Small regulatory RNAs (sRNAs) acting in concert with the RNA chaperone Hfq are prevalent in many bacteria and typically act by base-pairing with multiple target transcripts. In the human pathogen Vibrio cholerae, sRNAs play roles in various processes including antibiotic tolerance, competence, and quorum sensing (QS). Here, we use RIL-seq (RNA-interaction-by-ligation-and-sequencing) to identify Hfq-interacting sRNAs and their targets in V. cholerae. We find hundreds of sRNA-mRNA interactions, as well as RNA duplexes formed between two sRNA regulators. Further analysis of these duplexes identifies an RNA sponge, termed QrrX, that base-pairs with and inactivates the Qrr1-4 sRNAs, which are known to modulate the QS pathway. Transcription of qrrX is activated by QrrT, a previously uncharacterized LysR-type transcriptional regulator. Our results indicate that QrrX and QrrT are required for rapid conversion from individual to community behaviours in V. cholerae.

与 RNA 伴侣 Hfq 协同作用的小调节 RNA (sRNA) 在许多细菌中普遍存在，通常通过与多个目标转录物进行碱基配对来发挥作用。在人类病原体霍乱弧菌中，sRNA 在多种过程中发挥作用，包括抗生素耐受性、能力和群体感应 (QS)。在这里，我们使用 RIL-seq（通过连接和测序进行的 RNA 相互作用）来识别 Hfq 相互作用的 sRNA 及其在霍乱弧菌中的靶标。我们发现了数百种 sRNA-mRNA 相互作用，以及在两个 sRNA 调节剂之间形成的 RNA 双链体。对这些双链体的进一步分析确定了一种称为 QrrX 的 RNA 海绵，它与已知可调节 QS 通路的 Qrr1-4 sRNA 碱基配对并使其失活。qrrX的转录由 QrrT 激活，QrrT 是一种先前未表征的 LysR 型转录调节因子。我们的结果表明，QrrX 和 QrrT 是霍乱弧菌从个体行为快速转变为群落行为所必需的。