During the course of EXORICO, we showed for the first time how the exosome, a central RNA degradation machine, physically interacts with protein translation machinery, the ribosome.
In the nuclear interaction with the ribosome precursor, the exosome degrades a protruding part of the pre-ribosome and thereby induces both compositional and structural changes. This interaction is transient and could only be observed because we were able to stall the process. To this end, an exosome with a mutated active site was engineered which halts the chemical reaction on the pre-ribosome and thus “freezes” the transient interaction. The resulting structural analysis showed how the exosome remodels the ribosome’s large subunit during maturation. The complex mechanistic investigation was performed using yeast as a model system. In further work we demonstrated that a functional human nuclear exosome can be reconstituted from its 14 building blocks and that it is remarkably similar to the yeast version, demonstrating a high conservation of an essential molecular machine in evolution.
In the cytosol, the exosome interacts with the mature, translating ribosome to control mRNA fate. Our studies using the yeast system showed that ribosomes bound to the exosome via a cytoplasmic cofactor, the Ski complex. This work served as a lauching point for us to characterize biochemically reconstituted human cytoplasmic ribosomes with human SKI bound to mRNA at high resolution. Strikingly, we identified a complex regulatory mechanism that controls the channeling of mRNA into the exosome, a mechanism employed by lower eukaryotes as well. Subsequent work revealed this mechanism is also used by exosome-cofactor complexes in the nucleus.
