Structural and functional insights into the cytoplasmic RNA exosome and its cofactors

Keidel, Achim (2023): Structural and functional insights into the cytoplasmic RNA exosome and its cofactors. Dissertation, LMU München: Fakultät für Chemie und Pharmazie

Abstract

In eukaryotic cells, the RNA exosome serves as the primary 3' to 5' exonuclease responsible for degrading and processing various RNA substrates. To carry out its diverse functions, the exosome relies on compartment-specific cofactors that provide substrate specificity. In the cytoplasm, the conserved Ski238 complex, centered around the ATP-dependent RNA helicase Ski2, assists the exosome. Additionally, the bridging factor Ski7 in yeast, or its equivalent Hbs1L3 in higher eukaryotes, facilitates the interaction between the Ski238 complex and the RNA-degrading exosome. It is suggested that the Ski238 complex directly associates with the exosome to guide the RNA substrate towards the exosome's nuclease domain. However, molecular structures as proof for the direct channeling are not available and the precise coordination among these cofactors, which ultimately leads to RNA degradation, remains largely unknown. This thesis presents a collection of structural snapshots that reveal the process of cytoplasmic 3' to 5' RNA degradation by the exosome and its cofactors. This series of complex structures provide unprecedented details regarding the interplay between different modules and reveal significant conformational changes within the Ski238 complex. These conformational rearrangements play a crucial role in coordinating the helicase and the nuclease activity during the degradation process. Based on this knowledge, for the first time, we were able to reconstitute a full Ski238-Ski7-exosome assembly and reveal its cryoEM structure. Remarkably, the interface between the exosome and its cytosolic helicase Ski2 resembles the nuclear complex where the exosome interacts with the helicase Mtr4. In summary, the presented results offer a holistic understanding of the individual steps involved in 3' to 5' RNA degradation by the exosome in the cytoplasm of eukaryotic cells. These findings reveal both the similarities and differences between yeast and human complexes, serving as a foundation for further elucidation of cytosolic RNA quality control mechanisms.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 540 Chemie
• Fakultäten: Fakultät für Chemie und Pharmazie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 13. September 2023
• 1. Bericht­erstatter:in: Conti, Elena