Sequence signal involved in the generation of an internally deleted defective interfering RNA from vesicular stomatitis virus.

Abstract

We have determined the nucleotide sequence at the 3' end of the vesicular stomatitis virus (VSV) polymerase or L gene and compared it to that obtained from a defective interfering particle (DI) RNA generated by this virus. The latter (DI 0.50) contains a large internal deletion within this gene. The deletion begins exactly 253 residues from the transcription start of the gene and extends to approximately 300 bases from the 5' end of the standard RNA genome. The flanking sequences bear no homology to the eukaryotic consensus splice sequence. The sequence immediately preceding the deletion is complementary to the ribosome binding site of the L gene transcript and also resembles genome transcription termination sites. In addition, we present the results of nuclease protection experiments which show that this DI RNA retains an exact copy of the 3' end half of the standard genome (leader, N, NS, M and G genes), although its own 3' end is non-genomic. The implications of these findings regarding mechanisms of DI generation are discussed.