Neo-functionalization in Saccharomyces cerevisiae: A Novel Nrg1-Rtg3 chimeric transcriptional modulator is essential to maintain mitochondrial DNA integrity

In Saccharomyces cerevisiae, the transcriptional repressor Nrg1 (Negative Regulator of Glucose-repressed genes) and the b/Zip transcription factor Rtg3 (ReTroGrade regulation) mediate glucose repression and mitochondria to nucleus signaling, respectively. Here we show a novel function for these two proteins, in which alanine promotes the formation of a chimeric Nrg1/Rtg3 regulator that represses the ALT2 gene (encoding an alanine transaminase paralogue of unknown function) expression. A NRG1/NRG2 paralogous pair, resulting from a post-wide genome, small scale duplication event, is extant in the Saccharomyces genus. Neo-functionalization of only one paralogue resulted in Nrg1, able to interact with Rtg3. Either nrg1{Delta} or rtg3{Delta} single mutant strains are unable to utilize ethanol and show a typical petite (small) phenotype on glucose. Neither of the WT genes complemented the petite phenotype, suggesting irreversible mitochondrial DNA damage in these mutants. Neither nrg1{Delta} nor rtg3{Delta} mutant strains express genes encoded by any of five polycistronic units transcribed from mitochondrial DNA in S. cerevisiae. This, and the direct measure of the mitochondrial DNA gene complement confirms that irreversible damage of the mitochondrial DNA occurred in both mutant strains and is consistent with an essential role of the chimeric Nrg1/Rtg3 regulator in mitochondrial DNA maintenance.