In the past year, we have made important progress in our understanding of the mechanism of action of two regulatory RNAs that respond to amino acid starvation in a variety of bacteria, including clinically important pathogens of genera such as Bacillus and Vibrio. The glycine riboswitch is thus far unique among gene-regulatory RNAs in that its architecture involves quaternary interactions. We have used solution methods to analyze how these interactions between independently folded, homologous subunits gives rise to function. The T-box riboswitch controls the expression of aminoacyl-tRNA synthetases, the enzymes responsible for specific charging of tRNA with amino acids, in response to intracellular amino acid levels in Gram-positive bacteria. It is essential for cell survival and virulence. Although this mRNA domain was discovered in 1993, it was not until our work published this year that the mechanism by which the T-box specifically recognizes tRNA was elucidated. In addition to resolving a long-standing question mechanistic, our work forms the starting point for analysis of RNA-RNA interactions in biological systems.

Project Start
Project End
Budget Start
Budget End
Support Year
3
Fiscal Year
2013
Total Cost
$941,172
Indirect Cost
Name
National Heart, Lung, and Blood Institute
Department
Type
DUNS #
City
State
Country
Zip Code
Warner, Katherine Deigan; Chen, Michael C; Song, Wenjiao et al. (2014) Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat Struct Mol Biol 21:658-63
Baird, Nathan J; Ferre-D'Amare, Adrian R (2014) Analysis of riboswitch structure and ligand binding using small-angle X-ray scattering (SAXS). Methods Mol Biol 1103:211-25
Zhang, Jinwei; Ferré-D'Amaré, Adrian R (2014) Dramatic improvement of crystals of large RNAs by cation replacement and dehydration. Structure 22:1363-71
Warner, Katherine Deigan; Homan, Philip; Weeks, Kevin M et al. (2014) Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem Biol 21:591-5
Zhang, Jinwei; Ferre-D'Amare, Adrian R (2013) Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature 500:363-6
Baird, Nathan J; Ferre-D'Amare, Adrian R (2013) Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA 19:167-76