Construction of a tunable promoter library to optimize gene expression in Methylomonas sp. DH-1, a methanotroph, and its application to cadaverine production

Hyunjoo Kim,Dokyun Na,Woo Young Kim,Hyang-Mi Lee,Junhao Shen,Jun Ren,Myeong-Sang Yu,Seung Min Yoo,Seong-il Eyun

doi:10.1186/s13068-021-02077-8

Abstract

BackgroundAs methane is 84 times more potent than carbon dioxide in exacerbating the greenhouse effect, there is an increasing interest in the utilization of methanotrophic bacteria that can convert harmful methane into various value-added compounds. A recently isolated methanotroph, Methylomonas sp. DH-1, is a promising biofactory platform because of its relatively fast growth. However, the lack of genetic engineering tools hampers its wide use in the bioindustry.ResultsThrough three different approaches, we constructed a tunable promoter library comprising 33 promoters that can be used for the metabolic engineering of Methylomonas sp. DH-1. The library had an expression level of 0.24–410% when compared with the strength of the lac promoter. For practical application of the promoter library, we fine-tuned the expressions of cadA and cadB genes, required for cadaverine synthesis and export, respectively. The strain with PrpmB-cadA and PDnaA-cadB produced the highest cadaverine titre (18.12 ± 1.06 mg/L) in Methylomonas sp. DH-1, which was up to 2.8-fold higher than that obtained from a non-optimized strain. In addition, cell growth and lysine (a precursor of cadaverine) production assays suggested that gene expression optimization through transcription tuning can afford a balance between the growth and precursor supply.ConclusionsThe tunable promoter library provides standard and tunable components for gene expression, thereby facilitating the use of methanotrophs, specifically Methylomonas sp. DH-1, as a sustainable cell factory.Graphical

Highlights

As methane is 84 times more potent than carbon dioxide in exacerbating the greenhouse effect, there is an increasing interest in the utilization of methanotrophic bacteria that can convert harmful methane into vari‐ ous value-added compounds
To identify potential promoters that can be used for gene expression optimization, we first utilized computational models to predict promoter sequence regions from the genomic sequence of Methylomonas sp
We evaluated the promoters of M. trichosporium OB3b, a model organism of type II methanotroph [25], because Methylomonas sp

Summary

Introduction

As methane is 84 times more potent than carbon dioxide in exacerbating the greenhouse effect, there is an increasing interest in the utilization of methanotrophic bacteria that can convert harmful methane into vari‐ ous value-added compounds. Gene expression is a fundamental process of living organisms, for processes, such as growth, metabolism, homeostasis, differentiation, and reproduction [1,2,3]. It has been evolutionarily optimized for robust cellular functions. The non-optimized expression of enzyme genes may facilitate the accumulation of toxic intermediate metabolites, which decreases the production yield. To resolve this problem, promoters with different strengths are widely employed to fine-tune the expression levels of enzyme genes [8, 9]

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Conclusion