Translational T-box riboswitches bind tRNA by modulating conformational flexibility

Eduardo Campos-Chavez, Sneha Paul, Zunwu Zhou, Dulce Alonso, Anjali R. Verma, Jingyi Fei () and Alfonso Mondragón ()
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Eduardo Campos-Chavez: Northwestern University
Sneha Paul: The University of Chicago
Zunwu Zhou: The University of Chicago
Dulce Alonso: Northwestern University
Anjali R. Verma: Columbia University
Jingyi Fei: The University of Chicago
Alfonso Mondragón: Northwestern University

Nature Communications, 2024, vol. 15, issue 1, 1-17

Abstract: Abstract T-box riboswitches are noncoding RNA elements involved in genetic regulation of most Gram-positive bacteria. They regulate amino acid metabolism by assessing the aminoacylation status of tRNA, subsequently affecting the transcription or translation of downstream amino acid metabolism-related genes. Here we present single-molecule FRET studies of the Mycobacterium tuberculosis IleS T-box riboswitch, a paradigmatic translational T-box. Results support a two-step binding model, where the tRNA anticodon is recognized first, followed by interactions with the NCCA sequence. Furthermore, after anticodon recognition, tRNA can transiently dock into the discriminator domain even in the absence of the tRNA NCCA-discriminator interactions. Establishment of the NCCA-discriminator interactions significantly stabilizes the fully bound state. Collectively, the data suggest high conformational flexibility in translational T-box riboswitches; and supports a conformational selection model for NCCA recognition. These findings provide a kinetic framework to understand how specific RNA elements underpin the binding affinity and specificity required for gene regulation.

Date: 2024
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DOI: 10.1038/s41467-024-50885-x

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