The single distinct leader protease encoded by alpinia oxyphylla mosaic virus (the genus Macluravirus) suppresses RNA silencing through interfering with double-stranded RNA synthesis

The genomic 5′-terminal regions of viruses in the family Potyviridae (potyvirids) encode two types of leader proteases, serine-protease (P1) and cysteine-protease (HCPro), which differ greatly in the arrangement and sequence composition among inter-genus viruses. Most potyvirids have the same tandemly-arranged P1 and HCPro, whereas viruses in the genus Macluravirus encode single distinct leader protease - a truncated version of HCPro with yet-unknown functions. We investigated the RNA silencing suppression (RSS) activity and its underpinning mechanism of the distinct HCPro from alpinia oxyphylla mosaic macluravirus (aHCPro). Sequence analysis revealed that macluraviral HCPros have obvious truncations in the N-terminal and middle regions, when aligned to their counterparts in potyviruses (well-characterized viral suppressors of RNA silencing). Nearly all defined-elements essential for the RSS activity of potyviral counterparts are not discriminated in macluraviral HCPros. Here, we demonstrated that aHCPro exhibits the similar anti-silencing activity with potyviral counterpart. However, aHCPro fails to block both the local and systemic spreading of RNA silencing. In line, aHCPro interferes with the dsRNA synthesis, an upstream step in RNA silencing pathway. Affinity-purification and NanoLC-MS/MS analysis revealed that aHCPro has no association with core components or their potential interactors involving in dsRNA synthesis from the protein layer. Instead, the ectopic expression of aHCPro significantly reduces the transcript abundance of RDR2, RDR6, SGS3 and SDE5. This study represents the first report of the anti-silencing function of macluravirus-encoded HCPro and the underlying molecular mechanism.