Quality control mechanisms operate in various steps of ribosomal biogenesis to ensure the production of functional ribosome particles. It was reported previously that mature ribosome particles containing nonfunctional mutant rRNAs are also recognized and selectively removed by a cellular quality control system (nonfunctional rRNA decay [NRD]). Here, we show that the NRD of 25S rRNA requires a ubiquitin E3 ligase component Rtt101p and its associated protein Mms1p, identified previously as factors involved in DNA repair. We revealed that a group of proteins associated with nonfunctional ribosome particles are ubiquitinated in a Rtt101-Mms1-dependent manner. 25S NRD was disrupted when ubiquitination was inhibited by the overexpression of modified ubiquitin molecules, demonstrating a direct role for ubiquitin in this pathway. These results uncovered an unexpected connection between DNA repair and the quality control of rRNAs. Our findings support a model in which responses to DNA and rRNA damages are triggered by a common ubiquitin ligase complex during genotoxic stress harmful to both molecules.[Keywords: Ubiquitin; ribosome; genotoxic stress; quality control; rRNA] Supplemental material is available at http://www.genesdev.org. Gene mutations often result in the production of nonfunctional RNA molecules. In addition, RNA itself is continuously damaged by endogenous and exogenous stress, including ionizing radiation, exposure to certain chemical compounds, and the intracellular generation of reactive oxygen species (Bregeon and Sarasin 2005). Rare but measurable errors in transcription also produce mutant RNAs that do not properly fulfill their roles and aims. In order to avoid a breakdown of cellular order, it is important for cells to detect and selectively dismantle such irregular RNA molecules continuously. It is well documented that various types of aberrant RNAs are selectively removed in eukaryotic cells (Doma and Parker 2007). Three pathways requiring distinct factors degrade different classes of aberrant mRNAs, including mRNAs with a nonsense mutation in their ORFs (nonsensemediated mRNA decay) (Isken and Maquat 2007), mRNAs with no termination codon (nonstop mRNA decay) van Hoof et al. 2002), and mRNAs with a highly stable structure that prevents ribosomal progression (no-go mRNA decay) (Doma and Parker 2006). Recently, it has been reported that tRNAs with hypomodifications are also selectively degraded in vivo, indicating that stable RNAs are monitored by cellular quality control systems (Kadaba et al. 2004;Chernyakov et al. 2008). However, it is not clear how the quality control of ribosomal RNAs (rRNAs), another species of stable RNAs, is achieved, although rRNAs are highly abundant and essential for life.The eukaryotic ribosome is a massive ribonucleoprotein (RNP) complex that consists of four rRNAs and about 80 ribosomal proteins (Venema and Tollervey 1999). The precursor 35S rRNA transcribed by RNA polymerase (Pol) I is processed into three parts; 18S, 5.8S, and 25S rRNA. 5S rRNA is synthesized indep...

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Eukaryotic cells have quality control systems that eliminate nonfunctional rRNAs with deleterious mutations (nonfunctional rRNA decay, NRD). We have previously reported that 25S NRD requires an E3 ubiquitin ligase complex, which is involved in ribosomal ubiquitination. However, the degradation process of nonfunctional ribosomes has remained unknown. Here, using genetic screening, we identified two ubiquitin-binding complexes, the Cdc48-Npl4-Ufd1 complex (Cdc48 complex) and the proteasome, as the factors involved in 25S NRD. We show that the nonfunctional 60S subunit is dissociated from the 40S subunit in a Cdc48 complex-dependent manner, before it is attacked by the proteasome. When we examined the nonfunctional 60S subunits that accumulated under proteasome-depleted conditions, the majority of mutant 25S rRNAs retained their full length at a single-nucleotide resolution. This indicates that the proteasome is an essential factor triggering rRNA degradation. We further showed that ribosomal ubiquitination can be stimulated solely by the suppression of the proteasome, suggesting that ubiquitin-proteasome-dependent RNA degradation occurs in broader situations, including in general rRNA turnover.

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Background: Increased oxidative stress is associated with various complications in hemodialysis (HD) patients. Methods: We examined the effect of coenzyme Q10 (CoQ10) administration on the plasma oxidative products and antioxidant capacity in 36 HD patients for 6 months. Results: The advanced oxidation protein products (AOPP), malondialdehyde and the percentage of ubiquinone in total CoQ10 were significantly higher in HD patients than in healthy subjects before administration (0 month). Oxygen radical absorbing capacity (ORAC) and Trolox equivalent antioxidant capacity (TEAC), indicators of total antioxidant capacity, were also paradoxically higher in the HD patients at 0 month. AOPP and the percentage of ubiquinone significantly decreased during CoQ10 administration, but increased again after the discontinuation. ORAC and TEAC were also decreased during CoQ10 administration. Conclusion: The CoQ10 administration was partially effective for suppressing the oxidative stress in HD patients. The unexpected decrease of ORAC and TEAC by CoQ10 seemed to be associated with a decreased oxidative stress.