Position of the kissing-loop interaction associated with PTE-type 3′CITEs can affect enhancement of cap-independent translation

•Proximity to the 5′ end of the kissing-loop interaction can negatively impact translation of SCV.•Phylogenetically conserved 5′ terminal hairpin in carmoviruses is involved in translation.•Natural upstream out-of-frame AUG in SCV genomic RNA significantly reduces translation of a reporter mRNA.

The Panicum mosaic virus-like translation enhancer (PTE) functions as a cap-independent translation enhancer (3′CITE) in members of several Tombusviridae genera including 7/19 carmoviruses. For nearly all PTE, a kissing-loop connects the element with a hairpin found in several conserved locations in the genomic RNA (5′ terminal hairpin or ~100 nt from the 5′ end) and small subgenomic RNA (~63 nt from the 5′ end). Moving the interaction closer to the 5′ end in reporter mRNAs using Saguaro cactus virus (SCV) sequences had either a minimal or substantial negative effect on translation. Movement of the kissing loop from position 104 to the SCV 5′ terminal hairpin also reduced translation by 4-fold. These results suggest that relocating the PTE kissing loop closer to the 5′ end reduces PTE efficiency, in contrast to results for the Barley yellow dwarf BTE and Tomato bushy stunt virus Y-shaped 3′CITEs, suggesting that different 3′CITEs have different bridging requirements.