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Background  Unlike xylose-converting natural yeasts, recombinant strains of  Saccharomyces cerevisiae  expressing the same xylose assimilation pathway produce under anaerobic conditions xylitol rather than ethanol from xylose at low specific xylose conversion rates. Despite intense research efforts over the last two decades, differences in these phenotypes cannot be explained by current metabolic and kinetic models. To improve our understanding how metabolic flux of xylose carbon to ethanol is controlled, we developed a novel kinetic model based on enzyme mechanisms and applied quantitative metabolite profiling together with enzyme activity analysis to study xylose-to-ethanol metabolisms of  Candida tenuis  CBS4435 ( q  xylose  = 0.10 g/g dc /h, 25 °C;  Y  ethanol  = 0.44 g/g;  Y  xylitol  = 0.09 g/g) and the recombinant  S. cerevisiae  strain BP000 ( q  xylose  = 0.07 g/g dc /h, 30 °C;  Y  ethanol  = 0.24 g/g;  Y  xylitol  = 0.43 g/g), both expressing the same xylose reductase (XR), comprehensively.    Results  Results from strain-to-strain metabolic control analysis indicated that activity levels of XR and the maximal flux capacity of the upper glycolysis (UG; both ≥ tenfold higher in CBS4435) contributed predominantly to phenotype differentiation while reactions from the oxidative pentose phosphate pathway played minor roles. Intracellular metabolite profiles supported results obtained from kinetic modeling and indicated a positive correlation between pool sizes of UG metabolites and carbon flux through the UG. For CBS4435, fast carbon flux through the UG could be associated with an allosteric control of 6-phosphofructokinase (PFK) activity by fructose 6-phosphate. The ability of CBS4435 to keep UG metabolites at high levels could be explained by low glycerol 3-phosphate phosphatase (GPP, 17-fold lower in CBS4435) and high XR activities.    Conclusions  By applying a systems biology approach in which we combined results obtained from metabolic control analysis based on kinetic modeling with data obtained from quantitative metabolite profiling and enzyme activity analyses, we could provide new insights into metabolic and kinetic interactions contributing to the control of carbon flux from xylose to ethanol. Supported by evidences presented two new targets, PFK and GPP, could be identified that aside from XR play pivotal roles in phenotype differentiation. Design of efficient and fast microbial ethanol producers in the future can certainly benefit from results presented in this study.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-015-0340-x) contains supplementary material, which is available to authorized users.

Identification of novel metabolic interactions controlling carbon flux from xylose to ethanol in natural and recombinant yeasts