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

Nucleic Acids Research
Kathrin S FröhlichZemer Gitai

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...Continue Reading

Associated Software

Oct 16, 2018·Zemer GitaiKonrad U. Förstner
Oct 16, 2018·Zemer GitaiKonrad U. Förstner

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Citations

May 6, 2020·Molecular Microbiology·Kathrin S Fröhlich, Kai Papenfort
Feb 16, 2021·Frontiers in Cellular and Infection Microbiology·Jia WangYanguang Cong

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Datasets Mentioned

BETA
GSE104186
NA1000

Methods Mentioned

BETA
PCR
immunoprecipitation
Illumina sequencing
dRNA-seq
co-immunoprecipitation
co-IP

Software Mentioned

READemption
Unix Shell script
Integrated Genome Browser
segemehl
cutadapt
RNAfold
BLAST
DESeq2

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