Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II

Abstract

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.

Figure 1. Relationships of Arabidopsis Pol II, IV, and V Subunits to E. coli, Archaeai, and Yeast RNA Pol II Subunits

Numbers indicate percent protein coverage represented by peptides unique to that protein. “*” indicates that all peptides match both closely related proteins. Unshaded numbers represent alternate subunits detected at trace levels relative to the predominant subunit.

Figure 2. Verification of Pol V Subunit Associations

(A) Pol V includes subunits shared with other polymerases as well as a unique RPB5 family variant. Pol I, II, III, IV, and V were immunoprecipitated by virtue of FLAG-tagged catalytic subunits alongside NRPE6a, NRPE8b, NRPE10, NRPE11, and NRPE5 FLAG-tagged subunits. Duplicate immunoblots were probed with anti-FLAG, anti-NRPE1, anti-NRPE2/NRPD2 (abbreviated anti-NRPE2/D2), or an antibody recognizing the second-largest subunits of Pol I, II, or III. The two panels in the top row are from the same blot but focus on different size ranges. (B) Control immunoblot showing that the multiple high-molecular-mass bands characteristic of NRPE1 are lost in an nrpe1 null mutant (allele nrpd1b-11), indicating that the antibody is specific for NRPE1. (C) NRPE6b and NRPE9a are subunits of Pol V as well as Pol I, II, or III. Immunoprecipitation and immunoblot detection was as in (A). NRPE5 and NRPB2 immunoprecipitations serve as controls for Pol V and Pol II, respectively. “*” denotes a nonspecific band detected by the anti-FLAG antibody. (D) Phylogenetic tree based on a CLUSTALW alignment of Arabidopsis RPB9-like proteins with the RPB9 (Pol II), RPC11 (Pol III), and RPA12 (Pol I) subunit equivalents of yeast. (E) NRPE8a and NRPE6a associate with Pol V. Immunoprecipitation and immunoblot detection was as in (A). NRPE5 and NRPB7 serve as controls for Pol V and Pol II, respectively.

Figure 3. Pol V Utilizes a Distinct RPB3 Variant, NRPE3b, as well as an NRPE3a Variant Corresponding to the Pol II NRPB3 Subunit

(A) Alignment of the two Arabidopsis RPB3 family proteins with yeast RPB3. (B) HA-tagged NRPE3a/NRPB3 and NRPE3b were Immunoprecipitated and resulting immunoblots were probed using the indicated antibodies.

Figure 4. ColP Tests of Pol V, IV, and II Subunit Associations

(A) Pol I, II, III, IV, and V were immunoprecipitated by virtue of FLAG-tagged catalytic subunits along-side immunoprecipitated NRPE6a, NRPE8b, NRPE9a, NRPE10, NRPE11, and NRPE3b FLAG-tagged subunits. Duplicate immunoblots were probed with anti-FLAG, anti-NRPD1 (Pol IV), or anti-NRPB1-CTD (Pol II). The two panels in the top row show different exposures of the same blot, focused on different size ranges. (B) Pol I, II, III, IV, and V were immunoprecipitated using the indicated FLAG-tagged subunits and probed with anti-FLAG, anti-NRPE5, or anti-NRPE2/NRPD2. (C) Immunoprecipitation and immunoblotting using the indicated antibodies were as in (B).

Figure 5. nrpe5 Mutants Are Defective in RNA-Directed DNA Methylation and Retrotransposon Silencing

(A) Phylogenetic tree based on a CLUSTALW alignment of the five full-length RPB5-like proteins in Arabidopsis with the RPB5 subunits of yeast and human. (B) Locations of T-DNA insertions in the nrpb5-1/nrpe5-1 and nrpe5-1 alleles. Black boxes represent exons, black bars represent introns, and gray bars represent 5′ and 3′UTRs. (C) nrpe5-1 homozygous mutant plants display a delay in flowering under short-day conditions (8 hr light, 16 hr dark). The mean (±SEM) number of rosette leaves when the floral bolt reached 10 cm is graphed. All mutants are significantly different from wild-type based on a Student’s t test (p < 0.05). (D) Methylation-sensitive Southern blot analyses of wild-type, nrpe1, nrpd2/nrpd2, and nrpe5 mutants and three different nrpe5, 35S:FLAG-NRPE5 transgenic lines. Genomic DNA was digested with either HpaII (left, reports on ^meCG) or HaeIII (right, reports on ^meCNN) and probed for 5S rDNA repeats. Images for the HpaII or HaeIII digests are from the same exposures of the same Southern blots; the black vertical lines separate groups of lanes whose order was rearranged for clarity of presentation. (E and F) PCR-based methylation assay of AtSN1 and AtSN2 family retroelements. Genomic DNA was digested with HaeIII and subjected to PCR using AtSN1, AtSN2-1, or control primers that amplify sequences lacking HaeIII sites (At2g19920 in the case of [B], and an AtSN2 family element lacking HaeIII sites in the case of [C]). Diagrams show the relative positions of the primers flanking the HaeIII sites. (G) RT-PCR detection of AtSN1 and actin transcripts. (H) Small RNA blot analysis. Blots were probed for siRNAs corresponding to 45S or 5S rRNA genes, Copia or AtSN1 transposons, and miRNA 173 or trans-acting siRNA 255.

Figure 6. Comparison of RNA Polymerase Subunits in Pol II, IV, and V

(A) Subunits that are unique to Pol IV and/or Pol V compared to Pol II are shown in blue. Subunits common to Pol II, IV, and V are shown in green. The subunit interaction model is based on the yeast Pol II crystal structure (Armache et al., 2005; Cramer et al., 2001; Sampath et al., 2008). The thickness of lines connecting the subunits is proportional to the number of contacts. (B) Subunits that are unique to Pol V are shown in blue. Subunits common to Pol IV and Pol V are shown in green. The half-blue, half-green shading of the third-largest subunit reflects the fact that Pol V uses the NRPE3b variant that is not used appreciably by Pol IV in addition to the NRPE3a/NRPD3 variant that predominates in Pol IV. (C) Summary of the Arabidopsis genes that encode Pol II, IV, or V subunits.