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

<p>Abstract</p> <p>The family <it>Dicistroviridae </it>(order <it>Picornavirales</it>) 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' O...

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Bibliographic Details
Main Authors: Jan Eric, Wang Qing S, Firth Andrew E, Atkins John F
Format: Article
Language:English
Published: BMC 2009-11-01
Series:Virology Journal
Online Access:http://www.virologyj.com/content/6/1/193
Description
Summary:<p>Abstract</p> <p>The family <it>Dicistroviridae </it>(order <it>Picornavirales</it>) 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 <it>Dicistroviridae </it>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.</p>
ISSN:1743-422X