The primary structure and expression of the second open reading frame of the polymerase gene of the coronavirus MHV-A59; a highly conserved polymerase is expressed by an efficient ribosomal frameshifting mechanism

Abstract

Sequence analysis of a substantial part of the polymerase gene of the murine coronavirus MHV-A59 revealed the 3' end of an open reading frame (ORF1a) overlapping with a large ORF (ORF1b; 2733 amino acids) which covers the 3' half of the polymerase gene. The expression of ORF1b occurs by a ribosomal frameshifting mechanism since the ORF1a/ORF1b overlapping nucleotide sequence is capable of inducing ribosomal frameshifting in vitro as well as in vivo. A stem-loop structure and a pseudoknot are predicted in the nucleotide sequence involved in ribosomal frameshifting. Comparison of the predicted amino acid sequence of MHV ORF1b with the amino acid sequence deduced from the corresponding gene of the avian coronavirus IBV demonstrated that in contrast to the other viral genes this ORF is extremely conserved. Detailed analysis of the predicted amino acid sequence revealed sequence elements which are conserved in many DNA and RNA polymerases.

Toroviruses: replication, evolution and comparison with other members of the coronavirus-like superfamily

“…Apparently the ratio between the levels of ORF 1 a-and ORF 1 b-derived proteins in infected cells has to be regulated. Using reporter gene constructs, frameshifting efficiencies in expression systems of 25 to 40 %, 20 to 30 % and 15 to 20 % have been observed for corona-, toro-and arteriviruses, respectively (Brierley et al, 1989;Bredenbeek et al, 1990a;Snijder et al, 1990a;den Boon et al, 1991b).…”

Localization of mouse hepatitis virus open reading frame 1A derived proteins

“…The second open reading frame ORF1b, overlaps ORF1a for 75 nucleotides and is 2771 amino acids long. In vitro transcription and translation studies of gene 1 have indicated that these two ORFs are translated by a ribosomal frameshifting mechanism to yield a polyprotein of almost 800 000 kDa which is co-translationally cleaved (Breedenbeek et al, 1990). Analysis of the nucleotide sequence and the predicted amino acid sequence revealed that ORF1a contains several likely functional domains: two hydrophobic domains, three cysteine-rich domains, a picornavirus 3C-like protease domain, and two papain-like protease domains (Lee et al, 1989;Bonilla et al, 1994).…”

“…The relative positions of these ORF1a domains are depicted schematically in Figure 1. ORF1b is predicted to encode domains required for the MHV RNA-dependent RNA polymerase activity, including the canonical SDD polymerase motif, a nucleotide binding motif, a metal binding domain, and a helicase domain (Breedenbeek et al, 1990).…”

Internal Ribosome Entry in the Coding Region of Murine Hepatitis Virus mRNA 5

“…The unique region of MHV mRNA 1 contains two large ORFs that constitute the coronavirus RNA polymerase locus. Expression of viral proteins from this locus involves both ribosomal frameshifting and autoproteolytic processing (Baker et al, 1989;Bredenbeek et al, 1990;Denison et al, 1991Denison et al, , 1992. MHV mRNA 5 also contains two ORFs in its unique region, designated ORF 5a and ORF 5b.…”