The role of RNA polymerase I lobe-binding subunits in regulation of transcription, rRNA proofreading and quality control of ribosome biosynthesis

• Applicants: Professor Dr. Christoph Engel; Privatdozent Dr. Joachim Griesenbeck; Professor Dr. Herbert Tschochner
• Subject Area: Biochemistry
• Term: since 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 522934942

All three nuclear RNA polymerases (RNAPs) share a common core structure but differ in subunit composition conferring specific functional and structural features to each of the enzymes. The 14 subunits containing RNA polymerase I (Pol I) from the yeast S. cerevisiae is a specialized enzyme which transcribes only one gene - the rRNA gene- with high rate and efficiency. One significant difference between Pol I and RNA polymerase II (Pol II) is seen at the “lobe”, a structural domain within the second largest subunit of eukaryotic Pols: Whereas in Pol II only subunit Rpb9 binds to the lobe structure, three subunits bind to the lobe in S. cerevisiae Pol I, namely the RNA cleavage stimulating factor Rpa12.2 and subunit Rpa34.5 which forms a heterodimer with subunit Rpa49. The Pol I lobe-binding subunits are considered built-in transcription factors because they resemble the Pol II transcription factors TFIIS, TFIIE and TFIIF in structure and function. Despite their homology to Pol II factors and Pol III subunits, the Pol I lobe binding subunits contribute significantly to making Pol I a highly specialized and efficient enzyme. Thus, unraveling the function and structural contribution of these subunits in the transcription process will be the main topic of this proposal. The aim of this proposal is to unravel molecular mechanism of how lobe-binding subunits impact crucial steps of the Pol I transcription cycle. The project is divided into distinct but closely interconnected work packages which highlight the roles of the lobe-binding subunits in transcription initiation and elongation, Pol I passages through nucleosomes in vivo as well as their role(s) in quality control of ribosomal RNA. These aspects shall be analyzed using well-established in vitro systems as well as dedicated in vivo techniques, supervised by Herbert Tschochner and Joachim Griesenbeck, respectively. Christoph Engel will contribute with his expertise in structural analyses. This will allow to achieve a comprehensive picture about important specific features of the Pol I transcription machinery.

• DFG Programme: Research Grants