The simian immunodeficiency virus 5′ untranslated leader sequence plays a role in intracellular viral protein accumulation and in RNA packaging

We investigated the role of 5′ untranslated leader sequences of simian immunodeficiency virus (SIV_mac239) in RNA encapsidation and protein expression. A series of progressively longer deletion mutants was constructed with a common endpoint six nucleotides upstream of the gag initiation codon and another endpoint at the 3′ end of the primer binding site (PBS). We found that efficient intracellular Gag-Pol protein accumulation required the region between the PBS and splice donor (SD) site. Marked reduction of genomic RNA packaging was observed with all the deletion mutants that involved sequences at both the 5′ and at the 3′ ends of the major SD site, and increased nonspecific RNA incorporation could be detected in these mutants. RNA encapsidation was affected only modestly by a deletion of 54 nucleotides at the 3′ end of the SD site when the mutant construct pΔ54 was transfected alone. In contrast, the amount of pΔ54 genomic RNA incorporated into particles was reduced more than 10-fold when this mutant was cotransfected with a construct specifying an RNA molecule with a wild-type packaging signal. Therefore, we conclude that the 175 nucleotides located 5′ of the gag initiation codon are critical for efficient and selective incorporation of genomic RNA into virions. This location of the SIV Ψ element provides the means for efficient discrimination between viral genomic and spliced RNAs.