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Background   Zymomonas mobilis  produces near theoretical yields of ethanol and recombinant strains are candidate industrial microorganisms. To date, few studies have examined its responses to various stresses at the gene level. Hfq is a conserved bacterial member of the Sm-like family of RNA-binding proteins, coordinating a broad array of responses including multiple stress responses. In a previous study, we observed  Z. mobilis  ZM4 gene ZMO0347 showed higher expression under anaerobic, stationary phase compared to that of aerobic, stationary conditions.    Results  We generated a  Z. mobilis hfq  insertion mutant AcRIM0347 in an acetate tolerant strain (AcR) background and investigated its role in model lignocellulosic pretreatment inhibitors including acetate, vanillin, furfural and hydroxymethylfurfural (HMF).  Saccharomyces cerevisiae  Lsm protein (Hfq homologue) mutants and Lsm protein overexpression strains were also assayed for their inhibitor phenotypes. Our results indicated that all the pretreatment inhibitors tested in this study had a detrimental effect on both  Z. mobilis  and  S. cerevisiae , and vanillin had the most inhibitory effect followed by furfural and then HMF for both  Z. mobilis  and  S. cerevisiae . AcRIM0347 was more sensitive than the parental strain to the inhibitors and had an increased lag phase duration and/or slower growth depending upon the conditions. The  hfq  mutation in AcRIM0347 was complemented partially by trans-acting  hfq  gene expression. We also assayed growth phenotypes for  S. cerevisiae  Lsm protein mutant and overexpression phenotypes. Lsm1, 6, and 7 mutants showed reduced tolerance to acetate and other pretreatment inhibitors.  S. cerevisiae  Lsm protein overexpression strains showed increased acetate and HMF resistance as compared to the wild-type, while the overexpression strains showed greater inhibition under vanillin stress conditions.    Conclusions  We have shown the utility of the pKNOCK suicide plasmid for mutant construction in  Z. mobilis , and constructed a Gateway compatible expression plasmid for use in  Z. mobilis  for the first time. We have also used genetics to show  Z. mobilis  Hfq and  S. cerevisiae  Lsm proteins play important roles in resisting multiple, important industrially relevant inhibitors. The conserved nature of this global regulator offers the potential to apply insights from these fundamental studies for further industrial strain development.

The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors