title: A pH-responsive riboregulator.
abstract: The locus alx, which encodes a putative transporter, was discovered previously in a screen for genes induced under extreme alkaline conditions. Here we show that the RNA region preceding the alx ORF acts as a pH-responsive element, which, in response to high pH, leads to an increase in alx expression. Under normal growth conditions this RNA region forms a translationally inactive structure, but when exposed to high pH, a translationally active structure is formed to produce Alx. Formation of the active structure occurs while transcription is in progress under alkaline conditions and involves pausing of RNA polymerase at two distinct sites. Alkali increases the longevity of pausing at these sites and thereby interferes with formation of the inactive structure and promotes folding of the active one. The alx locus represents the first example of a pH-responsive riboregulator of gene expression, introducing a novel regulatory mechanism that involves RNA folding dynamics driven by pH.
authors.affiliation: Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
authors.forename: Gal
authors.initials: G
authors.lastname: Nechooshtan
authors.forename: Maya
authors.initials: M
authors.lastname: Elgrably-Weiss
authors.forename: Abigail
authors.initials: A
authors.lastname: Sheaffer
authors.forename: Eric
authors.initials: E
authors.lastname: Westhof
authors.forename: Shoshy
authors.initials: S
authors.lastname: Altuvia
mesh_terms: D020029:Base Pairing; D017124:Conserved Sequence; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D006863:Hydrogen-Ion Concentration; D009154:Mutation / Q000235:genetics; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000737:chemistry; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics
chemical_list: D029968:Escherichia coli Proteins; D012322:RNA Precursors; D012329:RNA, Bacterial