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 journalArticle

6 Citations (Scopus)

Abstract

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
Volume115
Issue number15
Early online date26 Mar 2018
DOIs
Publication statusPublished - 10 Apr 2018

Fingerprint

Riboswitch
Mycobacterium smegmatis
Transfer RNA
RNA, Transfer, Ile
RNA
Ligands
Transfer RNA Aminoacylation
Acylation
Actinobacteria
Hydroxyl Radical
Genes
Amino Acids

Keywords

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

Cite this

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title = "New tRNA contacts facilitate ligand binding in a Mycobacterium smegmatis T box riboswitch",
abstract = "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.",
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New tRNA contacts facilitate ligand binding in a Mycobacterium smegmatis T box riboswitch. / Sherwood, Anna V.; Frandsen, Jane K.; Grundy, Frank J.; Henkin, Tina M. (Lead / Corresponding author).

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 115, No. 15, 10.04.2018, p. 3894-3899.

Research output: Contribution to journalArticle

TY - JOUR

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AU - Sherwood, Anna V.

AU - Frandsen, Jane K.

AU - Grundy, Frank J.

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