Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway

Wai Shun Mak, Stephen Tran, Ryan Marcheschi, Steve Bertolani, James Thompson, David Baker, James C. Liao, Justin Siegel

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

The ability to biosynthetically produce chemicals beyond what is commonly found in Nature requires the discovery of novel enzyme function. Here we utilize two approaches to discover enzymes that enable specific production of longer-chain (C5-C8) alcohols from sugar. The first approach combines bioinformatics and molecular modelling to mine sequence databases, resulting in a diverse panel of enzymes capable of catalysing the targeted reaction. The median catalytic efficiency of the computationally selected enzymes is 75-fold greater than a panel of naively selected homologues. This integrative genomic mining approach establishes a unique avenue for enzyme function discovery in the rapidly expanding sequence databases. The second approach uses computational enzyme design to reprogramme specificity. Both approaches result in enzymes with >100-fold increase in specificity for the targeted reaction. When enzymes from either approach are integrated in vivo, longer-chain alcohol production increases over 10-fold and represents >95% of the total alcohol products.

Original languageEnglish (US)
Article number10005
JournalNature Communications
Volume6
DOIs
StatePublished - Nov 24 2015

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Biosynthetic Pathways
enzymes
engineering
Enzymes
alcohols
Alcohols
Databases
Sugar Alcohols
Molecular modeling
Bioinformatics
sugars
Computational Biology
products

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Chemistry(all)
  • Physics and Astronomy(all)

Cite this

Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. / Mak, Wai Shun; Tran, Stephen; Marcheschi, Ryan; Bertolani, Steve; Thompson, James; Baker, David; Liao, James C.; Siegel, Justin.

In: Nature Communications, Vol. 6, 10005, 24.11.2015.

Research output: Contribution to journalArticle

Mak, Wai Shun ; Tran, Stephen ; Marcheschi, Ryan ; Bertolani, Steve ; Thompson, James ; Baker, David ; Liao, James C. ; Siegel, Justin. / Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. In: Nature Communications. 2015 ; Vol. 6.
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