Mitochondrial cysteinyl-tRNA synthetase is expressed via alternative transcriptional initiation regulated by energy metabolism in yeast cells

Eukaryotes typically utilize two distinct aminoacyl-tRNA synthetase isoforms, one for cytosolic and one for mitochondrialprotein synthesis. However, the genome of budding yeast (Saccharomyces cerevisiae) contains only one cysteinyl-tRNA synthetase gene (YNL247W, also known as CRS1). In this study, we report that CRS1 encodes both cytosolic and mitochondrial isoforms. The 5′ complementary DNA end method and GFP reporter gene analyses indicatedthat yeast CRS1 expression yields two classes of mRNAs through alternative transcription starts: a long mRNA containing a mitochondrial targetingsequence and a short mRNA lacking this targeting sequence. We found that the mitochondrial Crs1 is the product of translationfrom the first initiation AUG codon on the long mRNA, whereas the cytosolic Crs1 is produced from the second in-frame AUGcodon on the short mRNA. Genetic analysis and a ChIP assay revealed that the transcription factor heme activator protein (Hap)complex, which is involved in mitochondrial biogenesis, determines the transcription start sites of the CRS1 gene. We also noted that Hap complex–dependent initiation is regulated according to the needs of mitochondrial energy production.The results of our study indicate energy-dependent initiation of alternative transcription of CRS1 that results in production of two Crs1 isoforms, a finding that suggests Crs1's potential involvement in mitochondrial energymetabolism in yeast.