UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, UK.
Nucleic Acids Res. 2021 Jun 21;49(11):6399-6419. doi: 10.1093/nar/gkab444.
sRNAs are a taxonomically-restricted but transcriptomically-abundant class of post-transcriptional regulators. While of major importance for adaption to the environment, we currently lack global-scale methodology enabling target identification, especially in species without known RNA hub proteins (e.g. Hfq). Using psoralen RNA cross-linking and Illumina-sequencing we identify RNA-RNA interacting pairs in vivo in Bacillus subtilis, resolving previously well-described interactants. Although sRNA-sRNA pairings are rare (compared with sRNA-mRNA), we identify a robust example involving the conserved sRNA RoxS and an unstudied sRNA RosA (Regulator of sRNA A). We show RosA to be the first confirmed RNA sponge described in a Gram-positive bacterium. RosA interacts with at least two sRNAs, RoxS and FsrA. The RosA/RoxS interaction not only affects the levels of RoxS but also its processing and regulatory activity. We also found that the transcription of RosA is repressed by CcpA, the key regulator of carbon-metabolism in B. subtilis. Since RoxS is already known to be transcriptionally controlled by malate via the transcriptional repressor Rex, its post-transcriptional regulation by CcpA via RosA places RoxS in a key position to control central metabolism in response to varying carbon sources.
sRNAs 是一类具有分类限制但转录丰富的转录后调控因子。虽然它们对适应环境具有重要意义，但我们目前缺乏能够进行靶标识别的全局规模方法，特别是在没有已知 RNA 枢纽蛋白（例如 Hfq）的物种中。我们使用补骨脂素 RNA 交联和 Illumina 测序，在枯草芽孢杆菌体内鉴定出 RNA-RNA 相互作用对，解决了以前描述过的相互作用。尽管 sRNA-sRNA 配对很少（与 sRNA-mRNA 相比），但我们发现了一个涉及保守 sRNA RoxS 和一个未研究的 sRNA RosA（sRNA A 的调节剂）的稳健例子。我们表明 RosA 是第一个在革兰氏阳性菌中被确认的 RNA 海绵。RosA 与至少两种 sRNA，RoxS 和 FsrA 相互作用。RosA/RoxS 相互作用不仅影响 RoxS 的水平，还影响其加工和调节活性。我们还发现 RosA 的转录受到 CcpA 的抑制，CcpA 是枯草芽孢杆菌碳代谢的关键调节剂。由于 RoxS 已经通过转录抑制剂 Rex 被转录调控，因此 CcpA 通过 RosA 对其进行的转录后调控使其处于控制中心代谢的关键位置，以响应不同的碳源。
