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

Authors

Shuang Li
Zhaoming Su
Jean Lehmann
Vassiliki Stamatopoulou
Nikoleta Giarimoglou
Frances E Henderson
Lixin Fan
Grigore D Pintilie
Kaiming Zhang
Muyuan Chen
Steven J Ludtke
Yun-Xing Wang
Constantinos Stathopoulos
Wah Chiu
Jinwei Zhang

Publication Date

12-1-2019

Journal

Nature Structural & Molecular Biology

DOI

10.1038/s41594-019-0326-7

PMID

31740854

PMCID

PMC6899168

PubMedCentral® Posted Date

5-18-2020

PubMedCentral® Full Text Version

Author MSS

Published Open-Access

yes

Keywords

Amino Acids, Aminoacylation, Bacillus subtilis, Cryoelectron Microscopy, Crystallography, X-Ray, Geobacillus, Models, Molecular, Nucleic Acid Conformation, RNA, Bacterial, RNA, Transfer, Riboswitch

Abstract

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.