Primary structure and translation of a defective interfering rna of murine coronavirus

Abstract

An intracellular defective-interfering (DI) RNA, DIssE, of mouse hepatitis virus (MHV) obtained after serial high multiplicity passage of the virus was cloned and sequenced. DIssE RNA is composed of three noncontiguous genomic regions, representing the first 864 nucleotides of the 5' end, an internal 748 nucleotides of the polymerase gene, and 601 nucleotides from the 3' end of the parental MHV genome. The DIssE sequence contains one large continuous open reading frame. Two protein products from this open reading frame were identified both by in vitro translation and in DI-infected cells. Sequence comparison of DIssE and the corresponding parts of the parental virus genome revealed that DIssE had three base substitutions within the leader sequence and also a deletion of nine nucleotides located at the junction of the leader and the remaining genomic sequence. The 5' end of DIssE RNA was heterogeneous with respect to the number of UCUAA repeats within the leader sequence. The parental MHV genomic RNA appears to have extensive and stable secondary structures at the regions where DI RNA rearrangements occurred. These data suggest that MHV DI RNA may have been generated as a result of the discontinuous and nonprocessive manner of MHV RNA synthesis.

Sequences of 3' end of genome and of 5' end of open reading frame 1a of lactate dehydrogenase-elevating virus and common junction motifs between 5' leader and bodies of seven subgenomic mRNAs

“…This model postulates that the plus-strand leader is transcribed by the replicase from a full-length minus-strand antigenome and that the leader then 'falls off' the template and reassociates at complementary sites in intergenic regions downstream in the minus-strand template acting as primer for continued transcription. The 3' end of the leader sequence in genomic MHV RNA is composed of two or three repeated 5' UCUAA 3' heptanucleotides followed by a consensus 5' UCUAAAC 3' sequence and two or three repeats of the same or closely related segments are found upstream of the initiation codon of every ORF (Baric et al, 1983;Makino et al, 1986Makino et al, , 1988Makino et al, , 1991Shieh et al, 1987;Spaan et al, 1988;Lai, 1990). For example, the intergenic segment preceding ORF 7 of MHV A59 contains an 18 nucleotide long segment that is identical to the 5' leader sequence.…”

Characterization of defective interfering RNAs of Berne virus

“…Since point mutations, insertions and deletions in the 5' end of DI RNAs have been described before, e.g. for coronaviruses (Makino et al, 1988), the conclusion that toroviral RNAs do not contain a common Y-terminal sequence would be premature. Both the results obtained with oligo D and the varying number of nucleotides upstream of the 'core promoter' motif could be explained by mutations in the 5' end of the DI RNA.…”

“…All coronaviral DI RNAs analysed to date have been found to contain the coronaviral leader sequence (Makino et al, 1988(Makino et al, , 1989van der Most et al, 1991). Therefore, they are 5'-coterminal with the genomic and sgRNAs of the standard virus.…”

Origin and Evolution of Defective Interfering RNAs of Tomato Bushy Stunt Virus

“…In actuality, a combination of these two explanations may operate. For instance, in the coronavirus mouse hepatitis virus (MHV), it is thought that deletions leading to formation of DIs involve recombination at conserved elements of secondary structure (Makino, et al, 1988). However, once generated, survival of the resulting recombinants depends upon maintaining the ability to be replicated.…”

“…The intergenic region of brome mosaic virus RNA3 contains is important for efficient RNA replication . In addition, it has been noted that animal virus DIs often contain internal regions of sequence (Makino, 1988;Schlesinger, 1988 The sequence motifs of TBSV DIs resemble in several ways those of the Similarly-sized DIs recently characterized in association with TCV (Li et ai., 1989). In both viruses, DI populations have been generated de novo and have been shown to retain all of the 5' non-coding region and a precisely modified 3' non-coding region consisting of the terminal 130-150 nt fused to variable portions of the C-terminus of the 3' -most ORF.…”