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Scientific article
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English

Genome-wide profiling of Hfq-bound RNAs reveals the iron-responsive small RNA RusT in Caulobacter crescentus

Published inMBio, e0315323
Publication date2024-03-21
First online date2024-03-21
Abstract

The alphaproteobacteriumCaulobacter crescentusthrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level inC. crescentus. Small RNAs (sRNAs) are a prominent class of regulators of bacterial gene expression, and most sRNAs characterized today engage in direct base-pairing interactions to modulate the translation and/or stability of target mRNAs. In many cases, the ubiquitous RNA chaperone, Hfq, contributes to the establishment of RNA-RNA interactions. Although the deletion of thehfqgene is associated with a severe loss of fitness inC. crescentus, the RNA ligands of the chaperone have remained largely unexplored. Here we report on the identification of coding and non-coding transcripts associated with Hfq inC. crescentusand demonstrate Hfq-dependent post-transcriptional regulation in this organism. We show that the Hfq-bound sRNA RusT is transcriptionally controlled by the NtrYX two-component system and induced in response to iron starvation. By combining RusT pulse expression with whole-genome transcriptome analysis, we determine 16 candidate target transcripts that are deregulated, many of which encode outer membrane transporters. We hence suggest RusT to support remodeling of theC. crescentuscell surface when iron supplies are limited.IMPORTANCEThe conserved RNA-binding protein Hfq contributes significantly to the adaptation of bacteria to different environmental conditions. Hfq not only stabilizes associated sRNAs but also promotes inter-molecular base-pairing interactions with target transcripts. Hfq plays a pivotal role for growth and survival, controlling central metabolism and cell wall synthesis in the oligotrophCaulobacter crescentus. However, direct evidence for Hfq-dependent post-transcriptional regulation and potential oligotrophy inC. crescentushas been lacking. Here, we identified sRNAs and mRNAs associated with Hfqin vivo, and demonstrated the requirement of Hfq for sRNA-mediated regulation, particularly of outer membrane transporters inC. crescentus.

eng
Keywords
  • Caulobacter
  • Hfq
  • NtrYX
  • Iron starvation
  • Small RNA
Citation (ISO format)
VOGT, Laura N et al. Genome-wide profiling of Hfq-bound RNAs reveals the iron-responsive small RNA RusT in Caulobacter crescentus. In: MBio, 2024, p. e0315323. doi: 10.1128/mbio.03153-23
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ISSN of the journal2150-7511
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