Multiomic studies of inhibitory effects of lignocellulose-derived inhibitors on xylose utilization in Zymomonas mobilis using chemical defined synthetic hydrolysates

Previously we found that modified Zymomonas mobilis is able to convert glucose to ethanol when fermenting highly concentrated hydrolysates such as 9% glucan-loading AFEX-pretreated corn stover hydrolysate (ACSH), but that xylose conversion after glucose depletion is greatly impaired. We hypothesized that impaired xylose conversion is caused by lignocellulose-derived inhibitors (LDIs) present in highly concentrated hydrolysates. To investigate the effects of LDIs on xylose utilization in Z. mobilis, we generated synthetic hydrolysates (SynHs) that contains nutrients and LDI at concentrations found in authentic 9% ACSH. Comparative fermentations of Z. mobilis 2032 using SynH with or without LDI were performed, and samples were collected for endproduct, transcriptomic, metabolomic, and proteomic analyses. Our data suggest that the overall flux of xylose metabolism is reduced in the presence of LDIs. However, the expression of most genes involved in glucose and xylose assimilation was not affected by LDIs nor did we observe blocks in glucose and xylose metabolic pathways. Several LDI-specific effects were observed including intracellular accumulation of mannose-1P and mannose-6P, down regulation of a Type I secretion system (ZMO0252-0255), and upregulation of sulfur metabolism genes and the RND family efflux pump system (ZMO0282_0283_0285). This efflux pump system is involved in detoxification. Together, our findings identify cellular responses to LDIs and possible causes of impaired xylose conversion that will enable future strain engineering of Z. mobilis.