S. elongatus PCC 7942 Circadian Control Bioproduction Transcriptomics

The industrial feasibility of photosynthetic bioproduction using cyanobacterial platforms remains challenging due to insufficient yields, particularly due to competition between product formation and cellular carbon demands. Here we demonstrate that circadian regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942, significantly affecting production efficiency. After entrainment to light-dark cycles, cultures maintained under the constant light revealed distinct temporal patterns in sucrose production, exhibiting three-fold higher productivity during subjective night despite moderate down-regulation of the photosynthetic apparatus. This enhanced productivity coincided with reduced glycogen accumulation and halted cell division, suggesting temporal separation of competing processes. Transcriptome analysis revealed coordinated circadian-driven adjustment of the cell cycle and rewiring of energy and carbon metabolism. The subjective night was characterized by altered expression of cell division-related genes and reduced expression of genes involved in glycogen synthesis, while showing upregulation of glycogen degradation pathways, alternative electron flow components, the pentose phosphate pathway, and oxidative decarboxylation of pyruvate. These molecular changes created favorable conditions for product formation through enhanced availability of major sucrose precursors (glucose-1-phosphate and fructose-6-phosphate) and maintained redox balance. Our findings suggest that understanding the circadian regulatory rewiring of carbon metabolism could enable two distinct approaches for improving cyanobacterial bioproduction. First, accounting and leveraging natural circadian rhythms for optimizing cultivation conditions, timing of heterologous pathway induction and harvesting patterns. Second, engineering strains that mimic circadian-driven metabolic shifts through controlled carbon flux redistribution and redox rebalancing to enable efficient cycling between growth, storage accumulation, and production phases. Overall design: The synchronized cultures were divided to enable parallel sampling for the first two 8-hour periods: subjective day (12:00-20:00) and subjective night (20:00-04:00). For both conditions, samples were collected throughout the 8-hour experimental period, with time 0 corresponding to the start of each period (12:00 for subjective day and 20:00 for subjective night). Sucrose production, biomass (OD750), cell number, and glycogen content were monitored at hours 0, 0.5, 1, 2, 4, 6, and 8. For transcriptome analysis, samples were collected at hours 0, 2, 4, and 8. Both conditions were maintained under continuous light.