A pH-responsive riboregulator

Gal Nechooshtan, Maya Elgrably-Weiss, Abigail Sheaffer, Eric Westhof, Shoshy Altuvia*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

111 Scopus citations


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.

Original languageAmerican English
Pages (from-to)2650-2662
Number of pages13
JournalGenes and Development
Issue number22
StatePublished - 15 Nov 2009


  • Alkaline conditions
  • RNA regulator
  • Transcriptional pausing
  • Translation control


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