Functional Consequences of Subunit Diversity in RNA Polymerases II and V

SummaryMultisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved as specialized forms of Pol II that mediate RNA-directed DNA methylation (RdDM) and transcriptional silencing of transposons, viruses, and endogenous repeats in plants. Among the subunits common to Arabidopsis thaliana Pols II, IV, and V are 93% identical alternative ninth subunits, NRP(B/D/E)9a and NRP(B/D/E)9b. The 9a and 9b subunit variants are incompletely redundant with respect to Pol II; whereas double mutants are embryo lethal, single mutants are viable, yet phenotypically distinct. Likewise, 9a or 9b can associate with Pols IV or V but RNA-directed DNA methylation is impaired only in 9b mutants. Based on genetic and molecular tests, we attribute the defect in RdDM to impaired Pol V function. Collectively, our results reveal a role for the ninth subunit in RNA silencing and demonstrate that subunit diversity generates functionally distinct subtypes of RNA polymerases II and V.

Graphical AbstractFigure optionsDownload as PowerPoint slideHighlights
► Arabidopsis RNA polymerases II, IV, and V use either of two ninth subunit proteins
► The alternative ninth subunits affect Pol II and Pol V functions
► RNA-directed DNA methylation requires the 9b-containing form of Pol V
► Unlike yeast and archaea, an NRPB9 subunit of Pol II is essential in Arabidopsis