Fig. 1: In silico identification of latent carbon fixation pathways.

a The GED cycle, the simplest carbon fixation pathway that can be generated from E. coli endogenous enzymes. The pathway is based on the reductive carboxylation of ribulose 5-phosphate (Ru5P) to 6-phosphogluconate (6PG) by Gnd, followed by the activity of the Entner–Doudoroff pathway (enzymes Edd and Eda) to produce pyruvate and glyceraldehyde-3-phosphate (GAP). Pyruvate is converted to GAP via gluconeogenesis and the intermediates phosphoenolpyruvate (PEP) and 3-phosphoglycerate (3PG). To close the cycle, GAP is recycled to Ru5P via the pentose phosphate pathway. The GED cycle mirrors the ribulose bisphosphate cycle (i.e., Calvin–Benson cycle), which is shown in gray. b, c Two other general archetypes of carbon fixation pathways that were computationally uncovered. Both are based on integrated cycles, which together reduce CO₂ to formate and then assimilate formate into pyruvate. AcCoA corresponds to acetyl-CoA and PrCoA corresponds to propionyl-CoA. CH₂-THF corresponds to methylene-THF. d A phylogenetic tree of bacteria, showing the three phyla that harbor all key enzymes of the GED cycle (shown in color). Numbers in parentheses correspond to the number of species in which the key pathway enzymes were found.