title: Quantitative effect of target translation on small RNA efficacy reveals a novel mode of interaction.
abstract: 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.
authors.affiliation: Department of Physics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Anat
authors.initials: A
authors.lastname: Lavi-Itzkovitz
authors.affiliation: Department of Physics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Neil
authors.initials: N
authors.lastname: Peterman
authors.affiliation: Department of Physics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Jost
authors.affiliation: Department of Physics and FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA elevine@fas.harvard.edu.
authors.forename: Erel
authors.initials: E
authors.lastname: Levine
mesh_terms: D020121:5' Untranslated Regions; D001665:Binding Sites; D020868:Gene Silencing; D008957:Models, Genetic; D014176:Protein Biosynthesis; D058727:RNA, Small Untranslated / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism
chemical_list: D020121:5' Untranslated Regions; D058727:RNA, Small Untranslated