Improved production of the non-native cofactor F420 in Escherichia coli

Mihir V Shah,Colin Scott,Colin J Jackson,James Antoney,Hadi Nazem-Bokaee,Suk Woo Kang

doi:10.1038/s41598-021-01224-3

Mihir V Shah, Colin Scott + Show 4 more

Open Access

https://doi.org/10.1038/s41598-021-01224-3

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Abstract

The deazaflavin cofactor F420 is a low-potential, two-electron redox cofactor produced by some Archaea and Eubacteria that is involved in methanogenesis and methanotrophy, antibiotic biosynthesis, and xenobiotic metabolism. However, it is not produced by bacterial strains commonly used for industrial biocatalysis or recombinant protein production, such as Escherichia coli, limiting our ability to exploit it as an enzymatic cofactor and produce it in high yield. Here we have utilized a genome-scale metabolic model of E. coli and constraint-based metabolic modelling of cofactor F420 biosynthesis to optimize F420 production in E. coli. This analysis identified phospho-enol pyruvate (PEP) as a limiting precursor for F420 biosynthesis, explaining carbon source-dependent differences in productivity. PEP availability was improved by using gluconeogenic carbon sources and overexpression of PEP synthase. By improving PEP availability, we were able to achieve a ~ 40-fold increase in the space–time yield of F420 compared with the widely used recombinant Mycobacterium smegmatis expression system. This study establishes E. coli as an industrial F420-production system and will allow the recombinant in vivo use of F420-dependent enzymes for biocatalysis and protein engineering applications.

Highlights

The deazaflavin cofactor F420 is a low-potential, two-electron redox cofactor produced by some Archaea and Eubacteria that is involved in methanogenesis and methanotrophy, antibiotic biosynthesis, and xenobiotic metabolism
Preliminary findings suggest that variation of phospho-carbohydrate moiety has less effect on F420-dependent enzymes than variations of tail length[30], we report that cofactor F 420 biosynthesis in E. coli is heavily influenced by the carbon source
This work establishes that intracellular phospho-enol pyruvate (PEP) concentration is the key limiting metabolic bottleneck for heterologous F420 biosynthesis in E. coli, at least when using biosynthetic enzymes, such as those from M. smegmatis, that natively use PEP

Summary

Introduction

The deazaflavin cofactor F420 is a low-potential, two-electron redox cofactor produced by some Archaea and Eubacteria that is involved in methanogenesis and methanotrophy, antibiotic biosynthesis, and xenobiotic metabolism. It is not produced by bacterial strains commonly used for industrial biocatalysis or recombinant protein production, such as Escherichia coli, limiting our ability to exploit it as an enzymatic cofactor and produce it in high yield. We have utilized a genome-scale metabolic model of E. coli and constraint-based metabolic modelling of cofactor F420 biosynthesis to optimize F420 production in E. coli This analysis identified phospho-enol pyruvate (PEP) as a limiting precursor for F420 biosynthesis, explaining carbon source-dependent differences in productivity. FO synthase accepts two molecules of S-adenosyl-l-methionine as substrate in addition to tyrosine, producing two molecules of l-methionine, one molecule of ammonia, and two molecules of 5’-deoxyadenosine (Fig. 1A)

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