Short report

A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa product

Andrew E Firth¹ and John F Atkins^1,2

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

Virology Journal 2009, 6:136 doi:10.1186/1743-422X-6-136

Published: 8 September 2009

Abstract

The genus Torovirus (order Nidovirales) includes a number of species that infect livestock. These viruses have a linear positive-sense ssRNA genome of ~25-30 kb, encoding a large polyprotein that is expressed from the genomic RNA, and several additional proteins expressed from a nested set of 3'-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5' end of the polyprotein coding sequence, ORF1a, in the +2 reading frame. The new ORF has a strong coding signature and, in fact, is more conserved at the amino acid level than the overlapping region of ORF1a. We propose that the new ORF utilizes a non-AUG initiation codon - namely a conserved CUG codon in a strong Kozak context - upstream of the ORF1a AUG initiation codon, resulting in a novel 258 amino acid protein, dubbed '30K'.