title: 40S subunit dissociation and proteasome-dependent RNA degradation in nonfunctional 25S rRNA decay.
abstract: 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.
authors.affiliation: Institute for Virus Research, Kyoto University, Kyoto, Japan.
authors.forename: Kotaro
authors.initials: K
authors.lastname: Fujii
authors.forename: Makoto
authors.initials: M
authors.lastname: Kitabatake
authors.forename: Tomoko
authors.initials: T
authors.lastname: Sakata
authors.forename: Mutsuhito
authors.initials: M
authors.lastname: Ohno
mesh_terms: D000251:Adenosine Triphosphatases / Q000378:metabolism; D018797:Cell Cycle Proteins / Q000378:metabolism; D029543:Nucleocytoplasmic Transport Proteins / Q000378:metabolism; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism*; D011485:Protein Binding; D020871:RNA Stability; D012335:RNA, Ribosomal / Q000378:metabolism*; D054682:Ribosome Subunits, Small, Eukaryotic / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D025801:Ubiquitin / Q000378:metabolism; D000074405:Valosin Containing Protein; D033921:Vesicular Transport Proteins / Q000378:metabolism
chemical_list: D018797:Cell Cycle Proteins; C104361:NPL4 protein, S cerevisiae; D029543:Nucleocytoplasmic Transport Proteins; D012335:RNA, Ribosomal; D029701:Saccharomyces cerevisiae Proteins; C444652:UFD1 protein, S cerevisiae; D025801:Ubiquitin; D033921:Vesicular Transport Proteins; C065039:RNA, ribosomal, 25S; D046988:Proteasome Endopeptidase Complex; D000251:Adenosine Triphosphatases; C000614177:CDC48 protein, S cerevisiae; D000074405:Valosin Containing Protein