Molecular events during the release of delta-aminolevulinate dehydratase from catabolite repression

Long-read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae reveals condition-dependent intron abundance

Mitochondria fulfil many essential roles and have their own genome, which is expressed as polycistronic transcripts that undergo co- or posttranscriptional processing and splicing. Due to the inherent complexity and limited technical accessibility of the mitochondrial transcriptome, fundamental questions regarding mitochondrial gene expression and splicing remain unresolved, even in the model eukaryote Saccharomyces cerevisiae. Long-read sequencing could address these fundamental questions. Therefore, a method for the enrichment of mitochondrial RNA and sequencing using Nanopore technology was developed, enabling the resolution of splicing of polycistronic genes and the quantification of spliced RNA. This method successfully captured the full mitochondrial transcriptome and resolved RNA splicing patterns with single-base resolution and was applied to explore the transcriptome of S. cerevisiae grown with glucose or ethanol as the sole carbon source, revealing the impact of growth conditions on mitochondrial RNA expression and splicing. This study uncovered a remarkable difference in the turnover of Group II introns between yeast grown in either mostly fermentative or fully respiratory conditions. Whether this accumulation of introns in glucose medium has an impact on mitochondrial functions remains to be explored. Combined with the high tractability of the model yeast S. cerevisiae, the developed method enables to monitor mitochondrial transcriptome responses in a broad range of relevant contexts, including oxidative stress, apoptosis and mitochondrial diseases.

Cloning of the δ-aminolevulinic acid synthase structural gene in yeast

HEM1, the structural gene for δ-aminolevulinic acid synthase, has been isolated on recombinant plasmids. A yeast genomic pool constructed in the E. coli - yeast shuttle vector YEp13 was used to clone the HEM1 gene by complementation. A leu2 hem1 yeast mutants was transformed with the yeast genomic pool and hybrid YEp13 plasmids carrying the HEM1 gene were cloned by their ability to complement both the leu2 and hem1 mutations in the recipient strain. The yeast transformants, bearing the HEM1-containing plasmids pYe(HEM1), showed a 24-28 fold increase in δ-aminolevulinic acid synthase activity and in the intracellular content of δ-aminolevulinic acid (5-8 fold) as compared to wild type strains, suggesting that the p(HEM1) gene is being expressed as a catalytically active enzyme which can be transported into the mitochondria. However, the transformant strains did not present higher-than-normal content of heme or cytochromes either in glucose or in glycerol media, indicating that the production of δ-aminolevulinic acid is not the rate-limiting step in heme biosynthesis in yeast.

Porphyrin biosynthesis in normal and haem mutants of Saccharomyces cerevisiae. Studies on the inheritance of the HEM R+ phenotype

Heme biosynthesis was studied in the segregants of Saccharomyces cerevisiae (DW10 tetrade 2) from D27 and D27/C6 mating, as a function of the carbon source in the growth medium and the physiological state of the cells. The effects of the HEM R+ gene on the 5-aminolevulinate synthase (ALA-S) and 5-aminolevulinate dehydratase (ALA-D) activities of heme biosynthesis in cells grown on nonfermentable and fermentable carbon sources were compared. Profiles obtained for both strains grown on a fermentable carbon source (glucose) were identical. However, in the presence of a nonfermentable carbon source (ethanol), they behave quite different, as if the mutation could only be expressed under these growth conditions. Moreover, their behavior is similar to that found for the parental strains, indicating that for the mutant its particular behavior might be inheritedly linked to the HEM R+ gene, which in turn affects some regulatory aspects of ALA synthesis explaining its characteristic phenotype.

The role of ALA-S and ALA-D in regulating porphyrin biosynthesis in a normal and a HEM R+ mutant strain of Saccharomyces cerevisiae

Catabolite repression and derepression on delta-aminolevulinate synthase (ALA-S) and delta-aminolevulinate dehydratase (ALA-D) in a normal yeast strain, D27, and its derived D27/C6 (HEM R+) were investigated. ALA-S and ALA-D activities and intracellular ALA (I-ALA) at different physiological states of the cells were measured. In YPD medium, under conditions of repression and when glucose was exhausted, both strains behaved identically as if the mutation was not expressed. In YPEt medium, however, both ALA-S and ALA-D activities were higher than in YPD, but the I-ALA content and the enzymic activity profiles shown by the two strains were quite different. It appears, therefore, that the mutation causes a deregulation of ALA-S, so that its activity is kept at a high level throughout the cell cycle. This would explain the increased levels of cytochromes present in the mutant. This mutation may affect some regulatory aspect of ALA formation and renders an ALA-S of high activity; moreover, this enzyme species seems to be more stable than in the normal strain.

Distinctly regulated tandem upstream activation sites mediate catabolite repression of the CYC1 gene of S. cerevisiae

The upstream activation site (UAS) of the yeast CYC1 gene is shown to contain two homologous subsites, UAS1 and UAS2. Each site, when placed upstream of the transcriptional initiation region of the yeast LEU2 gene, activates LEU2 transcription which is regulated by catabolite repression. UAS1 is responsible for most of the transcription under glucose repressed conditions, while UAS1 and UAS2 contribute equally to lactate derepressed transcription. A single point mutation in UAS2 increases its activity in glucose 10- to 20-fold. Several experiments indicate that UAS1 and UAS2 are regulated distinctly at the molecular level. First, UAS1 but not UAS2 is fully depressed in glucose by increasing the levels of intracellular heme. Second, trans-acting regulatory mutations, hap1-1 and hap2-1, selectively abolish the activity of UAS1 or UAS2. HAP1 appears to encode a protein that mediates catabolite repression of UAS1 by responding to intracellular heme levels.

Modulation of cytochrome biosynthesis in yeast by antimetabolite action of levulinic acid

Levulinic acid, a competitive inhibitor of delta-aminolevulinic acid dehydratase, was used to inhibit cytochrome biosynthesis in growing yeast cells. In Saccharomyces cerevisiae the antimetabolite acts by inhibiting delta-aminolevulinic acid dehydratase in vivo, causing an accumulation of intracellular delta-aminolevulinic acid and simultaneous decreases in all classes of mitochondrial cytochromes. Changes in cellular cytochrome content with increasing levulinic acid concentration suggested the existence of different regulatory patterns in S. cerevisiae and Candida utilis. In C. utilis, cytochrome a.a3 formation is very resistant to the antimetabolite action of levulinic acid. In this aerobic yeast, cytochrome c+c1 is the most sensitive to levulinic acid, and cytochrome b exhibits intermediate sensitivity.