Fig. 6: Structure-based model of TSWV L activation and its dual-targeted inhibition mechanisms.

In TSWV-infected plants, the newly synthesized L protein (apo L) remains in an inactivated state with a disordered active site. When the viral genome with a double-stranded terminus binds to the L protein, the proximal double strand unwinds; the 3′ end becomes single-stranded and enters the polymerase active centre, and nucleotides 1–10 of the 5′ end enter the hook-binding pocket to form a hook-like stem–loop. The protruding base C5 at the bend of the hook structure makes hydrogen bonds with Lys1291 of the fingertips (motif F), resulting in an ordered motif F. New hydrogen bonds (Arg1294–Gln1455 and Arg1289–Lys1008) between motif F and other motifs contribute to the formation of a complete polymerase active centre. These alterations in the active site together with the ordered endo and CTD engage TSWV L in an activated state to initiate replication and transcription processes. In ribavirin-treated plants, ribavirin or its triphosphate disrupts both vRNA recognition and the formation of a complete catalytic centre by occupying both the 5′-hook-binding pocket entry tunnel and the enzyme’s active centre, locking the polymerase in an inactivated state.