In a dynamic nutrient environment, cells commit to metabolic pathways to utilize the nutrients that are available, which is determined at the level of gene regulation. Specifically, yeast Saccharomyces cerevisiae cells undergo a metabolic shift from glycolysis to gluconeogenesis in the absence of the fermentable carbon source glucose before they enter stationary phase. This phenomenon is known as a diauxic shift and is conserved among all eukaryotic and aerobic prokaryote species. A gene tightly regulated during this process, GCR1, encodes a transcription factor also known to regulate about 75% of all RNA Polymerase II transcripts in the cell. For these reasons understanding how GCR1 itself is regulated will not only expand our understanding of basic mechanisms of gene expression, but will also contribute to fields including cancer biology, wherein dynamic gene regulation plays a major role. Here, we demonstrate Gcr1 protein levels are regulated in a manner that is glucose- dependent. Unexpectedly, GCR1 generates multiple protein isoforms when cells are grown in a glucose-rich environment. Remarkably, exclusive expression of each isoform causes overlapping and distinct effects on genome- wide RNA expression, suggesting that changing the ratio of Gcr1 isoforms provides a means by which the cell can elicit highly specific changes in gene expression. Consistent with this, GCR1 isoforms are differentially regulated in response to glucose depletion, supporting a model whereby the cell alters the Gcr1 isoform ratio to enable robust metabolic adjustment when exposed to a fluctuating glucose environment

The transcription factor Gcr1 controls expression of over 75% of the genes in actively growing yeast. Yet despite its widespread effects, regulation of Gcr1 itself remains poorly understood. Here, we show that posttranscriptional Gcr1 regulation is nutrient dependent. Moreover, GCR1 RNA contains a long, highly conserved intron, which allows the cell to generate multiple RNA and protein isoforms whose levels change upon glucose depletion. Intriguingly, an isoform generated by intron retention is exported from the nucleus, and its translation is initiated from a conserved, intronic translation start site. Expression of gene products from both the spliced and unspliced RNAs is essential, as cells expressing only one isoform cannot adjust their metabolic program in response to environmental changes. Finally, we show that the Gcr1 proteins form dimers, providing an elegant mechanism by which this one gene, through its regulation, can perform the repertoire of transcriptional activities necessary for fine-tuned environmental response.