Data for "Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates and 37 components"

Jeffrey M. Skerker, Dacia Leon, Morgan Price, Jordan Mar, Dan Tarjan, Jason Baumohl, Stefan Bauer, Ana Ibanez, Valerie Mitchell, Cindy Wu, Ping Hu, Terry Hazen, Adam P. Arkin
Energy Biosciences Institute
UC Berkeley Dept. of Bioengineering
LBNL Physical Biosciences Division
LBNL Earth Sciences Division

Abstract: Efficient fermentation of sugars from plant hydrolysates is a major hurdle for the development of economically efficient cellulosic biofuels. In addition to fermentable sugars, plant hydrolysates contain a wide variety of organic compounds that are potent inhibitors of microbial growth and fermentation. Here, we use chemogenomic profiling of DNA-barcoded mutant libraries to uncover the genetic basis of hydrolysate tolerance in both Zymomonas mobilis and Saccharomyces cerevisiae. We identified 44 genes in Z. mobilis and 28 genes in S. cerevisiae that are important for growth in miscanthus and switchgrass plant hydrolysates. By systematic overexpression of tolerance genes in Z. mobilis, we identified a gene of unknown function, ZMO1875, that improves specific ethanol productivity 2.4-fold in the presence of miscanthus hydrolysate. In both bacteria and yeast, we found that a synthetic hydrolysate mixture of 37 hydrolysate-derived compounds was not sufficient to explain the fitness profile of real plant hydrolysates. To further understand this difference, we profiled our Z. mobilis mutant library in each of these 37 compounds and modeled average hydrolysate fitness as a linear combination of the fitness profiles of components. We used outliers in our model to discover that methylglyoxal is a component of our miscanthus hydrolysate and contributes to overall toxicity. Our work provides a general strategy to dissect how microbes respond to a complex chemical stress, and will enable future strain engineering efforts in both Z. mobilis and S. cerevisiae that will help enable industrial-scale production of cellulosic biofuels.

Molecular Systems Biology 2013, 9:674

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