Phosphoproteomic analysis identifies proteins involved in transcription-coupled mRNA decay as targets of Snf1 signaling

The exoribonuclease Xrn1 participates in mRNA homeostasis downstream of the energy and nutrient-sensing kinase Snf1. Cells Adapt with Snf1 and Xrn1 Cells adapt to starvation in part through activation of the AMPK family of protein kinases. In yeast, the AMPK family member Snf1 responds to the lack of glucose by phosphorylating various proteins, including those that activate transcription of genes involved in the consumption of other nutrient sources. Braun et al. analyzed the proteome for changes in phosphorylation in normal and Snf1 activity–deficient yeast grown under glucose-deficient conditions and found Snf1-dependent changes in more than 100 proteins, including several proteins involved in the synthesis and decay of mRNA. One such protein known as Xrn1, which may couple mRNA synthesis and decay, was required for the activation of Snf1-dependent genes in the absence of glucose and their subsequent degradation when yeast were fed with glucose. Understanding Snf1-regulated proteins in yeast could inform studies in human cellular nutrient metabolism. Stresses, such as glucose depletion, activate Snf1, the Saccharomyces cerevisiae ortholog of adenosine monophosphate–activated protein kinase (AMPK), enabling adaptive cellular responses. In addition to affecting transcription, Snf1 may also promote mRNA stability in a gene-specific manner. To understand Snf1-mediated signaling, we used quantitative mass spectrometry to identify proteins that were phosphorylated in a Snf1-dependent manner. We identified 210 Snf1-dependent phosphopeptides in 145 proteins. Thirteen of these proteins are involved in mRNA metabolism. Of these, we found that Ccr4 (the major cytoplasmic deadenylase), Dhh1 (an RNA helicase), and Xrn1 (an exoribonuclease) were required for the glucose-induced decay of Snf1-dependent mRNAs that were activated by glucose depletion. Unexpectedly, deletion of XRN1 reduced the accumulation of Snf1-dependent transcripts that were synthesized during glucose depletion. Deletion of SNF1 rescued the synthetic lethality of simultaneous deletion of XRN1 and REG1, which encodes a regulatory subunit of a phosphatase that inhibits Snf1. Mutation of three Snf1-dependent phosphorylation sites in Xrn1 reduced glucose-induced mRNA decay. Thus, Xrn1 is required for Snf1-dependent mRNA homeostasis in response to nutrient availability.