Hierarchy in Hfq Chaperon Occupancy of Small RNA Targets Plays a Major Role in Their Regulation.

Cell Reports
Raya Faigenbaum-RommHanah Margalit

Abstract

Bacterial small RNAs (sRNAs) are posttranscriptional regulators of gene expression that base pair with complementary sequences on target mRNAs, often in association with the chaperone Hfq. Here, using experimentally identified sRNA-target pairs, along with gene expression measurements, we assess basic principles of regulation by sRNAs. We show that the sRNA sequence dictates the target repertoire, as point mutations in the sRNA shift the target set correspondingly. We distinguish two subsets of targets: targets showing changes in expression levels under overexpression of their sRNA regulator and unaffected targets that interact more sporadically with the sRNA. These differences among targets are associated with their Hfq occupancy, rather than with the sRNA-target base-pairing potential. Our results suggest that competition among targets over Hfq binding plays a major role in the regulatory outcome, possibly awarding targets with higher Hfq binding efficiency an advantage in the competition over binding to the sRNA.

Citations

Jun 4, 2020·MSystems·Lars Barquist
Mar 12, 2021·Molecular Cell·Ewelina M Małecka, Sarah A Woodson
Oct 21, 2020·Trends in Genetics : TIG·Evelyne Ng Kwan LimEric Massé
Jul 25, 2021·International Journal of Molecular Sciences·Katrin M H EisenhardtGabriele Klug
Aug 10, 2021·Frontiers in Microbiology·Paolo CostaRoberto Mazzoli

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Datasets Mentioned

BETA
E-MTAB-8224
E-MTAB-8229

Methods Mentioned

BETA
immunoprecipitation
RIL-seq
RNA-seq
dissection
PCR
Assay
profiler

Software Mentioned

MEME
cutadapt
ppcor R package
MUSCLE
R
RNAduplex
ArcZ
RNAfold
DESeq2
Conservation profiler

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