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RNA motifs that determine specificity between a viral replicase and its promoter

Nature Structural Biology volume 7, pages 415–423 (2000)Cite this article

An Erratum to this article was published on 01 June 2000

Abstract

The 3′ end of brome mosaic virus RNA contains a tRNA-like sequence that directs its RNA synthesis. A stem loop structure in this sequence, stem loop C (SLC), was investigated using NMR, and correlated with its ability to direct RNA synthesis by its replicase. SLC consists of two discrete domains, a flexible stem with an internal loop and a rigid stem containing a 5′-AUA-3′ triloop. Efficient RNA synthesis requires the sequence on only one side of the flexible stem and a specific compact conformation of the triloop. A high resolution structure of the triloop places the 5′ adenine out in solution, and the 3′ adenine within the triloop, held tightly through stacking and unusual hydrogen bonds. This high resolution structure of an RNA promoter from a (+)-strand RNA virus provides new insights into how the RNA-dependent RNA polymerase binds to the RNA to initiate synthesis.

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Figure 1: Secondary structure of the brome mosaic virus RNA (BMV) 3′ end.
Figure 2: D2O NOESY spectrum of SLC1 at 30° C.
Figure 3: The role of the internal loop-stem in directing RNA synthesis.
Figure 4: H2O NOESY spectra of SLC+8 and SLT+8.
Figure 5: The high resolution structure of SL13.
Figure 6: H2O NOESY spectra of SLC+8 and SLT+8.
Figure 7: The role of the triloop in directing RNA synthesis.
Figure 8: Features of SLC are conserved in other bromoviruses.

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Acknowledgements

We thank B. Dengler for general lab management and D. Koh for DNA template synthesis. We also thank J. Pelton for NMR advice and H.-J. Park for his work in RNA sample preparation. Funding was provided by a National Institute of Health grant and a Department of Energy grant to I.T., and by a National Science Foundation grant to C.K.

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Authors and Affiliations

  1. Department of Chemistry, and Physical Biosciences Division, University of California, Berkeley, Lawrence Berkeley National Laboratory, Berkeley, 94720-1460, California, USA

    Chul-Hyun Kim & Ignacio Tinoco Jr.

  2. Department of Biology, Indiana University, Bloomington, 47405-3700, Indiana, USA

    C. Cheng Kao

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Kim, CH., Kao, C. & Tinoco, I. RNA motifs that determine specificity between a viral replicase and its promoter. Nat Struct Mol Biol 7, 415–423 (2000). https://doi.org/10.1038/75202

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