rRNA processing is surveilled by the mRNA guard protein Npl3

Ribosomes mature stepwise on a long precursor-rRNA, the 35S rRNA in Saccharomyces cerevisiae. Successive cleavage and protein association generates the small and large subunits that join each other for translation. If the maturation encounters difficulties, pre-rRNA cleavage occurs irrevocably at site A3, generating the aberrant 23S rRNA that is degraded. We show that the mRNA guard protein Npl3 functions in rRNA maturation and its surveillance. In its absence, the early SSU processome assembly is disturbed as the ETS1 accumulates and some proteins are not loaded properly onto the rRNA. Additionally, the amount of the 23S rRNA increases, which indicates a novel role of Npl3 its removal. For this quality control function, Npl3 binds to the nascent pre-rRNA in a complex with the TRAMP-complex component Air1, but independently of Trf5. Although Trf5 is still able to mark such RNAs with an oligo d(T) sequence in npl3?, this signal is not sufficient for full TRAMP complex assembly. Rather, the Npl3-mediated loading of Air1 supports the exosome recruitment and the elimination of the 23S rRNA. Thus, Npl3 represents a general RNA surveillance factor that clears the cell from faulty mRNA and rRNA products by recognition of processing defects and guiding degrading enzymes. Overall design: To investigate the role of Npl3 in the rRNA quality control, we sequenced rRNA in wild type cells and in the deletion strain npl3?.