Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation

Abstract

By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions. We identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. We rediscovered known and identified novel sRNA seed sequences. The sRNA-mRNA interactions identified by CLASH have strong base-pairing potential and are highly enriched for complementary sequence motifs, even those supported by only a few reads. Yet, steady state levels of most mRNA targets were not significantly affected upon over-expression of the sRNA regulator. Our results reinforce the idea that the reproducibility of the interaction, not base-pairing potential, is a stronger predictor for a regulatory outcome.

Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping

“…The predominant target for FtsO in the RIL-seq datasets was the sRNA RybB ( Figure 8A ) followed by the sRNA CpxQ ( Melamed et al, 2020 ). The Hfq-mediated FtsO-RybB interaction was also detected in an independent CLASH dataset ( Iosub et al, 2020 ). We hypothesized that FtsO functions as a sponge for RybB and CpxQ, which are induced by misfolded outer membrane proteins and inner membrane proteins, respectively, and down-regulate the corresponding classes of proteins (reviewed in Hör et al, 2020 ).…”

The mRNA derived MalH sRNA contributes to alternative carbon source utilization by tuning maltoporin expression in E. coli

“…Thus, MalT and MalH join both promote lamB expression, forming a mixed coherent FFL. The grey lines indicate interactions that were detected by Hfq CLASH and RIL-seq [33,34] and experimentally verified interactions either by other groups (MicA and lamB [20]) or in this work (MalH, ompC). The bold black line connecting MalH and OmpA indicates that the interaction was detected in Hfq CLASH and RIL-seq data [33,34], verified by over-expression but not fully verified by our GFP reporter experiments.…”

Regulatory roles of 5′ UTR and ORF-internal RNAs detected by 3′ end mapping

“…The predominant target for FtsO in the RIL-seq datasets was the sRNA RybB ( Figure 8A) followed by the sRNA CpxQ (Melamed et al, 2020). The Hfq-mediated FtsO-RybB interaction was also detected in an independent CLASH dataset (Iosub et al, 2020).…”