An E. coli small RNA inhibits translation initiation from a distance

In bacterial systems, small RNA (sRNA)-dependent translational repression is commonly carried out via sRNA-mRNA base pairing interactions near the Shine-Dalgarno (SD) region. In this so-called “canonical” mechanism, the sRNA is the direct regulator; it competes with the initiating ribosomes while the chaperone protein Hfq plays a supporting role. Contrary to this widely accepted model, there are a few examples in the literature where the sRNA base pairs far from the SD region, yet translation of the target mRNA is still inhibited. Mechanistically, non-canonical translation regulation is one of the least understood aspects of sRNA biology. In the targetome of an E. coli sRNA SgrS, manXYZ is a non-canonical target where SgrS base pairs at two distinct sites that are far from the SD regions of manX and manY, yet translation of these two cistrons are repressed by SgrS. We found that manX translation is controlled by a molecular role-reversal mechanism where an Hfq binding site is directly adjacent to the manX ribosome binding site. In this regulatory mechanism, SgrS plays the role of a guide to recruit Hfq to the appropriate binding site to form the silencing complex. We also report that SgrS forms a duplex with a uridine-rich translation-enhancing element in the manY 5' untranslated region. Notably, we show that the enhancer is ribosome-dependent and that the small ribosomal subunit protein S1 interacts with the enhancer to promote translation of manY. In collaboration with the chaperone protein Hfq, SgrS interferes with the interaction between the translation enhancer and the r-protein S1 to repress translation of manY mRNA. Since bacterial translation is often initiated from a nonlinear ribosome binding site, sRNA-mediated enhancer silencing could be a common mode of gene regulation.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Microbiology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2020

Author dc:creator

• Azam, Muhammad Shafiul

Contributors dc:contributor

• Vanderpool, Carin K.
• Whitaker, Rachel J.
• Slauch, James M.
• Olsen, Gary J.

• sRNA, Hfq, Enhancer

Statement dc:rights

• Copyright 2019 Muhammad Shafiul Azam

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/106189

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/106189