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In silico analysis of IRES RNAs of foot-and-mouth disease virus and related picornaviruses

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Abstract

Foot-and-mouth disease virus (FMDV) uses an internal ribosome entry site (IRES), a highly structured segment of its genomic RNA, to hijack the translational apparatus of an infected host. Computational analysis of 162 type II picornavirus IRES RNA sequences yielded secondary structures that included only base pairs supported by comparative or experimental evidence. The deduced helical sections provided the foundation for a hypothetical three-dimensional model of FMDV IRES RNA. The model was further constrained by incorporation of data derived from chemical modification and enzymatic probing of IRES RNAs as well as high-resolution information about IRES RNA-bound proteins.

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Acknowledgments

This research was supported by grants from the Alabama Agricultural Experiment Station Foundation to I.K.W. and J.W. and an Auburn University Biogrant to J.W. Publication costs were supported in part by the Upchurch Fund for Excellence. J.M.B. was supported by the National Science Foundation under Grant No. 0091853 and NSF-EPS 0447675. The molecular graphics image in Fig. 4 was produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR-01081).

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Authors and Affiliations

  1. Department of Animal Sciences, Auburn University, 210 Upchurch Hall, Auburn, AL, 36849-5415, USA

    Jody M. Burks, Iwona K. Wower & Jacek Wower

  2. Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229-3900, USA

    Christian Zwieb

  3. PENTAFOLIUM-SOFT, Am Bauernholz 1, 21224, Rosengarten, Germany

    Florian Müller

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Correspondence to Jacek Wower.

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Supplementary material 1 (PDF 78 kb)

FMDVIRES-alignment.fas. Picornavirus type II IRES RNA alignment

162 Sequences from aphthoviruses, cardioviruses and parechoviruses were aligned in fasta format as described in the text (PDB 2340 kb)

FMDV-PTBd34-model.pdb. Model of FMDV IRES RNA complexed with PTB domains III and IV

Coordinates in PDB format of tertiary structure model of FMDV IRES RNA complexed with structure of PTB domains III and IV as described in text (FAS 109 kb)

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Burks, J.M., Zwieb, C., Müller, F. et al. In silico analysis of IRES RNAs of foot-and-mouth disease virus and related picornaviruses. Arch Virol 156, 1737–1747 (2011). https://doi.org/10.1007/s00705-011-1043-7

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  • DOI: https://doi.org/10.1007/s00705-011-1043-7

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