We have investigated the possible involvement of the ubiquitin-proteasome system (UPS) in ribosome biogenesis. We find by immunofluorescence that ubiquitin is present within nucleoli and also demonstrate by immunoprecipitation that complexes associated with pre-rRNA processing factors are ubiquitinated. Using short proteasome inhibition treatments, we show by fluorescence microscopy that nucleolar morphology is disrupted for some but not all factors involved in ribosome biogenesis. Interference with proteasome degradation also induces the accumulation of 90S preribosomes, alters the dynamic properties of a number of processing factors, slows the release of mature rRNA from the nucleolus, and leads to the depletion of 18S and 28S rRNAs. Together, these results suggest that the UPS is probably involved at many steps during ribosome biogenesis, including the maturation of the 90S preribosome.The nucleolus serves many functions (4, 23, 36, 51); however, its most prominent function remains ribosome biogenesis. This process comprises rRNA gene transcription; processing of the 47S pre-rRNA to mature 18S, 5.8S, and 28S rRNAs; and assembly of preribosomal particles (21). Ribosome biogenesis is spatially organized in distinct compartments within the nucleolus. Transcriptionally active ribosomal genes are thought to be situated at either the boundaries of the fibrillar centers (FCs) and dense fibrillar components (DFCs) or in DFCs (45), whereas both the pre-rRNA processing and the assembly of preribosomal particles occur in the DFCs and granular components (GCs) (46). Ribosome biogenesis is regulated at multiple levels, including the transcription of ribosomal genes and the phosphorylation, methylation, and acetylation of component nucleolar factors, plus the trafficking and interaction of these factors (30).Proteasomal regulation has been implicated in many processes, including cell cycle progression, transcription, and antigen processing (24) (18,34,58). Indirect evidence has hinted at a possible role for the ubiquitin-proteasome system (UPS) in ribosomal biogenesis. Two different ubiquitination patterns have been reported for the late processing factor B23 (25,48). Several other ribosomal factors may be ubiquitinated, as suggested by a recent proteomic analysis in yeast (37). It has also been known for many years that two ubiquitin precursors are ribosomal fusion proteins (5,16,47). A large ribosomal subunit protein (L28) forms the most abundant ubiquitin-protein conjugate in yeast, and this modification is essential for ribosome function and efficient translation (53). A possible role for ubiquitin in nucleolus disassembly was also suggested (54). In addition, a ubiquitin ligase is known to regulate the processing and nuclear export of rRNA, as well as tRNA and mRNA in yeast (35). Finally, a temperature-sensitive point mutation of the Cic1p/Nsa3p yeast protein, an adaptor for the 26S proteasome, associates with early pre-60S particles (49), and inhibits both the synthesis of the mature 5.8S and 25S rRNAs and the releas...