A potential mechanism for selective control of cap-independent translation by a viral RNA sequence in cis and in trans

Highly efficient cap-independent translation initiation at the 5\u27- proximal AUG is facilitated by the 3\u27 translation enhancer sequence (3\u27TE) located near the 3\u27 end of barley yellow dwarf virus (BYDV) genomic RNA. The role of the 3\u27TE in regulating viral translation was examined. The 3\u27TE is required for translation and thus replication of the genomic RNA that lacks a 5\u27 cap (Allen et al., 1999, Virology 253:139-144). Here we show that the 3\u27TE also mediates translation of uncapped viral subgenomic mRNAs (sgRNA1 and sgRNA2). A 109-nt viral sequence is sufficient for 3\u27TE activity in vitro, but additional viral sequence is necessary for cap-independent translation in vivo. The 5\u27 extremity of the sequence required in the 3\u27 untranslated region (UTR) for cap-independent translation in vivo coincides with the 5\u27 end of sgRNA2. Thus, sgRNA2 has the 3\u27TE in its 5\u27 UTR. Competition studies using physiological ratios of viral RNAs showed that, in trans, the 109-nt 3\u27TE alone, or in the context of 869-nt sgRNA2, inhibited translation of genomic RNA much more than it inhibited translation of sgRNA1. The divergent 5\u27 UTRs of genomic RNA and sgRNA1 contribute to this differential susceptibility to inhibition. We propose that sgRNA2 serves as a novel regulatory RNA to carry out the switch from early to late gene expression. Thus, this new mechanism for temporal control of translation control involves a sequence that stimulates translation in cis and acts in trans to selectively inhibit translation of viral mRNA