Rat1p and Rai1p function with the nuclear exosome in the processing and degradation of rRNA precursors

Exoribonucleases function in the processing and degradation of a variety of RNAs in all organisms. These enzymes play a particularly important role in the maturation of rRNAs and in a quality-control pathway that degrades rRNA precursors upon inhibition of ribosome biogenesis. Strains with defects in 3′–5′ exoribonucleolytic components of the RNA processing exosome accumulate polyadenylated precursor rRNAs that also arise in strains with ribosome biogenesis defects. These findings suggested that polyadenylation might target pre-rRNAs for degradation by the exosome. Here we report experiments that indicate a role for the 5′–3′ exoribonuclease Rat1p and its associated protein Rai1p in the degradation of poly(A) + pre-rRNAs. Depletion of Rat1p enhances the amount of poly(A) + pre-rRNA that accumulates in strains deleted for the exosome subunit Rrp6p and decreases their 5′ heterogeneity. Deletion of RAI1 results in the accumulation of poly(A) + pre-rRNAs, and inhibits Rat1p-dependent 5′-end processing and Rrp6p-dependent 3′-end processing of 5.8S rRNA. RAT1 and RAI1 mutations cause synergistic growth defects in the presence of rrp6 -Δ, consistent with the interdependence of 5′-end and 3′-end processing pathways. These findings suggest that Rai1p may coordinate the 5′-end and 3′-end processing and degradation activities of Rat1p and the nuclear exosome.