Sequence relationships between the genome and the intracellular RNA species 1,3,6 and 7 of mouse hepatitis virus strain A59

Abstract

We have shown by T1 oligonucleotide fingerprinting that the genome of mouse hepatitis virus strain A59 and its intracellular RNA 1 have identical fingerprints and that RNA 1 and the subgenomic RNAs 3, 6, and 7 contain common sequences. To localize the homologous region between the RNAs, we compared fingerprints of the 3Œ terminus of the genome with those of RNA 7. The genome was partially degraded with alkali, and polyadenylate-containing fragments were purified by oligodeoxythymidylate-cellulose chromatography. The fragments were size fractionated by agarose-urea gel electrophoresis, and two pools, x and z, containing 3Œ-derived fragments of the genome with apparent molecular weights of 0.1 ~ 106 to 0.14 ~ 106 and 0.6 ~ 106 to 0.8 ~ 106, respectively, were further analyzed by RNase T1 oligonucleotide fingerprinting. Comparison of the fingerprints of RNAs 6 and 7 with those of pools x and z showed that these subgenomic RNAs extend inwards from the 3Œ terminus of the genome. The RNA fragments present in pool z were on average slightly larger than RNA 7 as confirmed by the presence in pool z of T1 oligonucleotide spots specific for RNA 6 but not present in RNA 7. However, two large oligonucleotide spots derived from RNA 7, which were also present in RNAs 1, 3, and 6 and in the virion RNA, were not found in the T1 oligonucleotide map of pool z. A possible explanation is that the two spots were derived from a leader sequence. The results of UV transcription mapping experiments (L. Jacobs, W. J. M. Spaan, M. C. Horzinek, and B. A. M. van der Zeijst, J. Virol. 39:401-406, 1981) excluded the possibility that such a leader sequence arises by splicing from a larger precursor molecule, but either a virus-specific RNA primer molecule for the synthesis of mRNAs or an RNA polymerase jumping mechanism could explain the presence of a leader sequence.