A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics

Abstract

Lack of active export system often limits the industrial bio-based production processes accumulating the intracellular product and hence complexing the purification steps. L-lysine, an essential amino acid, is produced biologically in quantities exceeding two million tons per year; yet, L-lysine production is challenged by efficient export system at high titers during fermentation. To address this issue, new exporter candidates for efficient efflux of L-lysine are needed. Using metagenomic functional selection, we identified 58 genes encoded on 28 unique metagenomic fragments from cow gut microbiome library that improved L-lysine tolerance. These genes include a novel L-lysine transporter, belonging to a previously uncharacterized EamA superfamily, which is further <i>in vivo</i> characterized as L-lysine exporter using <i>Xenopus oocyte</i> expression system as well as <i>Escherichia coli</i> host. This novel exporter improved L-lysine tolerance in <i>E. coli</i> by 40% and enhanced yield, titer, and the specific production of L-lysine in an industrial <i>Corynebacterium glutamicum</i> strain by 7.8%, 9.5%, and 12%, respectively. Our approach allows the sequence-independent discovery of novel exporters and can be deployed to increase titers and productivity of toxicity-limited bioprocesses.