Previously, we described a novel pH-responsive RNA element in Escherichia coli that resides in the 5′ untranslated region of the alx gene and controls its translation in a pH-dependent manner. Under normal growth conditions, this RNA region forms a translationally inactive structure, but when transcribed under alkaline conditions, it forms an active structure producing the Alx protein. We identified two distinct transcriptional pause sites and proposed that pausing at these sites interfered with the formation of the inactive structure while facilitating folding of the active one. Alkali increases the longevity of pausing at these sites, thereby promoting folding of the translationally active form of alx RNA. We show here that mutations that modify the extent and/or position of pausing, although silent with regard to structure stability per se, greatly influence the dynamics of folding and thereby translation. Our data illustrate the mechanistic design of alx regulation, relying on precise temporal and spatial characteristics. We propose that this unique design provides an opportunity for environmental signals such as pH to introduce structural changes in the RNA and thereby modulate expression.
Bibliographical noteFunding Information:
This work was supported by the Israel Science Foundation founded by The Israel Academy of Sciences and Humanities [911/09]; by Deutsche Forschungsgemeinschaft research grant [VO 875/5-1]; and by Israel Centers of Research Excellence (ICORE), Chromatin and RNA [1796/12]. Funding for open access charge: The Israel Science Foundation founded by The Israel Academy of Sciences and Humanities [911/09] and Deutsche Forschungsgemeinschaft research grant [VO 875/5-1].