title: Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus.
abstract: To process plant-based renewable biofuels, pretreatment of plant feedstock with ionic liquids has significant advantages over current methods for deconstruction of lignocellulosic feedstocks. However, ionic liquids are often toxic to the microorganisms used subsequently for biomass saccharification and fermentation. We previously isolated Enterobacter lignolyticus strain SCF1, a lignocellulolytic bacterium from tropical rain forest soil, and report here that it can grow in the presence of 0.5 M 1-ethyl-3-methylimidazolium chloride, a commonly used ionic liquid. We investigated molecular mechanisms of SCF1 ionic liquid tolerance using a combination of phenotypic growth assays, phospholipid fatty acid analysis, and RNA sequencing technologies. Potential modes of resistance to 1-ethyl-3-methylimidazolium chloride include an increase in cyclopropane fatty acids in the cell membrane, scavenging of compatible solutes, up-regulation of osmoprotectant transporters and drug efflux pumps, and down-regulation of membrane porins. These findings represent an important first step in understanding mechanisms of ionic liquid resistance in bacteria and provide a basis for engineering microbial tolerance.
authors.affiliation: Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA.
authors.forename: Jane I
authors.initials: JI
authors.lastname: Khudyakov
authors.forename: Patrik
authors.initials: P
authors.lastname: D'haeseleer
authors.forename: Sharon E
authors.initials: SE
authors.lastname: Borglin
authors.forename: Kristen M
authors.initials: KM
authors.lastname: Deangelis
authors.forename: Hannah
authors.initials: H
authors.lastname: Woo
authors.forename: Erika A
authors.initials: EA
authors.lastname: Lindquist
authors.forename: Terry C
authors.initials: TC
authors.lastname: Hazen
authors.forename: Blake A
authors.initials: BA
authors.lastname: Simmons
authors.forename: Michael P
authors.initials: MP
authors.lastname: Thelen
mesh_terms: D001483:Base Sequence; D057005:Bioengineering / Q000379:methods; D056804:Biofuels; D004351:Drug Resistance / Q000502:physiology*; D004754:Enterobacter / Q000187:drug effects / Q000254:growth & development* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D007093:Imidazoles; D052578:Ionic Liquids / Q000633:toxicity*; D008969:Molecular Sequence Data; D010743:Phospholipids / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012988:Soil Microbiology; D059467:Transcriptome / Q000187:drug effects* / Q000235:genetics; D014197:Trees; D014329:Tropical Climate
chemical_list: D056804:Biofuels; D007093:Imidazoles; D052578:Ionic Liquids; D010743:Phospholipids; C518739:1-ethyl-3-methylimidazolium