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Appl Environ Microbiol. 2015 Nov 6;82(2):528-37. doi: 10.1128/AEM.02838-15. Print 2016 Jan 15.

Identification of Genes Conferring Tolerance to Lignocellulose-Derived Inhibitors by Functional Selections in Soil Metagenomes.

Author information

1
Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA.
2
Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3
Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA dantas@wustl.edu.

Abstract

The production of fuels or chemicals from lignocellulose currently requires thermochemical pretreatment to release fermentable sugars. These harsh conditions also generate numerous small-molecule inhibitors of microbial growth and fermentation, limiting production. We applied small-insert functional metagenomic selections to discover genes that confer microbial tolerance to these inhibitors, identifying both individual genes and general biological processes associated with tolerance to multiple inhibitory compounds. Having screened over 248 Gb of DNA cloned from 16 diverse soil metagenomes, we describe gain-of-function tolerance against acid, alcohol, and aldehyde inhibitors derived from hemicellulose and lignin, demonstrating that uncultured soil microbial communities hold tremendous genetic potential to address the toxicity of pretreated lignocellulose. We recovered genes previously known to confer tolerance to lignocellulosic inhibitors as well as novel genes that confer tolerance via unknown functions. For instance, we implicated galactose metabolism in overcoming the toxicity of lignin monomers and identified a decarboxylase that confers tolerance to ferulic acid; this enzyme has been shown to catalyze the production of 4-vinyl guaiacol, a valuable precursor to vanillin production. These metagenomic tolerance genes can enable the flexible design of hardy microbial catalysts, customized to withstand inhibitors abundant in specific bioprocessing applications.

PMID:
26546427
PMCID:
PMC4711125
DOI:
10.1128/AEM.02838-15
[Indexed for MEDLINE]
Free PMC Article

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