Regulation of the association of the PAF53/PAF49 heterodimer with RNA polymerase I

•The association of the heterodimer of PAF53 and PAF49 with RNA Pol I is regulated.•PAF49 is acetylated.•The acetylation state of PAF49 affects the binding of the heterodimer to Pol I.•Heterodimers containing hypoacetylated PAF49 are more stably associated with Pol I.•The heterodimer interacts with Rrn3.

Mammalian PAF49 and PAF53 form a heterodimer and are essential for transcription. However their roles in transcription have not been specifically defined. While the yeast homologues are “not essential” proteins, yeast cells deficient in the homologue of PAF53 grow at 50–66% the wild-type rate at 30 °C, but fail to grow at 25 °C (Liljelund et al., 1992; Beckouet et al., 2008). There is increasing evidence that these proteins may play important roles in transcription initiation and elongation.We have found that while some cells regulated the protein levels of both PAF53 and PAF49, other cells did not. However, in either case they regulated the nucleolar levels of the PAFs. In addition, we found that the association of PAF49/PAF53 with Pol I is regulated. In examining the mechanism that might regulate this association, we have found that PAF49 is acetylated on multiple sites. The acetylation state of PAF49 does not affect heterodimerization. However, hypoacetylated heterodimer binds to Pol I with greater affinity than acetylated heterodimer. Further, we have found that the heterodimer interacts with Rrn3. We propose a model, in which there is a biochemical interaction between the Pol I-associated heterodimer and Rrn3 and that this interaction facilitates the recruitment of Rrn3 to the polymerase. As the binding of Rrn3 to Pol I is essential to transcription initiation in yeast and mammals, our results provide a greater understanding of the regulation of Rrn3 function and provide biochemical underpinning for the roles of the PAF49/PAF53 heterodimer in transcription initiation and elongation by Pol I.