Quantitative effect of target translation on small RNA efficacy reveals a novel mode of interaction

Anat Lavi-Itzkovitz, Neil Peterman, Daniel Jost, Erel Levine

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


Small regulatory RNAs (sRNAs) in bacteria regulate many important cellular activities under normal conditions and in response to stress. Many sRNAs bind to the mRNA targets at or near the 5' untranslated region (UTR) resulting in translation inhibition and accelerated degradation. Often the sRNA-binding site is adjacent to or overlapping with the ribosomal binding site (RBS), suggesting a possible interplay between sRNA and ribosome binding. Here we combine quantitative experiments with mathematical modeling to reveal novel features of the interaction between small RNAs and the translation machinery at the 5'UTR of a target mRNA. By measuring the response of a library of reporter targets with varied RBSs, we find that increasing translation rate can lead to increased repression. Quantitative analysis of these data suggests a recruitment model, where bound ribosomes facilitate binding of the sRNA. We experimentally verified predictions of this model for the cell-to-cell variability of target expression. Our findings offer a framework for understanding sRNA silencing in the context of bacterial physiology.

Original languageEnglish
Pages (from-to)12200-12211
Number of pages12
JournalNucleic Acids Research
Issue number19
StatePublished - 29 Oct 2014
Externally publishedYes

Bibliographical note

Publisher Copyright:
© The Author(s) 2014.


We thank Cari Vanderpool, Jorg Vogel, Richard A. Lease and Arvind Subramaniam for reagents, Nancy Kleckner and members of the Levine lab for discussions. National Science Foundation [MCB1121057]. Funding for open access charge: National Science Foundation [MCB1121057].

FundersFunder number
National Science FoundationMCB1121057
Directorate for Biological Sciences1121057


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