Tuning genetic control through promoter engineering

TLDR

Gene function is usually assessed by measuring expression at only a few discrete points such as knockouts or overexpression. The authors provide a library of engineered constitutive promoters to enable quantitative assessment of gene expression and use it to optimize phosphoenolpyruvate carboxylase and deoxy‑xylulose‑P synthase levels for improved growth and lycopene production. They generated a library of promoters with varying strengths through mutagenesis, integrated them into the chromosome, and employed the characterized library to evaluate expression effects on growth yield and product formation. Single‑cell characterization showed that optimal promoter strengths for ppc and dxs maximized growth and lycopene production, with a linear response in a preengineered strain and variable optima depending on genetic background, and the approach generalizes to yeast.

Abstract

Gene function is typically evaluated by sampling the continuum of gene expression at only a few discrete points corresponding to gene knockout or overexpression. We argue that this characterization is incomplete and present a library of engineered promoters of varying strengths obtained through mutagenesis of a constitutive promoter. A multifaceted characterization of the library, especially at the single-cell level to ensure homogeneity, permitted quantitative assessment correlating the effect of gene expression levels to improved growth and product formation phenotypes in Escherichia coli. Integration of these promoters into the chromosome can allow for a quantitative accurate assessment of genetic control. To this end, we used the characterized library of promoters to assess the impact of phosphoenolpyruvate carboxylase levels on growth yield and deoxy-xylulose-P synthase levels on lycopene production. The multifaceted characterization of promoter strength enabled identification of optimal expression levels for ppc and dxs, which maximized the desired phenotype. Additionally, in a strain preengineered to produce lycopene, the response to deoxy-xylulose-P synthase levels was linear at all levels tested, indicative of a rate-limiting step, unlike the parental strain, which exhibited an optimum expression level, illustrating that optimal gene expression levels are variable and dependent on the genetic background of the strain. This promoter library concept is illustrated as being generalizable to eukaryotic organisms (Saccharomyces cerevisiae) and thus constitutes an integral platform for functional genomics, synthetic biology, and metabolic engineering endeavors.