Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites.

Abstract:

:Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia coli. We show that transcription factor decoys can effectively regulate expression of native and heterologous genes. Tunability of the decoy can be engineered via changes in copy number or modifications to the DNA decoy site sequence. Using arginine biosynthesis as a showcase, we observed a 16-fold increase in arginine production when we introduced the decoy system to steer metabolic flux towards increased arginine biosynthesis, with negligible growth differences compared to the wild type strain. The decoy-based production strain retains high genetic integrity; in contrast to a gene knock-out approach where mutations were common, we detected no mutations in the production system using the decoy-based strain. We further show that transcription factor decoys are amenable to multiplexed library screening by demonstrating enhanced tolerance to pinene with a combinatorial decoy library. Our study shows that transcription factor decoy binding sites are a powerful and compact tool for metabolic engineering.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Wang T,Tague N,Whelan SA,Dunlop MJ

doi

10.1093/nar/gkaa1234

subject

Has Abstract

pub_date

2021-01-25 00:00:00

pages

1163-1172

issue

2

eissn

0305-1048

issn

1362-4962

pii

6047286

journal_volume

49

pub_type

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