Changes in transcriptional pausing modify the folding dynamics of the pH-responsive RNA element.
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.
Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
Gal
G
Nechooshtan
Maya
M
Elgrably-Weiss
Shoshy
S
Altuvia
D020121:5' Untranslated Regions; D001483:Base Sequence; D004926:Escherichia coli / Q000235:genetics; D029968:Escherichia coli Proteins / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D006863:Hydrogen-Ion Concentration; D026901:Membrane Transport Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D059370:RNA Folding; D012329:RNA, Bacterial / Q000737:chemistry*; D038621:Regulatory Sequences, Ribonucleic Acid; D014158:Transcription, Genetic
D020121:5' Untranslated Regions; C586476:Alx protein, E coli; D029968:Escherichia coli Proteins; D026901:Membrane Transport Proteins; D012329:RNA, Bacterial; D038621:Regulatory Sequences, Ribonucleic Acid