Phosphorylation Patterns of Preribosomal Proteins Associated with the RNA Exosome

The RNA exosome is an essential and ubiquitous RNase with exonucleolytic activity that is involved in ribosome biogenesis and RNA quality control in eukaryotes. It is present both in the nucleus and cytoplasm and interacts with specific cofactors in each cell compartment, which are essential for the recruitment and activity control of the exosome. Post-translational modifications are known to regulate enzyme activity and protein interaction, although their precise roles are individually specific. In this study, we investigated the phosphorylation status of proteins associated with the nuclear (Rrp6) and core (Rrp46) subunits of the RNA exosome in Saccharomyces cerevisiae. Using coimmunoprecipitation followed by phosphopeptide enrichment and high-resolution mass spectrometry, we identified 114 phosphorylation sites on proteins functionally related to rRNA processing. Differential phosphorylation patterns between Rrp6 and Rrp46 coimmunoprecipitations are consistent with distinct exosome assemblies and suggest potential regulatory roles for phosphorylation. Several phosphosites were identified in exosome subunits and cofactors, revealing potential regulatory mechanisms for fine-tuning exosome function. The results shown here highlight the role of phosphorylation in the recruitment and control of the exosome in RNA processing and degradation, offering new insights into the post-transcriptional control of gene expression.