Structural insights into transcription initiation by yeast RNA polymerase I

Abstract

In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre‐rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi‐subunit pre‐initiation complex (PIC) at the ribosomal RNA promoter. In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3, and Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11. Here, we present the cryo‐EM structure of the 18‐subunit yeast Pol I PIC bound to a transcription scaffold. The cryo‐EM map reveals an unexpected arrangement of the DNA and CF subunits relative to Pol I. The upstream DNA is positioned differently than in any previous structures of the Pol II PIC. Furthermore, the TFIIB‐related subunit Rrn7 also occupies a different location compared to the Pol II PIC although it uses similar interfaces as TFIIB to contact DNA. Our results show that although general features of eukaryotic transcription initiation are conserved, Pol I and Pol II use them differently in their respective transcription initiation complexes.

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

“…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]. As expected by the presence of nucleic acids in the cleft, the DNA-mimicking loop is disordered.…”

“…Promoter-attached initiation factors foster binding of RNA polymerase I (Pol I) in complex with the Rrn3 protein [11–13]. The complete assembly of enzyme and factors on the promoter constitutes the pre-initiation complex (PIC) that has been proposed to evolve from a closed to an open complex upon DNA melting, which in Pol I is independent from ATP hydrolysis [14–16]. As proposed by these authors, an initially transcribing complex (ITC) forms upon addition of the first RNA nucleotides in the presence of initiation factors, and subsequent enzyme dissociation from the PIC leads to the formation of an elongation complex (EC).…”

“…Additional cryo-EM studies reported the structures of Pol I engaged in elongation [22,25]. Finally, the structures of a minimal PIC comprising the CF, Rrn3 and Pol I in the absence and presence of melted DNA provided hints into the initiation process [14–16]. …”

Breaking the mold: structures of the RNA polymerase I transcription complex reveal a new path for initiation

“…Module I includes Rrn11 and the Rrn6 β-propeller domain whereas module II includes Rrn7 and the Rrn6 C-terminal helical headlock domain. Surprisingly, the Rrn7 cyclin folds, although similar in structure, have an altered rotational axis compared to TFIIB that is likely due to its unique interaction with the rDNA promoter [3–5]. …”

“…Given that the Pols share an evolutionarily conserved core and a set of conserved initiation factors, it was anticipated that the Pol I initiation complex may resemble that of the Pol II system [1]. However, these recent Pol I structures reveal an entirely new paradigm for eukaryotic Pol initiation factor architecture that breaks the mold of how initiation complexes assemble and interact with promoter DNA [3–5]. In this point of view, we summarize recent progress in understanding the molecular architecture of the yeast Pol I initiation complex.…”