Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions

Nat Struct Mol Biol. 2019 Dec;26(12):1094-1105. doi: 10.1038/s41594-019-0326-7. Epub 2019 Nov 18.


Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box-tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate 'discriminator' structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.

Publication types

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

MeSH terms

  • Amino Acids / metabolism*
  • Aminoacylation
  • Bacillus subtilis / chemistry
  • Bacillus subtilis / metabolism*
  • Cryoelectron Microscopy
  • Crystallography, X-Ray
  • Geobacillus / chemistry
  • Geobacillus / metabolism*
  • Models, Molecular
  • Nucleic Acid Conformation
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / metabolism*
  • RNA, Bacterial / ultrastructure
  • RNA, Transfer / chemistry
  • RNA, Transfer / metabolism*
  • RNA, Transfer / ultrastructure
  • Riboswitch*


  • Amino Acids
  • RNA, Bacterial
  • Riboswitch
  • RNA, Transfer

Supplementary concepts

  • Geobacillus kaustophilus