Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics

Pierre-Yves Colin, Balint Kintses, Fabrice Gielen, Charlotte M. Miton, Gerhard Fischer, Mark F. Mohamed, Marko Hyvönen, Diego P. Morgavi, Dick B Janssen and Florian Hollfelder ()
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Pierre-Yves Colin: University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
Balint Kintses: University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
Fabrice Gielen: University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
Charlotte M. Miton: University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
Gerhard Fischer: University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
Mark F. Mohamed: University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
Marko Hyvönen: University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
Diego P. Morgavi: INRA, UMR1213 Herbivores
Dick B Janssen: Groningen Biomolecular Science and Biotechnology Institute, University of Groningen
Florian Hollfelder: University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK

Nature Communications, 2015, vol. 6, issue 1, 1-12

Abstract: Abstract Unculturable bacterial communities provide a rich source of biocatalysts, but their experimental discovery by functional metagenomics is difficult, because the odds are stacked against the experimentor. Here we demonstrate functional screening of a million-membered metagenomic library in microfluidic picolitre droplet compartments. Using bait substrates, new hydrolases for sulfate monoesters and phosphotriesters were identified, mostly based on promiscuous activities presumed not to be under selection pressure. Spanning three protein superfamilies, these break new ground in sequence space: promiscuity now connects enzymes with only distantly related sequences. Most hits could not have been predicted by sequence analysis, because the desired activities have never been ascribed to similar sequences, showing how this approach complements bioinformatic harvesting of metagenomic sequencing data. Functional screening of a library of unprecedented size with excellent assay sensitivity has been instrumental in identifying rare genes constituting catalytically versatile hubs in sequence space as potential starting points for the acquisition of new functions.

Date: 2015
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DOI: 10.1038/ncomms10008

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