Yeast Edc3 targets RPS28B mRNA for decapping by binding to a 3' untranslated region decay-inducing regulatory element

mRNA decapping commits a transcript to complete turnover in eukaryotic cells. In yeast, general mRNA decapping requires the Dcp1/Dcp2 decapping enzyme and a set of decapping activators, including Pat1, Dhh1, Edc3, and the Lsm1-7 complex. The exact function and mode of action of each of these decapping activators in mRNA decapping largely remain elusive. Here, we analyzed the role of Edc3 in the decay of yeast RPS28B mRNA, a pathway triggered by a negative-feedback autoregulatory mechanism. We show that Edc3-mediated RPS28B mRNA decay requires either of two orthologous proteins, Rps28a and Rps28b, expressed from the RPS28A and RPS28B genes, respectively. Contrary to a generally accepted model, we found that Rps28b does not bind to the 3'-untranslated region (UTR) regulatory element in RPS28B mRNA. Instead, Edc3 is directly involved in binding the element, and Rps28b binds Edc3 and regulates its activity. Decay of RPS28B mRNA requires the Lsm and YjeF-N domains of Edc3, but surprisingly, decay of YRA1 pre-mRNA, the only other known substrate of Edc3, requires only the Lsm domain. Collectively, our experiments reveal a new role for Edc3 in mRNA substrate recognition and suggest that this activity is subject to intricate regulation by additional factors, including the Rps28 ribosomal protein.