Regulation of the Ysh1 endonuclease of the mRNA cleavage/polyadenylation complex by ubiquitin-mediated degradation

Mutation of the essential yeast protein Ipa1 has previously been demonstrated to cause defects in pre-mRNA 3ʹ end processing and growth, but the mechanism underlying these defects was not clear. In this study, we show that the <i>ipa1-1</i> mutation causes a striking depletion of Ysh1, the evolutionarily conserved endonuclease subunit of the 19-subunit mRNA Cleavage/Polyadenylation (C/P) complex, but does not decrease other C/P subunits. <i>YSH1</i> overexpression rescues both the growth and 3ʹ end processing defects of the <i>ipa1-1</i> mutant. <i>YSH1</i> mRNA level is unchanged in <i>ipa1-1</i> cells, and proteasome inactivation prevents Ysh1 loss and causes accumulation of ubiquitinated Ysh1. Ysh1 ubiquitination is mediated by the Ubc4 ubiquitin conjugating enzyme and Mpe1, which in addition to its function in C/P, is also a RING ubiquitin ligase. In summary, Ipa1 affects mRNA processing by controlling availability of the C/P endonuclease, and may represent a regulatory mechanism that could be rapidly deployed to facilitate reprogramming of cellular responses.