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

Abstract

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.

Xylose assimilation enhances the production of isobutanol in engineered Saccharomyces cerevisiae

“…Glucose induces the Crabtree effect in S. cerevisiae (Diaz‐Ruiz, Rigoulet, & Devin, ) and is known to repress mitochondria biogenesis compared with nonfermentative carbon sources such as glycerol (Egner et al, ). In contrast, xylose is not recognized as a fermentable carbon source and induces a respiratory response in yeast engineered to consume it (Belinchón & Gancedo, ; Brink, Borgström, Tueros, & Gorwa‐Grauslund, ; Jin et al, ; Osiro, Borgström, Brink, Fjölnisdóttir, & Gorwa‐Grauslund, ; Osiro et al, ). Considering that the isobutanol production pathway in SR8‐Iso is compartmentalized in the mitochondria, it is likely that increased mitochondrial biogenesis is a major contributor to the enhanced isobutanol yields from xylose we observe.…”

“…Glucose induces the Crabtree effect in S. cerevisiae (Diaz-Ruiz, Rigoulet, & Devin, 2011) and is known to repress mitochondria biogenesis compared with nonfermentative carbon sources such as glycerol (Egner et al, 2002). In contrast, xylose is not recognized as a fermentable carbon source and induces a respiratory response in yeast engineered to consume it (Belinchón & Gancedo, 2003;Brink, Borgström, Tueros, & Gorwa-Grauslund, 2016;Jin et al, 2004;Osiro, Borgström, Brink, Fjölnisdóttir, & Gorwa-Grauslund, 2019;Osiro et al, 2018).…”

Metabolic Changes Induced by Deletion of Transcriptional Regulator GCR2 in Xylose-Fermenting Saccharomyces cerevisiae

“…Although there have been a number of successful strategies to implement xylose metabolism in S. cerevisiae , their efficiency so far has not been comparable to that of glucose [ 10 , 18 ]. Xylose paradox is a paradoxical phenomenon in the engineered yeast that do not sense xylose as a fermentable carbon source despite being able to grow on and ferment xylose [ 29 ]. Many studies showed that high xylose concentrations would trigger cellular signals similar to those generated due to low glucose concentrations, resulting in a starvation response rather than a fermentation response [ 29 , 30 ].…”

“…Xylose paradox is a paradoxical phenomenon in the engineered yeast that do not sense xylose as a fermentable carbon source despite being able to grow on and ferment xylose [ 29 ]. Many studies showed that high xylose concentrations would trigger cellular signals similar to those generated due to low glucose concentrations, resulting in a starvation response rather than a fermentation response [ 29 , 30 ]. The results of the current study support the notion of xylose paradox and associated cellular signaling pathways, involving GCR2 as a metabolic regulator.…”

Structure-based directed evolution improves S. cerevisiae growth on xylose by influencing in vivo enzyme performance

“…0.1 g PirXI per g biomass estimated based on on 25% of the total protein being XI, and a total protein content of 0.4 g per g biomass [46,47]), V max (8.3 U/mg, from k cat = 6.9 s −1 with Mn 2+ ) and K M (6.2 mM) have their usual meaning. Y represents the yield on xylose (0.25 g cell dry weight/g xylose converted) estimated from a previous study performed with S. cerevisiae grown in a similar condition [48]. This predicts a PirXI activity at [S] = 1-10 mM (reasonable intracellular substrate concentration) [49,50] of 1-4.6 g xylose converted per g biomass per h, [6,51].…”