Fig 5.

RNA traffic signal hypothesis for regulation of BYDV translation and replication. Black line indicates BYDV genomic RNA showing relevant secondary structural elements with key regions in color (not to scale). Black boxes indicate ORFs 1 and 2. For simplicity, other ORFs, nascent proteins, and (−) strand RNA are not shown. (A) Base pairing between the 3′ TE and 5′ UTR (magenta) (25) and between the LDFE and ADSL (gold) allow ribosomes (gray ovals) to translate ORF 1 and ORF 2. (B) As the viral RdRp molecules (blue spheres) accumulate, they initiate (−) strand synthesis at the 3′-terminal structure (46). They proceed upstream along the template and melt out the ADSL:LDFE base pairing. This blocks frameshifting (vertical bars), clearing ORF 2 of ribosomes, briefly allowing translation of ORF1 only. (C) Next, the RdRp reaches the 3′ TE and disrupts the 3′TE:5′ UTR base pairing, preventing translation initiation. This clears ORF1 and the entire RNA of ribosomes, allowing the RdRps to continue to the 5′ end. Subsequent rounds of replication would cause (+) strand RNA to accumulate in excess of RdRp molecules, returning the process to A as shown.