title: Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates.
abstract: The efficient production of biofuels from cellulosic feedstocks will require the efficient fermentation of the sugars in hydrolyzed plant material. Unfortunately, plant hydrolysates also contain many compounds that inhibit microbial growth and fermentation. We used DNA-barcoded mutant libraries to identify genes that are important for hydrolysate tolerance in both Zymomonas mobilis (44 genes) and Saccharomyces cerevisiae (99 genes). Overexpression of a Z. mobilis tolerance gene of unknown function (ZMO1875) improved its specific ethanol productivity 2.4-fold in the presence of miscanthus hydrolysate. However, a mixture of 37 hydrolysate-derived inhibitors was not sufficient to explain the fitness profile of plant hydrolysate. To deconstruct the fitness profile of hydrolysate, we profiled the 37 inhibitors against a library of Z. mobilis mutants and we modeled fitness in hydrolysate as a mixture of fitness in its components. By examining outliers in this model, we identified methylglyoxal as a previously unknown component of hydrolysate. Our work provides a general strategy to dissect how microbes respond to a complex chemical stress and should enable further engineering of hydrolysate tolerance.
authors.affiliation: Energy Biosciences Institute, University of California, Berkeley, CA, USA.
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Skerker
authors.forename: Dacia
authors.initials: D
authors.lastname: Leon
authors.forename: Morgan N
authors.initials: MN
authors.lastname: Price
authors.forename: Jordan S
authors.initials: JS
authors.lastname: Mar
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Tarjan
authors.forename: Kelly M
authors.initials: KM
authors.lastname: Wetmore
authors.forename: Adam M
authors.initials: AM
authors.lastname: Deutschbauer
authors.forename: Jason K
authors.initials: JK
authors.lastname: Baumohl
authors.forename: Stefan
authors.initials: S
authors.lastname: Bauer
authors.forename: Ana B
authors.initials: AB
authors.lastname: Ibáñez
authors.forename: Valerie D
authors.initials: VD
authors.lastname: Mitchell
authors.forename: Cindy H
authors.initials: CH
authors.lastname: Wu
authors.forename: Ping
authors.initials: P
authors.lastname: Hu
authors.forename: Terry
authors.initials: T
authors.lastname: Hazen
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
mesh_terms: D018533:Biomass; D002482:Cellulose / Q000737:chemistry / Q000378:metabolism*; D004791:Enzyme Inhibitors / Q000302:isolation & purification / Q000494:pharmacology; D000431:Ethanol / Q000378:metabolism*; D005285:Fermentation; D015723:Gene Library; D005798:Genes, Bacterial; D005800:Genes, Fungal; D006868:Hydrolysis; D008956:Models, Chemical; D008957:Models, Genetic; D009154:Mutation; D011765:Pyruvaldehyde / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D013312:Stress, Physiological; D017355:Zymomonas / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*
chemical_list: D004791:Enzyme Inhibitors; D000431:Ethanol; D011765:Pyruvaldehyde; D002482:Cellulose