title: Detection of signature sequences in overlapping genes and prediction of a novel overlapping gene in hepatitis G virus.
abstract: In viruses an increased coding ability is provided by overlapping genes, in which two alternative open reading frames (ORFs) may be translated to yield two distinct proteins. The identification of signature sequences in overlapping genes is a topic of particular interest, since additional out-of-frame coding regions can be nested within known genes. In this work, a novel feature peculiar to overlapping coding regions is presented. It was detected by analysis of a sample set of 21 virus genomic sequences and consisted in the repeated occurrence of a cluster of basic amino acid residues, encoded by a frame, combined to a stretch of acidic residues, encoded by the corresponding overlapping frame. A computer scan of an additional set of virus sequences demonstrated that this feature is common to several other known overlapping ORFs and led to prediction of a novel overlapping gene in hepatitis G virus (HGV). The occurrence of a bifunctional coding region in HGV was also supported by its extremely lower rate of synonymous nucleotide substitutions compared to that observed in the other gene regions of the HGV genome. Analysis of the amino acid sequence that was deduced from the putative overlapping gene revealed a high content of basic residues and the presence of a nuclear targeting signal; these characteristics suggest that a core-like protein may be expressed by this novel ORF.
authors.affiliation: Department of Evolutionary and Functional Biology, University of Parma, Parco Area delle Scienze 11/A, I-43100 Parma, Italy. maestri@unipr.it
authors.forename: A
authors.initials: A
authors.lastname: Pavesi
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003062:Codon; D019143:Evolution, Molecular; D018067:Flaviviridae / Q000235:genetics*; D005807:Genes, Overlapping; D005814:Genes, Viral; D016247:Information Storage and Retrieval; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D017386:Sequence Homology, Amino Acid; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D003062:Codon; D014764:Viral Proteins