Complete sequences of the ribosome recognition sites in vesicular stomatitis virus messenger rna recognition by the 40s and 80s complexes

Rose, J. K.

Nucleotide sequences of the [rabbit reticulocyte] ribosome-protected translation initiation sites from the vesicular stomatitis virus (VSV) M and L protein mRNA were determined, completing the sequences of the sites from all the VSV mRNA. A low level of protection at 2 internal AUG-containing sites in the N mRNA is also described. Small homologies are evident among some of the sites, but there are no obvious features common to all the sites other than a single AUG codon. A large homology between the VSV M mRNA site and the alfalfa mosaic virus coat mRNA site is noted. This homology suggests the existence of a common ancestral gene for these 2 apparently unrelated viruses. For each VSV mRNA species, the smallest sites protected in either the 40S or 80S initiation complexes are identical. These sites always contained the initiation codon, but only contained the capped 5' end in those mRNA having the 5' end near the initiation site. If 40S ribosomes bind to the capped 5' end, either they do not protect it from nuclease digestion or the protection is only transitory in some VSV mRNA. Consideration of the structures of the ribosome binding sites suggests that the differential effects of hypertonic shock on translation may be related to the distance between the 5' end of the mRNA and the initiation codon.