New tRNA contacts facilitate ligand binding in a Mycobacterium smegmatis T box riboswitch

Anna V. Sherwood, Jane K. Frandsen, Frank J. Grundy, Tina M. Henkin (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

16 Citations (Scopus)


T box riboswitches are RNA regulatory elements widely used by organisms in the phyla Firmicutes and Actinobacteria to regulate expression of amino acid-related genes. Expression of T box family genes is down-regulated by transcription attenuation or inhibition of translation initiation in response to increased charging of the cognate tRNA. Three direct contacts with tRNA have been described; however, one of these contacts is absent in a subclass of T box RNAs and the roles of several structural domains conserved in most T box RNAs are unknown. In this study, structural elements of a Mycobacterium smegmatis ileS T box riboswitch variant with an Ultrashort (US) Stem I were sequentially deleted, which resulted in a progressive decrease in binding affinity for the tRNAIle ligand. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) revealed structural changes in conserved riboswitch domains upon interaction with the tRNA ligand. Cross-linking and mutational analyses identified two interaction sites, one between the S-turn element in Stem II and the T arm of tRNAIle and the other between the Stem IIA/B pseudoknot and the D loop of tRNAIle. These newly identified RNA contacts add information about tRNA recognition by the T box riboswitch and demonstrate a role for the S-turn and pseudoknot elements, which resemble structural elements that are common in many cellular RNAs.

Original languageEnglish
Pages (from-to)3894-3899
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number15
Early online date26 Mar 2018
Publication statusPublished - 10 Apr 2018


  • Pseudoknot
  • Regulation
  • S-turn
  • T box riboswitch
  • TRNA

ASJC Scopus subject areas

  • General


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