Multivariate modular metabolic engineering for enhanced l-methionine biosynthesis in Escherichia coli

BACKGROUND: l-Methionine is the only bulk amino acid that has not been industrially produced by the fermentation method. Due to highly complex and strictly regulated biosynthesis, the development of microbial strains for high-level l-methionine production has remained challenging in recent years. RESULTS: By strengthening the l-methionine terminal synthetic module via site-directed mutation of l-homoserine O-succinyltransferase (MetA) and overexpression of metA(fbr), metC, and yjeH, l-methionine production was increased to 1.93 g/L in shake flask fermentation. Deletion of the pykA and pykF genes further improved l-methionine production to 2.51 g/L in shake flask fermentation. Computer simulation and auxotrophic experiments verified that during the synthesis of l-methionine, equimolar amounts of l-isoleucine were accumulated via the elimination reaction of cystathionine γ-synthetase MetB due to the insufficient supply of l-cysteine. To increase the supply of l-cysteine, the l-cysteine synthetic module was strengthened by overexpression of cysE(fbr), serA(fbr), and cysDN, which further increased the production of l-methionine by 52.9% and significantly reduced the accumulation of the byproduct l-isoleucine by 29.1%. After optimizing the addition of ammonium thiosulfate, the final metabolically engineered strain MET17 produced 21.28 g/L l-methionine in 64 h with glucose as the carbon source in a 5 L fermenter, representing the highest l-methionine titer reported to date. CONCLUSIONS: In this study, a high-efficiency strain for l-methionine production was derived from wild-type Escherichia coli W3110 by rational metabolic engineering strategies, providing an efficient platform for the industrial production of l-methionine. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13068-023-02347-7.