriptional level through direct base-pairing. Fine-mapping of the ChvR-chvT interaction revealed the requirement of two distinct base-pairing sites for full target regulation. Finally, we show that ChvR-controlled repression of chvT is independent of the ubiquitous RNA-chaperone Hfq, and therefore distinct from previously reported mechanisms employed by prototypical bacterial sRNAs. These findings have implications for the mechanism and evolution of sRNA function across bacterial species.
细菌小 RNA（sRNA）是一组异质的转录后调控因子，它们通常处于大型网络的核心。通过全基因组筛选已经发现了数百种 sRNA，其中大多数通过与靶 mRNA 碱基配对来发挥作用。然而，针对 sRNA 分子作用的研究主要局限于γ-变形菌，如大肠杆菌。在这里，我们从α-变形菌新月柄杆菌中鉴定并表征了一种新型 sRNA ChvR。ChvR 的转录受保守的双组分系统 ChvI-ChvG 控制，并响应 DNA 损伤、低 pH 值和在最小培养基中生长而表达。ChvR 的瞬时过表达与全基因组转录组谱分析相结合，确定了 TonB 依赖性受体 ChvT 的 mRNA 是 ChvR 的唯一靶标。遗传和生化分析表明，ChvR 通过直接碱基配对在转录后水平抑制 ChvT。ChvR-chvT 相互作用的精细定位揭示了完全靶标调节所需的两个不同的碱基配对位点。最后，我们表明 ChvR 控制的 chvT 抑制不依赖于普遍存在的 RNA 伴侣 Hfq，因此与先前报道的典型细菌 sRNA 所采用的机制不同。这些发现对 sRNA 功能在细菌物种中的机制和进化具有重要意义。
