Targeted metabolomics-guided rational refinement of cyanobacterial metabolism enables enhanced photosynthetic production of L-lysine

Cyanobacteria are capable of fixing CO₂ using sunlight as the sole energy source and are promising microbial platforms for sustainable bioproduction of fuels, commodity chemicals, food and pharmaceuticals. L-lysine is an essential amino acid to humans and animals and is a precursor to synthesis of building blocks for nylon and polyesters. Its industrial production is currently solely based upon fermenting sugars by heterotrophic microorganisms such as Corynebacterium and Escherichia coli. Engineering cyanobacteria to effectively redirect photosynthetically fixed carbon towards lysine biosynthesis would provide a carbon-negative route of lysine production. In this study, to address the bottlenecks of lysine biosynthesis in the cyanobacterium Synechococcus sp. PCC 7002 (also called Picosynechococcus sp. PCC 7002), we combined targeted metabolomics and synthetic biology approaches to progressively identify and mitigate the major rate-limiting steps, ultimately increasing lysine productivity by about 77 % compared to the parental strain. The best engineered lysine-producing Synechococcus strain was able to produce up to 2.92 mM lysine within 5 days, with flux partitioning towards lysine peaking at 23 % of total fixed carbon under phototrophic conditions. The strategies demonstrated in this study can be used to guide rational metabolic engineering to identify and overcome pathway bottlenecks that limit flux to other renewable bioproducts in cyanobacteria.