Identification of Multiple RNA Features That Influence CCR4 Deadenylation Activity

The CCR4 family proteins are 3′–5′-deadenylases that function in the first step of the degradation of poly(A) mRNA. Here we report the purification to homogeneity of the yeast CCR4 protein and the analysis of its substrate specificities. CCR4 deadenylated a 7N+23A substrate (seven nucleotides followed by 23 A residues) in a distributive manner. Only small differences in CCR4 activity for different A length substrates were observed until only 1 A residue remained. Correspondingly, the Km for a 25N+2A substrate was found to be at least 20-fold lower than that for a 26N+1A substrate, although their Vmax values differed by only 2-fold. In addition, the total length of the RNA was found to contribute to CCR4 activity: up to 17 nucleotides (not necessarily poly(A)) could be recognized by CCR4. Poly(U), poly(C), and poly(G) were also found to be 12–30-fold better inhibitors of CCR4 compared with poly(A), supporting the observation that CCR4 contains a non-poly(A)-specific binding site. Surprisingly, even longer substrates (≥45 nucleotides) stimulated CCR4 to become a processive enzyme, suggesting that CCR4 undergoes an additional transition in the presence of such substrates. CCR4 also displayed no difference in its activity with capped or uncapped RNA substrates. These results indicate that CCR4 recognition of its RNA substrates involves several features of the RNA that could be sites in vivo for controlling the rate of specific mRNA deadenylation.