Coordinated Control of rRNA Processing by RNA Polymerase I

Abstract

Ribosomal RNA (rRNA) is co- and post-transcriptionally processed into active ribosomes. This process is dynamically regulated by direct covalent modifications of the polymerase that synthesizes the rRNA, RNA polymerase I (Pol I), and by interactions with cofactors that influence initiation, elongation, and termination activities of Pol I. The rate of transcription elongation by Pol I directly influences processing of nascent rRNA, and changes in Pol I transcription rate result in alternative rRNA processing events that lead to cellular signaling alterations and stress. It is clear that in divergent species, there exists robust organization of nascent rRNA processing events during transcription elongation. This review evaluates the current state of our understanding of the complex relationship between transcription elongation and rRNA processing.

Keywords: RNA polymerase I; RNA processing; ribosome; transcription elongation.

Figure 1:. The RNA polymerases have structurally diverged to suit their cellular roles.

Structural studies of the eukaryotic nuclear RNA polymerases (Pol I PDB: 4C2M, Pol II PDB: 1WCM, and Pol III PDB: 5FJ9) have highlighted differences among the Pols. Yellow subunits are conserved among the Pols. The green Pol I A12.2 and Pol III C11 subunit is conserved between Pols I and III and the N-terminal domain of A12.2 and C11 is homologous to the Rpb9 subunit of Pol II. Teal Pol I subunit A34 and Pol III subunit C25 and purple Pol I subunit A49 and Pol III subunit C37 are conserved between Pols I and III. Pol III has 3 additional subunits as compared to Pols I and II, red subunit C31, pink subunit C34, and orange subunit C82.

Figure 2, Key Figure:. Elongation rate of Pol I drives rRNA folding and ribosome maturation.

A) Transcription of the rDNA (dark blue line) by wild type Pol I (light blue circle) results in properly folded ribosomal RNA (orange line) which is then properly processed into 20S rRNA and results in correct polysome profiling signifying properly folded, healthy ribosomes (green ovals). B) Slow polymerase mutants result in improperly folded rRNA which result in incorrectly cleaved pre-rRNAs (such as the 23S rRNA), polysome profiles with half-mers (denoted by H) and ultimately inactive ribosomes. [27].

Figure 3:. Nutrient limitations and stress result in alternative ribosome biogenesis pathways.

Studies suggest two distinct pathways for rRNA processing (orange line) influenced by TOR and CK2 signaling. CK2 signaling promotes A3 cleavage, which results in reduced functional ribosome synthesis. TOR signaling promotes A2 cleavage, resulting in mature, productive ribosomes.

Figure 4:. Ribosome biogenesis inhibitors CX-5461 and BMH-21 act through distinct mechanisms.

A) CX-5461 (red star) works by inhibiting two activities: 1) CX-5461 prevents SL1 (orange oval) binding to Pol I (blue circle) which results in lack of Pol I binding to the rDNA, 2) CX-5461 works in the nucleolus to stabilize g-quadruplexes and also results in DNA damage response pathways, likely by interacting with the rDNA. B) BMH-21 (red hexagon) is a DNA intercalator and is proposed to bind to the rDNA and inhibit Pol I elongation. Subsequent to impaired transcription elongation by BMH-21, the largest subunit of Pol I is subject to ubiquitination and proteasome-mediated degradation (yellow pacman).