Deletion of the GAPDH gene contributes to genome stability in Saccharomyces cerevisiae

Cellular metabolism is directly or indirectly associated with various cellular processes by producing a variety of metabolites. Metabolic alterations may cause adverse effects on cell viability. However, some alterations potentiate the rescue of the malfunction of the cell system. Here, we found that the alteration of glucose metabolism suppressed genome instability caused by the impairment of chromatin structure. Deletion of the TDH2 gene, which encodes glyceraldehyde 3-phospho dehydrogenase and is essential for glycolysis/gluconeogenesis, partially suppressed DNA damage sensitivity due to chromatin structure, which was persistently acetylated histone H3 on lysine 56 in cells with deletions of both HST3 and HST4, encoding NAD+-dependent deacetylases. tdh2 deletion also restored the short replicative lifespan of cells with deletion of sir2, another NAD+-dependent deacetylase, by suppressing intrachromosomal recombination in rDNA repeats increased by the unacetylated histone H4 on lysine 16. tdh2 deletion also suppressed recombination between direct repeats in hst3∆ hst4∆ cells by suppressing the replication fork instability that leads to both DNA deletions among repeats. We focused on quinolinic acid (QUIN), a metabolic intermediate in the de novo nicotinamide adenine dinucleotide (NAD+) synthesis pathway, which accumulated in the tdh2 deletion cells and was a candidate metabolite to suppress DNA replication fork instability. Deletion of QPT1, quinolinate phosphoribosyl transferase, elevated intracellular QUIN levels and partially suppressed the DNA damage sensitivity of hst3∆ hst4∆ cells as well as tdh2∆ cells. qpt1 deletion restored the short replicative lifespan of sir2∆ cells by suppressing intrachromosomal recombination among rDNA repeats. In addition, qpt1 deletion could suppress replication fork slippage between direct repeats. These findings suggest a connection between glucose metabolism and genomic stability.

Thepol3-tHyperrecombination Phenotype and DNA Damage-Induced Recombination inSaccharomyces cerevisiaeIsRAD50Dependent

The DNA polymeraseδ(POL3/CDC2) allelepol3-tofSaccharomyces cerevisiaehas previously been shown to be sensitive to methylmethanesulfonate (MMS) and has been proposed to be involved in base excision repair. Our results, however, show that thepol3-tmutation is synergistic for MMS sensitivity withMAG1, a known base excision repair gene, but it is epistatic withrad50Δ, suggesting thatPOL3may be involved not only in base excision repair but also in a RAD50 dependent function. We further studied the interaction ofpol3-twithrad50Δby examining their effect on spontaneous, MMS-, UV-, and ionizing radiation-induced intrachromosomal recombination. We found thatrad50Δcompletely abolishes the elevated spontaneous frequency of intrachromosomal recombination in thepol3-tmutant and significantly decreases UV- and MMS-induced recombination in bothPOL3andpol3-tstrains. Interestingly,rad50Δhad no effect onγ-ray-induced recombination in both backgrounds between 0 and 50 Gy. Finally, the deletion ofRAD50had no effect on the elevated frequency of homologous integration conferred by thepol3-tmutation.RAD50is possibly involved in resolution of replication forks that are stalled by mutagen-induced external DNA damage, or internal DNA damage produced by growing thepol3-tmutant at the restrictive temperature.