Ghandour Rabea, Devlitsarov Daniel, Popp Phillip, Melamed Sahar, Huber Michaela, Siemers Malte, Krüger Thomas, Kniemeyer Olaf, Klingl Andreas, Brakhage Axel A, Erhardt Marc, Papenfort Kai
Friedrich Schiller University, Institute of Microbiology, 07743 Jena, Germany.
Humboldt-Universität zu Berlin, Institute for Biology, 10115 Berlin, Germany.
Nucleic Acids Res. 2025 Feb 8;53(4). doi: 10.1093/nar/gkae1283.
Gene regulation at the post-transcriptional level is prevalent in all domains of life. In bacteria, ProQ-like proteins have emerged as important RNA chaperones facilitating RNA stability and RNA duplex formation. In the major human pathogen Vibrio cholerae, post-transcriptional gene regulation is key for virulence, biofilm formation, and antibiotic resistance, yet the role of ProQ has not been studied. Here, we show that ProQ interacts with hundreds of transcripts in V. cholerae, including the highly abundant FlaX small RNA (sRNA). Global analyses of RNA duplex formation using RIL-Seq (RNA interaction by ligation and sequencing) revealed a vast network of ProQ-assisted interactions and identified a role for FlaX in motility regulation. Specifically, FlaX base-pairs with multiple sites on the flaB flagellin mRNA, preventing 30S ribosome binding and translation initiation. V. cholerae cells lacking flaX display impaired motility gene expression, altered flagella composition and reduced swimming in liquid environments. Our results provide a global view on ProQ-associated RNA duplex formation and pinpoint the mechanistic and phenotypic consequences associated with ProQ-associated sRNAs in V. cholerae.
转录后水平的基因调控在生命的所有领域都很普遍。在细菌中，类ProQ蛋白已成为促进RNA稳定性和RNA双链体形成的重要RNA伴侣。在主要的人类病原体霍乱弧菌中，转录后基因调控是毒力、生物膜形成和抗生素抗性的关键，但ProQ的作用尚未得到研究。在这里，我们表明ProQ与霍乱弧菌中的数百种转录本相互作用，包括高度丰富的FlaX小RNA（sRNA）。使用RIL-Seq（通过连接和测序进行RNA相互作用）对RNA双链体形成进行的全局分析揭示了一个由ProQ辅助的相互作用的庞大网络，并确定了FlaX在运动调节中的作用。具体而言，FlaX与flaB鞭毛蛋白mRNA上的多个位点形成碱基对，阻止30S核糖体结合和翻译起始。缺乏flaX的霍乱弧菌细胞表现出运动基因表达受损、鞭毛组成改变以及在液体环境中的游动能力降低。我们的结果提供了关于ProQ相关RNA双链体形成的全局视图，并指出了与霍乱弧菌中ProQ相关sRNA相关的机制和表型后果。
