Improving xylose utilization by recombinant Zymomonas mobilis strain 8b through adaptation using 2-deoxyglucose

BACKGROUND: Numerous attempts have been made to improve xylose utilization in Z. mobilis including adaptive approaches. However, no one has yet found a way to overcome the reduced xylose utilization observed in fermentations carried out in the presence of glucose as well as the inhibitory compounds found within pretreated and saccharified biomass. Our goal was to generate Z. mobilis strains that are more robust than the wildtype strain with increased productivity in fermenting the glucose and xylose present in PCS. Through adaptation in the presence of 2-deoxyglucose, we have generated Zymomonas mobilis strain #7, which is better suited to utilizing xylose in pretreated corn stover (PCS) fermentations in the presence of both glucose and model inhibitory compounds of acetate and furfural. Strain #7 over performed the parent strain 8b both on simultaneous saccharification and fermentation (SFF) of PCS and fermentation of saccharified PCS slurry. At 65% neutralized PCS liquor level, strain #7 used 86% of the xylose present in the liquor while strain 8b was not able to ferment the liquor under similar conditions. Similarly, under SSF process conditions with 20% total solids loading of PCS, strain #7 used more than 50% of the xylose present, while strain 8b did not utilize any xylose under this condition. We have further identified genetic alterations in strain #7 in relation to the parental strain 8b that may be responsible for these phenotypic enhancements. RESULTS: We performed an extended lab-directed evolution of Z. mobilis strain 8b in the presence of acetate and a non-hydrolyzable glucose analogue 2-deoxyglucose. Following the adaptation, we identified and characterized numerous candidate strains and found a dramatic increase in xylose usage not only in shake flask, but also in a controlled PCS fermentation. We re-sequenced the genomes of evolved strains to identify genetic alterations responsible for these improved phenotypes, and identified two mutations that may be key to the improved xylose usage in these strains. CONCLUSION: We have generated Z. mobilis strain #7, which can ferment xylose efficiently in the presence of toxins present in pretreated corn stover. Genetic alterations responsible for the improvement have been identified.