title: The carboxyl-terminal part of the putative Berne virus polymerase is expressed by ribosomal frameshifting and contains sequence motifs which indicate that toro- and coronaviruses are evolutionarily related.
abstract: Sequence analysis of the 3' part (8 kb) of the polymerase gene of the torovirus prototype Berne virus (BEV) revealed that this area contains at least two open reading frames (provisionally designated ORF1a and ORF1b) which overlap by 12 nucleotides. The complete sequence of ORF1b (6873 nucleotides) was determined. Like the coronaviruses, BEV was shown to express its ORF1b by ribosomal frameshifting during translation of the genomic RNA. The predicted tertiary RNA structure (a pseudoknot) in the toro- and coronaviral frameshift-directing region is similar. Analysis of the amino acid sequence of the predicted BEV ORF1b translation product revealed homology with the ORF1b product of coronaviruses. Four conserved domains were identified: the putative polymerase domain, an area containing conserved cysteine and histidine residues, a putative helicase motif, and a domain which seems to be unique for toro- and coronaviruses. The data on the 3' part of the polymerase gene of BEV supplement previously observed similarities between toro- and coronaviruses at the level of genome organization and expression. The two virus families are more closely related to each other than to other families of positive-stranded RNA viruses.
authors.affiliation: Institute of Virology, Veterinary Faculty, State University of Utrecht, The Netherlands.
authors.forename: E J
authors.initials: EJ
authors.lastname: Snijder
authors.forename: J A
authors.initials: JA
authors.lastname: den Boon
authors.forename: P J
authors.initials: PJ
authors.lastname: Bredenbeek
authors.forename: M C
authors.initials: MC
authors.lastname: Horzinek
authors.forename: R
authors.initials: R
authors.lastname: Rijnbrand
authors.forename: W J
authors.initials: WJ
authors.lastname: Spaan
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D005075:Biological Evolution; D002460:Cell Line; D003001:Cloning, Molecular; D003332:Coronaviridae / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000378:metabolism; D005814:Genes, Viral; D006367:HeLa Cells; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D012328:RNA Viruses / Q000201:enzymology / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics; D015183:Restriction Mapping; D012270:Ribosomes / Q000378:metabolism*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D012367:RNA, Viral; D012321:DNA-Directed RNA Polymerases