The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription

Abstract

Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental process must be precisely regulated to satisfy cell needs at any time. We present in vivo evidence that, when growth is arrested by nutrient deprivation, cells induce rapid clearance of Pol I–Rrn3 complexes, followed by the assembly of inactive Pol I homodimers. This dual repressive mechanism reverts upon nutrient addition, thus restoring cell growth. Moreover, Pol I dimers also form after inhibition of either ribosome biogenesis or protein synthesis. Our mutational analysis, based on the electron cryomicroscopy structures of monomeric Pol I alone and in complex with Rrn3, underscores the central role of subunits A43 and A14 in the regulation of differential Pol I complexes assembly and subsequent promoter association.DOI: http://dx.doi.org/10.7554/eLife.20832.001

RNA polymerase I activation and hibernation: unique mechanisms for unique genes

“…As mentioned, ordering of the A43 C-terminal tail enables essential contacts for enzyme dimerization. Conformation II corresponds to free monomeric Pol I, and it has also been observed in Rrn3-bound Pol I [21–24]. This configuration presents a semi-expanded cleft of about 38 Å in width, a partially-unfolded bridge helix and a disordered DNA-mimicking loop.…”

“…In this conformation, the A12.2 C-terminal domain has been found either disordered or partially ordered inside the pore. The major difference between free monomeric and Rrn3-bound Pol I is the stalk, which appears flexible in the former while it is fixed upon Rrn3 interaction, with the exception of the A43 C-terminal tail [24]. Finally, conformation III corresponds to Pol I in the pre-initiation and elongation complexes, and is defined by a closed cleft of about 30 Å in width and a fully ordered bridge helix [14–16,22,25].…”

“…The bridge helix remains partially unfolded and the trigger loop is disordered. This transition, which implies disruption of Pol I homodimers into monomers and disordering of the DNA-mimicking loop, plays an important role in the regulation of rDNA transcription [24]. The transition between conformations II and III involves full closure of the cleft by further approach of the rigid shelf-clamp module towards the jaw-lobe (Figure 1(B)).…”

“…When detached from DNA, free monomeric Pol I cannot directly be recruited to rDNA promoters but requires prior binding to the activating factor Rrn3 [12,13]. This event allows direct downregulation of rRNA production by Rrn3 degradation [24,30]. In addition, rDNA transcription is also down-tuned by Pol I dimerization [24].…”

“…Two independent studies reported the crystal structure of Pol I in its inactive dimeric conformation [19,20]. More recently, electron cryomicroscopy (cryo-EM) analysis revealed the structures of Pol I in the free monomeric and Rrn3-bound states [21–24]. Additional cryo-EM studies reported the structures of Pol I engaged in elongation [22,25].…”