Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria

Vivek K. Mutalik (), Pavel S. Novichkov, Morgan N. Price, Trenton K. Owens, Mark Callaghan, Sean Carim, Adam M. Deutschbauer and Adam P. Arkin ()
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Vivek K. Mutalik: Lawrence Berkeley National Laboratory
Pavel S. Novichkov: Lawrence Berkeley National Laboratory
Morgan N. Price: Lawrence Berkeley National Laboratory
Trenton K. Owens: Lawrence Berkeley National Laboratory
Mark Callaghan: Lawrence Berkeley National Laboratory
Sean Carim: University of California
Adam M. Deutschbauer: Lawrence Berkeley National Laboratory
Adam P. Arkin: Lawrence Berkeley National Laboratory

Nature Communications, 2019, vol. 10, issue 1, 1-14

Abstract: Abstract A major challenge in genomics is the knowledge gap between sequence and its encoded function. Gain-of-function methods based on gene overexpression are attractive avenues for phenotype-based functional screens, but are not easily applied in high-throughput across many experimental conditions. Here, we present Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), a method that uses random DNA barcodes to greatly increase experimental throughput. As a demonstration of this approach, we construct a Dub-seq library with Escherichia coli genomic DNA, performed 155 genome-wide fitness assays in 52 experimental conditions, and identified overexpression phenotypes for 813 genes. We show that Dub-seq data is reproducible, accurately recapitulates known biology, and identifies hundreds of novel gain-of-function phenotypes for E. coli genes, a subset of which we verified with assays of individual strains. Dub-seq provides complementary information to loss-of-function approaches and will facilitate rapid and systematic functional characterization of microbial genomes.

Date: 2019
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DOI: 10.1038/s41467-018-08177-8

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