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

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 in this paper, 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.

Authors:
 [1];  [2];  [3];  [4];  [4];  [1];  [5];  [2]; ORCiD logo [2];  [6]; ORCiD logo [6];  [7];  [4];  [2]; ORCiD logo [1]
  1. National Inst. of Diabetes and Digestive and Kidney Diseases, Bethesda, MD (United States). Lab. of Molecular Biology
  2. Stanford Univ., CA (United States). James H. Clark Center
  3. Univ. Paris-Sud, Gif-sur-Yvette (France). Inst. for Integrative Biology of the Cell (I2BC)
  4. Univ. of Patras, Patras (Greece)
  5. National Cancer Inst., Frederick, MD (United States).Center for Cancer Research; Frederick National Lab. for Cancer Research, Frederick, MD (United States)
  6. Baylor College of Medicine, Houston, TX (United States)
  7. National Cancer Inst., Frederick, MD (United States). Structural Biophysics Lab., Center for Cancer Research
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH); European Union (EU)
OSTI Identifier:
1595138
Grant/Contract Number:  
AC02-76SF00515
Resource Type:
Accepted Manuscript
Journal Name:
Nature Structural & Molecular Biology
Additional Journal Information:
Journal Volume: 26; Journal Issue: 12; Journal ID: ISSN 1545-9993
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Li, Shuang, Su, Zhaoming, Lehmann, Jean, Stamatopoulou, Vassiliki, Giarimoglou, Nikoleta, Henderson, Frances E., Fan, Lixin, Pintilie, Grigore D., Zhang, Kaiming, Chen, Muyuan, Ludtke, Steven J., Wang, Yun-Xing, Stathopoulos, Constantinos, Chiu, Wah, and Zhang, Jinwei. Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. United States: N. p., 2019. Web. doi:10.1038/s41594-019-0326-7.
Li, Shuang, Su, Zhaoming, Lehmann, Jean, Stamatopoulou, Vassiliki, Giarimoglou, Nikoleta, Henderson, Frances E., Fan, Lixin, Pintilie, Grigore D., Zhang, Kaiming, Chen, Muyuan, Ludtke, Steven J., Wang, Yun-Xing, Stathopoulos, Constantinos, Chiu, Wah, & Zhang, Jinwei. Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. United States. doi:10.1038/s41594-019-0326-7.
Li, Shuang, Su, Zhaoming, Lehmann, Jean, Stamatopoulou, Vassiliki, Giarimoglou, Nikoleta, Henderson, Frances E., Fan, Lixin, Pintilie, Grigore D., Zhang, Kaiming, Chen, Muyuan, Ludtke, Steven J., Wang, Yun-Xing, Stathopoulos, Constantinos, Chiu, Wah, and Zhang, Jinwei. Mon . "Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions". United States. doi:10.1038/s41594-019-0326-7.
@article{osti_1595138,
title = {Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions},
author = {Li, Shuang and Su, Zhaoming and Lehmann, Jean and Stamatopoulou, Vassiliki and Giarimoglou, Nikoleta and Henderson, Frances E. and Fan, Lixin and Pintilie, Grigore D. and Zhang, Kaiming and Chen, Muyuan and Ludtke, Steven J. and Wang, Yun-Xing and Stathopoulos, Constantinos and Chiu, Wah and Zhang, Jinwei},
abstractNote = {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 in this paper, 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.},
doi = {10.1038/s41594-019-0326-7},
journal = {Nature Structural & Molecular Biology},
number = 12,
volume = 26,
place = {United States},
year = {2019},
month = {11}
}

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