The Saccharomyces cerevisiae Nrd1-Nab3 Transcription Termination Pathway Acts in Opposition to Ras Signaling and Mediates Response to Nutrient Depletion

Abstract

The Saccharomyces cerevisiae Nrd1-Nab3 pathway directs the termination and processing of short RNA polymerase II transcripts. Despite the potential for Nrd1-Nab3 to affect the transcription of both coding and noncoding RNAs, little is known about how the Nrd1-Nab3 pathway interacts with other pathways in the cell. Here we present the results of a high-throughput synthetic lethality screen for genes that interact with NRD1 and show roles for Nrd1 in the regulation of mitochondrial abundance and cell size. We also provide genetic evidence of interactions between the Nrd1-Nab3 and Ras/protein kinase A (PKA) pathways. Whereas the Ras pathway promotes the transcription of genes involved in growth and glycolysis, the Nrd1-Nab3 pathway appears to have a novel role in the rapid suppression of some genes when cells are shifted to poor growth conditions. We report the identification of new mRNA targets of the Nrd1-Nab3 pathway that are rapidly repressed in response to glucose depletion. Glucose depletion also leads to the dephosphorylation of Nrd1 and the formation of novel nuclear speckles that contain Nrd1 and Nab3. Taken together, these results indicate a role for Nrd1-Nab3 in regulating the cellular response to nutrient availability.

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ACKNOWLEDGMENTS

This work was supported by NIH/NIGMS grant numbers R01GM066108 to J.L.C. and R01HG002432 to J.D.B.

We thank Elisa Vidal-Cardenas for her help with initial Western blots, Robert Jensen (Johns Hopkins) for his advice on the mitochondrial overabundance phenotype, and Roy Parker (University of Arizona) for his advice on examining colocalization between Nrd1, stress granules, and P bodies. Pub1 and Dcp2 expression plasmids were a gift from the Parker laboratory. The Sik1-RFP strain was a gift from Erin O'Shea (Harvard), and the high-copy-number PDE2 plasmid was a gift from Paul Herman (Ohio State University). The template for mCherry tagging was a gift from Roger Tsien (University of California, San Diego).