@article {367,
	title = {Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {109},
	year = {2012},
	month = {2012 Aug 7},
	pages = {E2173-82},
	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.},
	issn = {1091-6490},
	doi = {10.1073/pnas.1112750109},
	author = {Khudyakov, Jane I and D{\textquoteright}haeseleer, Patrik and Borglin, Sharon E and Deangelis, Kristen M and Woo, Hannah and Lindquist, Erika A and Hazen, Terry C and Simmons, Blake A and Thelen, Michael P}
}
@article {371,
	title = {Complete genome sequence of "Enterobacter lignolyticus" SCF1.},
	journal = {Stand Genomic Sci},
	volume = {5},
	year = {2011},
	month = {2011 Oct 15},
	pages = {69-85},
	abstract = {In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated "Enterobacter lignolyticus" SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are net methane producers. Because of its ability to grow on lignin anaerobically, we sequenced the genome. The genome of "E. lignolyticus" SCF1 is 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohydrate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single gene cluster.},
	issn = {1944-3277},
	doi = {10.4056/sigs.2104875},
	author = {Deangelis, Kristen M and D{\textquoteright}haeseleer, Patrik and Chivian, Dylan and Fortney, Julian L and Khudyakov, Jane and Simmons, Blake and Woo, Hannah and Arkin, Adam P and Davenport, Karen Walston and Goodwin, Lynne and Chen, Amy and Ivanova, Natalia and Kyrpides, Nikos C and Mavromatis, Konstantinos and Woyke, Tanja and Hazen, Terry C}
}
