Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome

Abstract: Quality control requires discrimination between functional and aberrant species to selectively target substrates for destruction. Nuclear RNA quality control in Saccharomyces cerevisiae includes the TRAMP complex that marks RNA for decay via polyadenylation and helicase-dependent 3′ to 5′ degradation by the RNA exosome. Using reconstitution biochemistry we show that polyadenylation and helicase activities of TRAMP cooperate with processive and distributive exoribonuclease activities of the nuclear RNA exosome to selectively target and degrade an unmodified tRNA while leaving native tRNA intact. Inactivation of the distributive exoribonuclease activity of Rrp6 results in loss of substrate discrimination, leading to degradation of all RNAs. These data suggest that the activities of the Mtr4 helicase and Rrp6 exoribonuclease endow the TRAMP-RNA exosome complex with the ability to protect stable RNA while degrading defective RNA species. Rrp6 and its 3′-5′ exonuclease activity have previously been shown to contribute to quality control and processing of various types of nuclear RNAs. Our sequencing analysis further confirms that Rrp6 contributes to this process. Comparison of global RNA analysis of yeast strains containing either wild-type (WT) or exoribonuclease inactive Rrp6 (Rrp6 exo-) or lacking Rrp6 completely (rrp6Δ). Two biological replicates of each sample are included.