Not4-dependent targeting of MMF1 mRNA to mitochondria limits its expression via ribosome pausing, Egd1 ubiquitination, Caf130, No-Go-Decay and autophagy

The Ccr4-Not complex is a conserved multi protein complex with diverse roles in the mRNA life cycle. Recently we determined that the Not1 and Not4 subunits of Ccr4-Not inversely regulate mRNA solubility and thereby impact dynamics of co-translation events. One mRNA whose solubility is limited by Not4 is MMF1 encoding a mitochondrial matrix protein. In this work we determine that Not4 promotes the co-translational docking of MMF1 mRNA to mitochondria via the mitochondrial targeting sequence of the Mmf1 nascent chain, the Egd1 chaperone, the Om14 mitochondrial outer membrane protein and the co-translational import machinery. We observe that MMF1 mRNA is translated with ribosome pausing and uncover a mechanism that depends upon its targeting to the mitochondria and limits its overexpression. We have named this mechanism Mito-ENCay. It relies on Egd1 ubiquitination by Not4, the Caf130 subunit of the Ccr4-Not complex, the mitochondrial outer membrane protein Cis1, No-Go-Decay as well as autophagy. We propose that in fermenting yeast, mRNAs whose encoded proteins depend upon co-translational folding and/or assembly are regulated by Caf130-dependent quality control mechanisms similar to Mito-ENCay.