Quantitative assessment of DNA damage in the industrial ethanol production strain Saccharomyces cerevisiae PE-2.

Lignocellulosic hydrolysates remain one of the most abundantly used substrates for the sustainable production of second generation fuels and chemicals with Saccharomyces cerevisiae. Nevertheless, fermentation inhibitors such as acetic acid, furfural and hydroxymethylfurfural are formed during the process and can lead to slow or stuck fermentations and/or act as genotoxic agents leading to production strain genetic instability. We have developed a novel dominant deletion (DEL) cassette assay for quantification of DNA damage in both wild-type and industrial yeast strains. Using this assay, the ethanol production strain S. cerevisiae PE-2 was shown to be more resistant to hydrogen peroxide and furfural than the laboratory DEL strain RS112. Indeed, the PE-2 strain also showed a lower tendency for recombination, consistent with a more efficient DNA protection. The dominant DEL assay presented herein should prove to be a useful tool in the selection of robust yeast strains and process conditions for second generation feedstock fermentations.