Standard YPD, even supplemented with extra nutrients, does not always compensate growth defects of Saccharomyces cerevisiae auxotrophic strains

Abstract

Conventional complex media are routinely used to grow auxotrophic strains under the assumption that they can compensate the latter's nutritional deficiencies. We here demonstrate that this is not always true. This study compares the growth parameters of Saccharomyces cerevisiae (S288C) and its derived auxotrophic strains FY1679-14C and BY4741 in synthetic minimal medium (SD), standard YPD medium from two of the most commonly used suppliers, or modified YPD medium. Maximum specific growth rates of auxotrophic strains were slightly lower than the prototrophic case in all growth conditions tested. Also, the biomass production of auxotrophic strains in synthetic medium was slightly less than the prototrophic case. However in both of the two standard YPD media used, the biomass production of both auxotrophic strains was markedly lower than that of the prototrophic one. The extent of the differences depended on the medium used. Indeed in one of the two YPD media, the lower biomass production of auxotrophic strains was evident even at the diauxic shift. Uracil seems to be the main limiting growth factor for both auxotrophic strains growing in the two standard YPD medium tested. No YPD media or specific supplement was able to compensate for the effect of the auxotrophic mutations in the multiple auxotrophic marker strain BY4741. The fact that auxotrophic strains grew poorly on YPD when compared to their prototrophic counterpart indicates that standard YPD medium is not sufficient to overcome the effect of auxotrophic mutations.

Efficient fermentation of an improved synthetic grape must by enological and laboratory strains of Saccharomyces cerevisiae

“…S288C-derived BY strains are auxotrophic for several amino acids and uracil; thus, auxotrophic supplements must be added, appropriate concentrations of which have been determined by considering the composition of the final biomass and the type of energy metabolism (Pronk [2002]). Auxotrophic supplementation is also necessary when using a complex medium, such as Yeast extract Peptone Dextrose (YPD) or grape must (Corbacho et al [2011]; Hanscho et al [2012]; Harsch et al [2010]). The optimal concentration of these supplements is still under debate.…”

Construction of a Quadruple Auxotrophic Mutant of an Industrial Polyploid Saccharomyces cerevisiae Strain by Using RNA-Guided Cas9 Nuclease

“…However, this was expected because there had been many reports regarding the growth defect of auxotrophic strains. Even standard YPD could not compensate for the growth defects of S. cerevisiae auxotrophic strains (34,35). Nevertheless, the ATCC 4124 auxotroph still performed significantly better than three laboratory strains.…”

Evolution in changing environments : heavy metal adaptation in experimental yeast populations as a case study

“…However, in our case we consider it more likely that the systematic discrepancy between fitness values is caused by a change in medium composition, which in turn has affected the relative reductive effect of each of the metals. YPD is a rich, undefined medium, and subtle changes in such media can have crucial consequences (Joho et al 1988;O'Keefe et al 2006;Corbacho et al 2011). In a pilot assay performed prior to this study, clone fitness correlated strongly with population fitness (data not shown).…”

“…First, the main problem that I came across was that fitness assays were sometimes irreproducible, particularly between batches of media. This problem is not specific to yeast, and might have been found with any organism cultured in undefined nutrient media (O'Keefe et al 2006;Corbacho et al 2011). It is possible that the consequences of variation in medium composition were particularly pronounced in my experimental set-up because metals have steep reaction norms (Joho et al 1988;Gadd 1993), such that small changes in effective concentration have far-reaching consequences for fitness.…”

“…That is, the same concentrations of Ni and Zn reduced overall yield (number of colonies after competition) more strongly in our current assays, while Cd had a smaller reductive effect. This difference in reductive effect may be due to subtle differences in the composition of our -undefined -media, which can have large consequences (Joho et al 1988;O'Keefe et al 2006;Corbacho et al 2011). Since we were unable to remedy this problem, we chose to correct our measurements for this effect.…”