(A) Temporal expression profiles of genes encoding enzymes involved in sugar metabolism whose expression is abrogated in the rpaA- ‘clock rescue’ strain. Relative RNA levels were measured in the light/dark conditions by RNA sequencing. (B) A diagram representing carbon metabolism in S. elongatus PCC7942 in the dark. At night glycogen constitutes the store for energy and carbon skeletons. Glycogen degradation, glycolysis and oxidative pentose phosphate pathways are the key metabolic pathways operating at night. Deletion of operons with genes colored red leads to a strong viability defect specifically in light/dark conditions (Figure 3—figure supplement 1C and Doolittle and Singer 1974; Scanlan et al., 1995). glgP, glycogen phosphorylase; gap1, glyceraldehyde-3-phosphate dehydrogenase; gnd, 6-phosphogluconate dehydrogenase; zwf, glucose-6-phosphate dehydrogenase; opcA, glucose-6-phosphate dehydrogenase assembly protein; fbp, fructose-1,6-bisphosphatase, G6P, glucose-6-phosphate; 6-PGlcA, 6-phosphogluconate; F6P, fructose-6-phosphate; FBP, fructose-1,6-bisphosphate, Ru5-P, ribulose-5-phosphate (C) Enzymatic activities of glycogen phosphorylase, glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase in wild type, the rpaA- and negative control strains measured 3 hr after exposure to expected darkness. Error bars represent standard error of the mean of four independent experiments.