Controlled Carbon Loss: Threshold-Dependent Overflow Metabolism in <em>Synechocystis </em>sp.<em> PCC 6803</em>

Cyanobacteria such as Synechocystis sp. PCC 6803 are promising chassis for sustainable bioproduction. During nitrogen starvation, Synechocystis redirects fixed carbon from biomass growth toward glycogen accumulation as a carbon and energy reserve. Inhibiting glycogen synthesis results in the excretion of excess carbon as organic acids, predominantly pyruvate and 2-oxoglutarate. Efficiently rerouting this carbon toward the formation of value-added products such as the plastic alternative polyhydroxybutyrate requires a deeper understanding of carbon partitioning and overflow metabolism. To investigate this, we quantified intra- and extracellular metabolites in Synechocystis wild-type and mutant strains with altered glycogen metabolism (Δpgm, ΔglgC, ΔglgA1, ΔglgA2), nitrogen signaling (ΔglnB), and carbon allocation (ΔpirC), including the double mutant ΔglgCΔpirC. Metabolites were analyzed after two days of nitrogen-replete or -depleted growth using enzymatic glycogen quantification and liquid chromatography–mass spectrometry. Excretion was primarily triggered by inhibition of glycogen synthesis but modulated by other changes in carbon flow, such as pirC deletion. Besides pyruvate and 2-oxoglutarate, small amounts of glutamate, succinate, and malate were excreted. Our findings suggest that, rather than a passive consequence of metabolite accumulation, excretion is a selective, threshold-dependent process that limits intracellular metabolite buildup, revealing an additional layer of metabolic control relevant to cyanobacterial bioengineering.