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Nucleic Acids Res. 2018 Nov 16;46(20):10969-10982. doi: 10.1093/nar/gky765.

Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus.

Author information

1
Department of Molecular Biology, Princeton University, Lewis Thomas Laboratories, Princeton, NJ 08544, USA.
2
Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, D-82152 Martinsried, Germany.
3
Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany.

Abstract

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.

PMID:
30165530
PMCID:
PMC6237742
DOI:
10.1093/nar/gky765
[Indexed for MEDLINE]
Free PMC Article

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