19S late mRNAs of simian virus 40 have an internal ribosome entry site upstream of the virion structural protein 3 coding sequence.

The late mRNAs of simian virus 40 (SV40) are polycistronic. The 19S mRNAs encode primarily the virion structural proteins VP2 and VP3. The VP2 and VP3 coding sequences are located in the same reading frame, and the VP3 AUG is an internal AUG for VP2. We tested whether an internal ribosome entry site (IRES) might be located upstream of the VP3 AUG that would facilitate its utilization, especially late in infection when cap-dependent translation is reduced (19). Using dicistronic reporter systems for IRES detection, we detected IRES activity within SV40 nucleotides (nts) 565 to 916, the region between the VP2 and VP3 AUGs. Nuclease protection analysis and primer extension analysis indicate no aberrant transcription or splicing that could account for false prediction of an IRES. Deletion analysis of the region indicates the presence of two functional IRESs, one within nts 661 to 830 and the other within nts 771 to 915. These two regions, each containing one IRES, have essentially the same IRES activity as the entire region spanning nts 616 to 915, which contains both IRESs. This suggests that potential secondary structures in the overlapping regions spanning nts 661 to 830 and nts 771 to 915 may be in dynamic equilibrium, such that there is only one functional IRES at any one time. These data strongly suggest that an IRES can be utilized for VP3 translation from the SV40 19S late mRNAs.