Ionic liquids have been shown to be effective deconstructors of biomass to release sugars for fermentation. However, ILs are partially retained in the hydrolystates, and are not readily tolerated by the fermentative microorganisms—such as yeast—that do the work of fermentation.

Ionic liquids are a particularly promising technology for deconstructing biomass, but their toxicity to fermentative microbes has posed a challenge. To really harness the power of this solvent—and to enable a bio-based economy—we need microbes specifically tailored to tolerate the specific toxicity of ionic liquids.

—Jeff Piotrowski, senior author

Using a technique called chemical genomics that integrates chemical-genetic and genetic interaction data to find the pathways and targets of inhibitory compounds, the researchers set out to engineer a yeast strain that could tolerate ionic liquids. By identifying a number of genes that, when deleted, either made the yeast sensitive to ionic liquids or resistant to them, they were able to understand the precise nature of ionic liquids’ toxicity to yeast.

This guided them in successfully engineering the new strain of yeast that not only shows resistance to ionic liquids but also improves sugar conversion and biofuel production. Since removing residual ionic liquid after deconstruction is an added step incurring added expense, the new strain by itself could lower the costs of making biofuels.

The technique of chemical genomics-guided bio-design is novel, and rich in potential for future applications.

Our results illustrate a general paradigm by which chemical genomics can enable rapid strain design in response to emerging bioconversion technologies. Both lignocellulose deconstruction technologies and the resulting landscape of fermentation inhibitors continue to evolve. Continued strain development will be necessary to keep pace with these new technologies and chemical stressors like IILs. Further, different industrial settings often necessitate use of different strain backgrounds; thus, it will be important that advantageous traits can be introduced rationally into diverse strain backgrounds. Our chemical genomics approach enables identification of such readily exploited traits for rational engineering. As our discovery system is based on S. cerevisiae, the primary lignocellulosic biorefinery microbe, the gene identified can be directly modified in other yeast strains to rapidly tailor proven strains for new hydrolysates.

Chemical genomics-guided biodesign for strain engineering can also be applied to other bioproducts in addition to ethanol. Drugs, green chemicals, and next-generation fuels can be produced by yeast and other engineered microbes, and many of these end-products can be toxic to the biocatalyst microbe. The chemical genomics approach is a general way to define their mechanism of toxicity and discover means to engineer tolerance and improve their production. This approach is not limited to yeast; genome-wide mutant and overexpression collections exist in a number of industrially relevant microbes, including Escherichia coli and Zymomonas mobilis, making the chemical genomics approach translatable to these microbes as well.

—Dickinson et al.

Resources

• Quinn Dickinson, Scott Bottoms, Li Hinchman, Sean McIlwain, Sheena Li, Chad L. Myers, Charles Boone, Joshua J. Coon, Alexander Hebert, Trey K. Sato, Robert Landick and Jeff S. Piotrowski (2016) “Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain” Microbial Cell Factories 15:17 doi: 10.1186/s12934-016-0417-7

• Ainslie B Parsons, Renée L Brost, Huiming Ding, Zhijian Li, Chaoying Zhang, Bilal Sheikh, Grant W Brown, Patricia M Kane, Timothy R Hughes & Charles Boone (2004) “Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways” Nature Biotechnology 22, 62 - 69 doi: 10.1038/nbt919