Intergenic sequences of the vesicular stomatitis virus genome (New Jersey serotype): evidence for two transcription initiation sites within the L gene.

The intergenic sequences of vesicular stomatitis virus of the New Jersey serotype [VSV (NJ): Ogden strain] have been determined by dideoxy sequencing across the gene junctions of the viral RNA genome using deoxyoligonucleotide primers. The N-NS, NS-M, and M-G intergenic sequences of VSV (NJ) are identical to the consensus intergenic sequence for VSV of the Indiana serotype [VSV (IND)]: 3'-AUACU7GAUUGUCNNNAG-5' (genome sense; N denotes any nucleotide), where 3'-AUACU7-5' encodes the 3' terminus and the start of the polyadenylate tract of the preceding mRNA, 3'-UUGUCNNNAG-5' encodes the 5' terminus of the succeeding mRNA, and 3'-GA-5' is a nontranscribed dinucleotide. Notably, the NS-M junction of VSV (NJ) does not contain the anomalous dinucleotide 3'-CA-5' which is found at the NS-M junction of VSV (IND). In striking contrast to VSV (IND), the G-L intergenic sequence of VSV (NJ) contains a 19-base insertion between the nontranscribed dinucleotide and the consensus mRNA start sequence. During in vitro transcription, the L mRNA of VSV (NJ) may initiate at two distinct sites: the first start site (3'-CCUUAUCUUC-5') is that flanking the nontranscribed dinucleotide, and the second start site is a consensus mRNA start sequence located 20 bases downstream from the nontranscribed dinucleotide. However, the L mRNA isolated form VSV (NJ)-infected cells appears to initiate only at the consensus start sequence. The possible role of these start sites in L mRNA synthesis is discussed.