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Structural insights into recognition of c-di-AMP by the ydaO riboswitch

Nature Chemical Biology volume 10, pages 787–792 (2014)Cite this article

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Abstract

Bacterial second messenger cyclic di-AMP (c-di-AMP) is implicated in signaling DNA damage and cell wall stress through interactions with several protein receptors and a widespread ydaO-type riboswitch. We report the crystal structures of c-di-AMP riboswitches from Thermoanaerobacter pseudethanolicus and Thermovirga lienii determined at ∼3.0-Å resolution. In both species, the RNA adopts an unforeseen 'square'-shaped pseudosymmetrical architecture that features two three-way junctions, a turn and a pseudoknot, positioned in the square corners. Uncharacteristically for riboswitches, the structure is stapled by two ligand molecules that span the interior of the structure and employ similar noncanonical interactions for RNA recognition. Mutations in either ligand-binding site negatively affect c-di-AMP binding, suggesting that the riboswitch-triggered genetic response requires contribution of both ligands. Our data provide what are to our knowledge the first insights into specific sensing of c-di-AMP and a molecular mechanism underlying the common c-di-AMP–dependent control of essential cellular processes in bacteria.

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Figure 1: Overall structure and schematics of the T. pseudethanolicus c-di-AMP riboswitch.
Figure 2: Structural elements of the T. pseudethanolicus c-di-AMP riboswitch.
Figure 3: Recognition of c-di-AMP molecules by the T. pseudethanolicus riboswitch.
Figure 4: Binding of c-di-AMP molecules to the riboswitch.

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Acknowledgements

We thank the personnel of beamlines X25 at the Brookhaven National Laboratory and 24-ID at the Argonne National Laboratory funded by the US Department of Energy. We thank O. Ouerfelli for the synthesis of iridium hexamine and L. Jaeger for discussions. A.S. was supported by funds from the New York University School of Medicine.

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  1. Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA

    Ang Gao & Alexander Serganov

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A.G. crystallized the riboswitches, determined their structures and conducted ITC experiments. A.G. and A.S. refined the structures and wrote the manuscript.

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Correspondence to Alexander Serganov.

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The authors declare no competing financial interests.

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Gao, A., Serganov, A. Structural insights into recognition of c-di-AMP by the ydaO riboswitch. Nat Chem Biol 10, 787–792 (2014). https://doi.org/10.1038/nchembio.1607

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