Comparative structural studies of bovine viral diarrhea virus IRES RNA

Jody M. Burks, Christian Zwieb, Florian Müller, Iwona K. Wower, Jacek Wower

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

The internal ribosomal entry site (IRES) RNA of bovine viral diarrhea virus (BVDV) has been implicated in virus propagation. To gain insight into the structure and potential function of the BVDV IRES RNA, we collected and aligned 663 of its sequences. Compensatory Watson-Crick and wobble G·U pairs were investigated to establish phylogenetically supported secondary structures for each of the BVDV IRES RNA sequences. The extensively folded BVDV IRES RNAs were composed of helices 2, 3 and 4. Helix 2 consisted of five helical sections. Helix 3 contained sections 3a to 3j as well as six helical insertions 3.1-3.6. Sections 3a and 3b together with helices 3.6 and 4 formed an RNA pseudoknot. Two highly variable regions corresponded to hairpins 3j and 3.4. Three-dimensional modeling of the BVDV-1b strain Osloss IRES RNA predicted an elongated structure with approximate dimensions of 170. Å by 65. Å by 90. Å. The model of the IRES RNA-ribosome complex suggested proximity between helix 2 of the BVDV IRES and ribosomal proteins S5 and S25.

Original languageEnglish (US)
Pages (from-to)136-142
Number of pages7
JournalVirus Research
Volume160
Issue number1-2
DOIs
Publication statusPublished - Sep 1 2011

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Keywords

  • BVDV
  • Comparative Sequence Analysis
  • IRES RNA
  • RNA model
  • RNA secondary structure

ASJC Scopus subject areas

  • Cancer Research
  • Virology
  • Infectious Diseases

Cite this

Burks, J. M., Zwieb, C., Müller, F., Wower, I. K., & Wower, J. (2011). Comparative structural studies of bovine viral diarrhea virus IRES RNA. Virus Research, 160(1-2), 136-142. https://doi.org/10.1016/j.virusres.2011.06.002