Pol I lobe binding subunits drive elongation

A significant difference between RNA polymerase II (Pol II) and RNA polymerase I (Pol I) transcribed genes is the dense packing of Pol I molecules on its gene which ensures fast and efficient rRNA synthesis. In such an arrangement frequent pausing, which includes backtracking and RNA cleavage might be disadvantageous. Pol I and Pol II differ also in the amount and features of subunits which bind to the lobe structure of the core enzyme. In Pol II only subunit Rpb9 is bound to the lobe whereas in Pol I the subunits Rpa34.5 which dimerizes with Rpa49 and the RNA cleaving subunit Rpa12.2 are associated to the lobe. Using reconstituted transcription assays, we analyzed the mutual dependency of the different domains of the lobe binding subunits to optimize the elongation process. We found that the tandem Wing Helix domain of Rpa49 including the linker (L-tWH) supports forward movement and NTP misincorporation and inhibits cleavage when Pol I is in elongation mode. In contrast, the dimerization domain enforces cleavage and transcription fidelity. We present a model, how the dynamic interaction of lobe binding domains accomplishes optimal RNA synthesis which includes prevention of transcriptional stops during favorable transcription conditions even despite a possible incorporation of wrong nucleotides.