Abstract
The exosome is a conserved multiprotein complex essential for RNA processing and degradation. The nuclear exosome is a key factor for pre-rRNA processing through the activity of its catalytic subunits, Rrp6 and Rrp44. In Saccharomyces cerevisiae, Rrp6 is exclusively nuclear and has been shown to interact with exosome cofactors. With the aim of analyzing proteins associated with the nuclear exosome, in this work, we purified the complex with Rrp6-TAP, identified the co-purified proteins by mass spectrometry, and found karyopherins to be one of the major groups of proteins enriched in the samples. By investigating the biological importance of these protein interactions, we identified Srp1, Kap95, and Sxm1 as the most important karyopherins for Rrp6 nuclear import and the nuclear localization signals recognized by them. Based on the results shown here, we propose a model of multiple pathways for the transport of Rrp6 to the nucleus.
Highlights
The exosome is a conserved multiprotein complex essential for RNA processing and degradation
Despite the difference in expression levels of the bait proteins, the band profile of the proteins coimmunoprecipitated with Rrp6-TAP was similar to that of the exosome co-immunoprecipitated with Rrp43-TAP [16], and all the exosome subunits were identified in the elution fraction (Fig. 1A)
For the identification of the proteins co-immunoprecipitated with Rrp6-TAP, the eluted fraction was analyzed by mass spectrometry
Summary
The exosome is a conserved multiprotein complex essential for RNA processing and degradation. The first identified sequence was the simian virus 40 large tumor antigen-like nuclear localization signal (classical NLS), which is recognized by karyopherin ␣ (Srp in yeast) and transported to the nucleus as a trimeric complex with karyopherin  (Kap in yeast) and the cargo protein [19, 20]. Another nuclear import route occurs through the recognition of a different NLS in the cargo by a karyopherin  and the transport of a heterodimer to the nucleus [21]. The results shown here provide evidence for alternative pathways of Rrp transport to the cell nucleus
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