NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA.

Nucleic Acids Research
Jiachen WangE P Nikonowicz

Abstract

Gram-positive bacteria utilize a tRNA-responsive transcription antitermination mechanism, designated the T box system, to regulate expression of many amino acid biosynthetic and aminoacyl-tRNA synthetase genes. The RNA transcripts of genes controlled by this mechanism contain 5' untranslated regions, or leader RNAs, that specifically bind cognate tRNA molecules through pairing of nucleotides in the tRNA anticodon loop with nucleotides in the Specifier Loop domain of the leader RNA. We have determined the solution structure of the Specifier Loop domain of the tyrS leader RNA from Bacillus subtilis. Fifty percent of the nucleotides in the Specifier Loop domain adopt a loop E motif. The Specifier Sequence nucleotides, which pair with the tRNA anticodon, stack with their Watson-Crick edges rotated toward the minor groove and exhibit only modest flexibility. We also show that a Specifier Loop domain mutation that impairs the function of the B. subtilis glyQS T box RNA disrupts the tyrS loop E motif. Our results suggest a mechanism for tRNA-Specifier Loop binding in which the phosphate backbone kink created by the loop E motif causes the Specifier Sequence bases to rotate toward the minor groove, which increases accessibility for pai...Continue Reading

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Citations

May 10, 2011·Nature Methods·José Almeida Cruz, Eric Westhof
Apr 17, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jason C GriggAilong Ke
Jul 17, 2013·Proceedings of the National Academy of Sciences of the United States of America·Nizar Y SaadHubert Dominique Becker
Jan 15, 2015·Proceedings of the National Academy of Sciences of the United States of America·Anna V SherwoodTina M Henkin
Sep 9, 2015·Chemical Biology & Drug Design·Jia LiuJennifer V Hines
May 13, 2014·Biochimica Et Biophysica Acta·Tina M Henkin
Apr 29, 2014·Biochimica Et Biophysica Acta·Jinwei ZhangAdrian R Ferré-D'Amaré
May 12, 2015·Wiley Interdisciplinary Reviews. RNA·Jinwei Zhang, Adrian R Ferré-D'Amaré
Feb 22, 2011·Journal of Molecular Biology·Jiachen Wang, Edward P Nikonowicz
Nov 12, 2013·Journal of Chemical Theory and Computation·Filip LeonarskiJoanna Trylska
Jul 28, 2018·Microbiology Spectrum·Kiel D Kreuzer, Tina M Henkin
Jun 18, 2017·Biochemistry·Xianyang FangEdward P Nikonowicz

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Methods Mentioned

BETA
nuclear magnetic resonance
in vitro transcription
chemical exchange

Software Mentioned

NIH
Xplor
Insight

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