Short report

Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses

Andrew E Firth^1*, Qing S Wang², Eric Jan² and John F Atkins^1,3*

• * Corresponding authors: Andrew E Firth A.Firth@ucc.ie - John F Atkins j.atkins@ucc.ie

Author Affiliations

¹ BioSciences Institute, University College Cork, Cork, Ireland

² Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada

³ Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA

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Virology Journal 2009, 6:193 doi:10.1186/1743-422X-6-193

Published: 6 November 2009

Abstract

The family Dicistroviridae (order Picornavirales) includes species that infect insects and other arthropods. These viruses have a linear positive-sense ssRNA genome of ~8-10 kb, which contains two long ORFs. The 5' ORF encodes the nonstructural polyprotein while the 3' ORF encodes the structural polyprotein. The dicistroviruses are noteworthy for the intergenic Internal Ribosome Entry Site (IGR-IRES) that mediates efficient translation initation on the 3' ORF without the requirement for initiator Met-tRNA. Acute bee paralysis virus, Israel acute paralysis virus of bees and Kashmir bee virus form a distinct subgroup within the Dicistroviridae family. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF in these viruses. The ORF overlaps the 5' end of the structural polyprotein coding sequence in the +1 reading frame. We also identify a potential 14-18 bp RNA stem-loop structure 5'-adjacent to the IGR-IRES. We discuss potential translation initiation mechanisms for the novel ORF in the context of the IGR-IRES and 5'-adjacent stem-loop.