A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

Nat Commun. 2022 Jan 11;13(1):199. doi: 10.1038/s41467-021-27790-8.


Riboswitches are structured non-coding RNAs often located upstream of essential genes in bacterial messenger RNAs. Such RNAs regulate expression of downstream genes by recognizing a specific cellular effector. Although nearly 50 riboswitch classes are known, only a handful recognize multiple effectors. Here, we report the 2.60-Å resolution co-crystal structure of a class I type I preQ1-sensing riboswitch that reveals two effectors stacked atop one another in a single binding pocket. These effectors bind with positive cooperativity in vitro and both molecules are necessary for gene regulation in bacterial cells. Stacked effector recognition appears to be a hallmark of the largest subgroup of preQ1 riboswitches, including those from pathogens such as Neisseria gonorrhoeae. We postulate that binding to stacked effectors arose in the RNA World to closely position two substrates for RNA-mediated catalysis. These findings expand known effector recognition capabilities of riboswitches and have implications for antimicrobial development.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Pairing
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Gene Expression Regulation, Bacterial
  • Genetic Vectors / chemistry
  • Genetic Vectors / metabolism
  • Green Fluorescent Proteins / genetics
  • Green Fluorescent Proteins / metabolism
  • Neisseria gonorrhoeae / genetics*
  • Neisseria gonorrhoeae / metabolism
  • Nucleic Acid Conformation
  • Nucleoside Q / biosynthesis
  • Nucleoside Q / chemistry*
  • Pyrimidinones / chemistry*
  • Pyrimidinones / metabolism
  • Pyrroles / chemistry*
  • Pyrroles / metabolism
  • RNA, Bacterial / chemistry*
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism
  • RNA, Messenger / chemistry*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Riboswitch*


  • 7-(aminomethyl)-7-deazaguanine
  • Pyrimidinones
  • Pyrroles
  • RNA, Bacterial
  • RNA, Messenger
  • Recombinant Proteins
  • Riboswitch
  • Green Fluorescent Proteins
  • Nucleoside Q