Differential activation mechanisms of two isoforms of Gcr1 transcription factor generated from spliced and un-spliced transcripts in Saccharomyces cerevisiae

Gcr1, an important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1(U) and Gcr1(S), produced from un-spliced and spliced transcripts, respectively. In this study, by generating strains expressing only Gcr1(U) or Gcr1(S) using the CRISPR/Cas9 system, we elucidate differential activation mechanisms of these two isoforms. The Gcr1(U) monomer forms an active complex with its coactivator Gcr2 homodimer, whereas Gcr1(S) acts as a homodimer without Gcr2. The USS domain, 55 residues at the N-terminus existing only in Gcr1(U), inhibits dimerization of Gcr1(U) and even acts in trans to inhibit Gcr1(S) dimerization. The Gcr1(S) monomer inhibits the metabolic switch from fermentation to respiration by directly binding to the ALD4 promoter, which can be restored by overexpression of the ALD4 gene, encoding a mitochondrial aldehyde dehydrogenase required for ethanol utilization. Gcr1(U) and Gcr1(S) regulate almost the same target genes, but show unique activities depending on growth phase, suggesting that these isoforms play differential roles through separate activation mechanisms depending on environmental conditions.