Subunit Compositions of Arabidopsis DNA-Dependent RNA Polymerases and the Roles of the Plant-Specific RNA Polymerases IV and V in Gene Silencing

In addition to RNA polymerases I, II and III, the essential RNA polymerases present in all eukaryotes, plants have two additional nuclear RNA polymerases, abbreviated as Pol IV and Pol V, that play non-redundant roles in siRNA-directed DNA methylation and gene silencing. Using a combination of affinity purification and protein identification by mass spectrometry, my studies show that Arabidopsis Pol IV and Pol V are composed of subunits that are paralogous or identical to the twelve subunits of Pol II. Four subunits of Pol IV are distinct from their Pol II paralogs, six subunits of Pol V are distinct from their Pol II paralogs, and four subunits differ between Pol IV and Pol V. Importantly, the subunit differences occur in key positions relative to the template entry and RNA exit paths. My findings support the hypothesis that Pol IV and Pol V are Pol II-like enzymes that evolved specialized roles in the production of noncoding transcripts for RNA silencing and genome defense. In addition, I have determined the subunit compositions of Arabidopsis RNA polymerases I, II and III, providing a novel framework for comparative and functional analyses of subunits from all five DNA-dependent RNA polymerases in plants