New Insights into nuclear import and nucleolar localization of yeast RNA exosome subunits

Neto, V. G.; Cepeda, L. P. P.; Queiroz, B. R. S.; Cantaloube, S.; Leger-Silvestre, I.; Mangeat, T.; Albert, B.; Gadal, O.; Oliveira, C. C.

doi:10.1101/2025.02.25.640171

bioRxiv · 10.1101/2025.02.25.640171

New Insights into nuclear import and nucleolar localization of yeast RNA exosome subunits

Neto, V. G.·Cepeda, L. P. P.·Queiroz, B. R. S.·Cantaloube, S.·Leger-Silvestre, I.·Mangeat, T.·Albert, B.·Gadal, O.·Oliveira, C. C.

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Abstract

The RNA exosome is a multiprotein complex essential for RNA maturation and degradation. In budding yeast, a nine-subunit protein complex (Exo9) associated with Rrp44 forms Exo10 in the cytoplasm and, in complex with Rrp6, Exo11 in the nucleus. Depending on its subcellular localization, the exosome interacts with different cofactors and RNA substrates. In the cytoplasm, Exo10 associates with the SKI complex via Ski7, while in the nucleus, Exo11 interacts with the TRAMP complex. Within the nucleolus, the exosome participates in ribosomal RNA (rRNA) processing, facilitated by Mtr4-dependent adaptors Utp18 and Nop53. In this manuscript, we have performed a comprehensive study that addresses the targeting mechanism and precise subcellular localization of all members of the Exo11 complex. We observed a high concentration of all Exo11 subunits in the nucleolus and identified the importins Srp1 () and Kap95 ({beta}) as responsible for the nuclear import of Exo9 subunits. Notably, Exo9 subunits localization was not significantly disrupted in the simultaneous absence of NLS-containing subunits Rrp6 and Rrp44, suggesting redundant nuclear import pathways for Exo9. Additionally, we show evidence that Ski7 may play a role in the Exo9 retention in the cytoplasm. To explore the exosome sub-nucleolar localization, we compared Rrp43 with nuclear exosome cofactors and show that it is enriched in the same nucleolar region as Mtr4 and Nop53. In conclusion, our findings provide a detailed characterization of Exo11 distribution, highlight the primary nuclear import mechanisms for Exo9, and reveal the specific localization of the exosome within the granular component (GC) of the yeast nucleolus, suggesting a spatial regulation of the RNA processing pathway. Highlights- Comprehensive study of the localization of all exosome subunits in yeast. - Identification of karyopherins involved in exosome nuclear import. - Ski7 dependent cytoplasmic retention of exosome. - Yeast sub-nucleolar organization of exosome and its cofactors.

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Neto, V. G., Cepeda, L. P. P., Queiroz, B. R. S., Cantaloube, S., Leger-Silvestre, I., Mangeat, T., Albert, B., Gadal, O., Oliveira, C. C.. 2025-03-01. New Insights into nuclear import and nucleolar localization of yeast RNA exosome subunits. https://doi.org/10.1101/2025.02.25.640171

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