Crt10 directs the cullin-E3 ligase Rtt101 to nonfunctional 25S rRNA decay

• Nonfunctional 25S rRNA decay (25S NRD) involves an E3 ubiquitin ligase complex.
• Crt10 is required for the ubiquitination of nonfunctional ribosomes.
• Crt10 confines the substrate specificity of the Rtt101-Mms1-containing E3 ubiquitin ligase.

Nonfunctional mutant ribosomal RNAs in 40S or 60S subunits are selectively degraded in eukaryotic cells (nonfunctional rRNA decay, NRD). We previously reported that NRD of 25S rRNA required cullin-E3 ligase Rtt101 and its associating factor Mms1, both of which are involved in DNA repair. Although Mms22, an accessory component of the E3 complex, was suggested to direct the E3 complex to DNA repair, the factor that directs the complex to 25S NRD currently remains unknown. We herein demonstrated that another accessory component, Crt10 was required for 25S NRD, but not for DNA repair, suggesting that this accessory component specifies the function of the E3 complex differently. We also identified two distinct Crt10-containing E3 complexes, one of which contained the Paf1 complex, a Pol-II binding complex that modulates the transcription of stress-related genes. Our results showed the convergence of multiple pathways for stresses that harm nucleic acids and provided a molecular framework for the substrate diversity of the E3 complex.