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Background  There have been many successful strategies to implement xylose metabolism in  Saccharomyces cerevisiae , but no effort has so far enabled xylose utilization at rates comparable to that of glucose (the preferred sugar of this yeast). Many studies have pointed towards the engineered yeast not sensing that xylose is a fermentable carbon source despite growing and fermenting on it, which is paradoxical. We have previously used fluorescent biosensor strains to in vivo monitor the sugar signalome in yeast engineered with xylose reductase and xylitol dehydrogenase (XR/XDH) and have established that  S. cerevisiae  senses high concentrations of xylose with the same signal as low concentration of glucose, which may explain the poor utilization.    Results  In the present study, we evaluated the effects of three deletions ( ira2 ∆,  isu1 ∆ and  hog1 ∆) that have recently been shown to display epistatic effects on a xylose isomerase (XI) strain. Through aerobic and anaerobic characterization, we showed that the proposed effects in XI strains were for the most part also applicable in the XR/XDH background. The  ira2 ∆ isu1 ∆ double deletion led to strains with the highest specific xylose consumption- and ethanol production rates but also the lowest biomass titre. The signalling response revealed that  ira2 ∆ isu1 ∆ changed the  low glucose -signal in the background strain to a simultaneous signalling of high and low glucose, suggesting that engineering of the signalome can improve xylose utilization.    Conclusions  The study was able to correlate the previously proposed beneficial effects of  ira2 ∆,  isu1 ∆ and  hog1 ∆ on  S. cerevisiae  xylose uptake, with a change in the sugar signalome. This is in line with our previous hypothesis that the key to resolve the xylose paradox lies in the sugar sensing and signalling networks. These results indicate that the future engineering targets for improved xylose utilization should probably be sought not in the metabolic networks, but in the signalling ones.    Electronic supplementary material  The online version of this article (10.1186/s12934-019-1141-x) contains supplementary material, which is available to authorized users.

Exploring the xylose paradox in Saccharomyces cerevisiae through in vivo sugar signalomics of targeted deletants