Molecular Basis of Rrn3-regulated RNA Polymerase I Initiation

Eukaryotic nuclear transcription is carried out by three different
Polymerases (Pol), Pol I, Pol II and Pol III. Among these, Pol I is
dedicated to transcription of the rRNA, which is the first step of
ribosome biogenesis, and cell growth is regulated during Pol I
transcription initiation by the conserved factor Rrn3/TIF-IA in
yeast/human. A wealth of structural information is available on Pol
II and its general transcription factors (GTFs). Recently, also the
architectures of Pol I and Pol III have been described by electron
microscopy and the additional subunits that are specific to Pol I
and Pol III have been identified as orthologs of the Pol II
transcription factors TFIIF and TFIIE. Nevertheless, we still lack
information about the architecture of the Pol I initiation complex
and structural data is missing explaining the regulation of Pol I
initiation mediated by its central transcription initiation factor
Rrn3. The Rrn3 structure solved in this study reveals a unique HEAT
repeat fold and indicates dimerization of Rrn3 in solution.
However, the Rrn3-dimer is disrupted upon Pol I binding. The Rrn3
structure further displays a surface serine patch. Phosphorylation
of this patch represses human Pol I transcription (Mayer et al,
2005; Mayer et al, 2004), and a phospho-mimetic patch mutation
prevents Rrn3 binding to Pol I in vitro, and reduces S. cerevisiae
cell growth and Pol I gene occupancy in vivo. This demonstrates a
conserved regulation mechanism of the Pol I-Rrn3 interaction.
Crosslinking indicates that Rrn3 does not only interact with Pol I
subunits A43/14, but the interface further extends past the RNA
exit tunnel and dock domain to AC40/19. The corresponding region of
Pol II binds the Mediator head (Soutourina et al., 2011) that
co-operates with TFIIB (Baek et al, 2006). Consistent with this,
the Rrn3 binding partner, core factor subunit Rrn7, is predicted to
be a TFIIB homologue. Taken together, our results provide the
molecular basis of Rrn3-regulated Pol I initiation and cell growth
and indicate a universally conserved architecture of eukaryotic
transcription initiation complexes.