Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II

Abstract

SUMMARY 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 nonredundant roles in siRNA-directed DNA methylation and gene silencing. We show that Arabidopsis Pol IV and Pol V are composed of subunits that are paralogous or identical to the 12 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. Our 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.

A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development

“…We recently found another subunit, RDM2/NRPD4, that is shared by Pol IV and Pol V, and that is also necessary for the RdDM pathway (He et al 2009b). Like Pol II (Cramer 2002), Pol IV and Pol V are multisubunit complexes (Huang et al 2009;Ream et al 2009). In addition to requiring various polymerase subunits, the functioning of Pol II as well as of Pol I and Pol III requires several positive and negative transcriptional regulators (Wade and Struhl 2008).…”

“…The 24-nt siRNAs are generated in a pathway involving the putative DNA-directed RNA polymerase IV (Pol IV), RDR2 (RNA-dependent RNA polymerase 2), and DCL3 (Dicer-like RNA Pol IV and Pol V have distinct largest subunits-NRPD1 and NRPE1, respectively-but share some common subunits such as NRPD/E2 and NRPD/E4 (He et al 2009b). Some subunits of Pol IV and Pol V are also shared with Pol II (Huang et al 2009;Ream et al 2009). It appears that the plant-specific RNA Pol IV and Pol V evolved from an ancestral RNA polymerase to function specifically in RdDM.…”

“…Some subunits of Pol IV and Pol V are also shared with Pol II (Huang et al 2009;Ream et al 2009). It appears that the plant-specific RNA Pol IV and Pol V evolved from an ancestral RNA polymerase to function specifically in RdDM.…”

The SUMO E3 Ligase-Like Proteins PIAL1 and PIAL2 Interact with MOM1 and Form a Novel Complex Required for Transcriptional Silencing

“…In the RdDM pathway, 24-nucleotide small interfering RNA (siRNA) mediates de novo DNA methylation (Hamilton et al, 2002;Aufsatz et al, 2002;Matzke and Mosher, 2014). DNAdependent RNA polymerases IV and V (Pol IV and Pol V) are two multisubunit DNA-dependent RNA polymerases that are unique to plants (Ream et al, 2009;Huang et al, 2009;Law and Jacobsen, 2010). NRPD1 and NRPE1 are the largest subunits of Pol IV and Pol V, respectively (Herr et al, 2005;Kanno et al, 2005;Pontier et al, 2005;Ream et al, 2009;Huang et al, 2009).…”

“…DNAdependent RNA polymerases IV and V (Pol IV and Pol V) are two multisubunit DNA-dependent RNA polymerases that are unique to plants (Ream et al, 2009;Huang et al, 2009;Law and Jacobsen, 2010). NRPD1 and NRPE1 are the largest subunits of Pol IV and Pol V, respectively (Herr et al, 2005;Kanno et al, 2005;Pontier et al, 2005;Ream et al, 2009;Huang et al, 2009). The generation of 24-nucleotide siRNA is dependent on Pol IV, RNA-dependent RNA polymerase 2 (RDR2), and Dicer-like 3 Haag and Pikaard, 2011).…”