The labs paper on post-transcriptional regulation in E. coli is now on BioRxiv!
Our latest paper on post-transcriptional regulation in E. coli is now online!
To better understand how Escherichia coli acclimatizes to changes in nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover sRNA-target interaction networks. Using this proximity-dependent RNA-RNA ligation method, we uncovered thousands of sRNA-target duplexes associated with the RNA chaperone Hfq at specific growth stages, many of which have not been described before. Our work revealed that 3’UTR-derived sRNAs and sRNA-sRNA interactions are more prevalent than previously anticipated. We uncovered sRNA-target interaction networks that play a role in adaptation to changes in nutrient availability by enhancing the uptake of nutrients from the environment. We describe detailed functional analyses of a novel sRNA (MdoR), the first example of a bacterial 3’UTR-derived sRNA that functions as part of a mixed coherent feed forward loop. MdoR enhances the effectiveness of maltose uptake by (a) inactivating repressive pathways that blocks the accumulation of specific maltose transporters and (b) by reducing the flux of general porins to the outer membrane. Our work suggests that many mRNAs encode regulatory sRNAs embedded within their 3’UTRs, allowing direct regulatory interactions between functionally related mRNAs. Small RNA sponging interactions appear frequently and reveal that major nutritional stress responses are coordinated post-transcriptionally. This provides striking examples of how cells utilize sRNA regulatory networks to integrate multiple signals and regulatory pathways to enhance nutrient stress adaptation.
This work was done in collaboration with the labs of Jai Tree and Gabriella Viero.
The link to the paper: