title: Metagenomic scaffolds enable combinatorial lignin transformation.
abstract: Engineering the microbial transformation of lignocellulosic biomass is essential to developing modern biorefining processes that alleviate reliance on petroleum-derived energy and chemicals. Many current bioprocess streams depend on the genetic tractability of Escherichia coli with a primary emphasis on engineering cellulose/hemicellulose catabolism, small molecule production, and resistance to product inhibition. Conversely, bioprocess streams for lignin transformation remain embryonic, with relatively few environmental strains or enzymes implicated. Here we develop a biosensor responsive to monoaromatic lignin transformation products compatible with functional screening in E. coli. We use this biosensor to retrieve metagenomic scaffolds sourced from coal bed bacterial communities conferring an array of lignin transformation phenotypes that synergize in combination. Transposon mutagenesis and comparative sequence analysis of active clones identified genes encoding six functional classes mediating lignin transformation phenotypes that appear to be rearrayed in nature via horizontal gene transfer. Lignin transformation activity was then demonstrated for one of the predicted gene products encoding a multicopper oxidase to validate the screen. These results illuminate cellular and community-wide networks acting on aromatic polymers and expand the toolkit for engineering recombinant lignin transformation based on ecological design principles.
authors: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;MetaMixis, Inc., Vancouver, BC, Canada V6J 3R3;
authors: Cameron R
authors: CR
authors: Strachan
authors: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;
authors: Rahul
authors: R
authors: Singh
authors: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;
authors: David
authors: D
authors: VanInsberghe
authors: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;
authors: Kateryna
authors: K
authors: Ievdokymenko
authors: Environment and Carbon Management, Alberta Innovates-Technology Futures, Edmonton, AB, Canada T6N 1E4;
authors: Karen
authors: K
authors: Budwill
authors: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;
authors: William W
authors: WW
authors: Mohn
authors: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; and.
authors: Lindsay D
authors: LD
authors: Eltis
authors: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;MetaMixis, Inc., Vancouver, BC, Canada V6J 3R3;Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 shallam@mail.ubc.ca.
authors: Steven J
authors: SJ
authors: Hallam
mesh_terms: D001483:Base Sequence; D001711:Biotransformation; D048168:Escherichia coli K12 / Q000235:genetics / Q000378:metabolism; D008031:Lignin / Q000378:metabolism*; D060847:Metabolic Engineering; D056186:Metagenomics; D008969:Molecular Sequence Data; D044223:Pseudomonas stutzeri / Q000235:genetics
chemical_list: D008031:Lignin
keywords: environmental genomics; synthetic biology