Saccharomyces cerevisiae
To enable construction of a minimal glycolysis yeast strain, a first goal was to identify the major paralogs that should be retained in the final strain design. This assessment was based on literature information on phenotypes of relevant deletion mutants and on non-glycolytic roles (moonlighting functions of glycolytic isoenzymes). Furthermore, a compendium of S. cerevisiae transcriptome data, obtained under a wide range of controlled cultivation conditions, was used to compare expression profiles of glycolytic paralogs. Major paralogs were elected based on the following, non-exclusive criteria highest transcript level over a range of growth conditions, ii) most extensive loss of enzyme activity in cell extracts upon deletion, iii) moonlighting functions with strong impact on specific growth rate or robustness (HXK2, ENO1 and ENO2), iv) strongest decrease in specific growth rate upon deletion. Based on these criteria, 11 of the 27 glycolytic genes S. cerevisiae were assessed to be major paralogs: HXK2, PGI, FBA1, TPI1, TDH3, GPM1, ENO2, PGI1, PYK1 (CDC19), PDC1 and ADH1, while 13 minor paralogs (i.e. HXK1, GLK1, TDH1, TDH2, GPM2, GPM3, ENO1, PYK2, PDC5, PDC6, ADH2, ADH4 and ADH5) were selected for gene deletion. In S. cerevisiae, the PKF1 and PFK2 paralogs have evolved into subunits of a heterooctameric phosphofructokinase. Since deletion of either gene substantially decreases fitness both were retained in the minimal glycolysis design. ADH3 encodes a mitochondrial alcohol dehydrogenase involved in an anaerobic redox shuttle across the mitochondrial inner membrane. To prevent reduced growth rates under anaerobic conditions, ADH3 was therefore also retained in minimal glycolysis design.
isolate
IMX372
collection_date
2014
geo_loc_name
Netherlands
isolation_source
CEN.PK102-12A
sample_type
pure culture
collected_by
Daniel Solis-Escalante
genotype
MATa ura3-52 his3-1 leu2-3,112 MAL2-8c SUC2 glk1::SpHis5, hxk1::KlLEU2, tdh1::KlURA3, tdh2, gpm2, gpm3, eno1, pyk2, pdc5, pdc6, adh2, adh5, adh4
mating_type
MATa
BioSampleModel
Microbe, viral or environmental