Functional Diversification of Maize RNA Polymerase IV and V Subtypes via Alternative Catalytic Subunits

Summary: Unlike nuclear multisubunit RNA polymerases I, II, and III, whose subunit compositions are conserved throughout eukaryotes, plant RNA polymerases IV and V are nonessential, Pol II-related enzymes whose subunit compositions are still evolving. Whereas Arabidopsis Pols IV and V differ from Pol II in four or five of their 12 subunits, respectively, and differ from one another in three subunits, proteomic analyses show that maize Pols IV and V differ from Pol II in six subunits but differ from each other only in their largest subunits. Use of alternative catalytic second subunits, which are nonredundant for development and paramutation, yields at least two subtypes of Pol IV and three subtypes of Pol V in maize. Pol IV/Pol V associations with MOP1, RMR1, AGO121, Zm_DRD1/CHR127, SHH2a, and SHH2b extend parallels between paramutation in maize and the RNA-directed DNA methylation pathway in Arabidopsis. : All known eukaryotes have three essential nuclear RNA polymerases, abbreviated as Pols I, II, and III. In plants, duplication of Pol II subunit genes gave rise to two additional enzymes, Pols IV and V, that specialize in RNA-mediated gene silencing. Here, Haag et al. show that functionally distinct subtypes of Pols IV and V exist in maize based on their differential use of alternative catalytic subunits, an indication of the ongoing diversification of these intriguing enzymes in plants