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

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

Author information

1
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
2
Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA.
3
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Campus Paris-Saclay, Gif-sur-Yvette, France.
4
Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece.
5
Small-Angle X-ray Scattering Core Facility, Center for Cancer Research of the National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA.
6
Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
7
Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
8
Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA. wahc@stanford.edu.
9
Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, Stanford University, Stanford, CA, USA. wahc@stanford.edu.
10
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA. jinwei.zhang@nih.gov.

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.

PMID:
31740854
PMCID:
PMC6899168
[Available on 2020-05-18]
DOI:
10.1038/s41594-019-0326-7

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