A comprehensive optimization of known prokaryotic autotrophic carbon dioxide (CO2) fixation pathways is presented that evaluates all their possible variants under different environmental conditions. This was achieved through a computational methodology recently developed that considers the trade-offs between energy efficiency (yield) and growth rate, allowing us to evaluate candidate metabolic modifications in silico for microbial conversions. The results revealed the superior configurations in terms of both yield (efficiency) and rate (driving force). The pathways from anaerobic organisms appear to fix carbon at lower net ATP cost than those found in aerobic organisms, and the reverse TCA cycle pathway shows the lowest overall energy cost and maximum adaptability across a broad range of CO2 and electron donor (H2) concentrations. The reverse tricarboxylic acid cycle and Wood-Ljungdahl pathways appear highly efficient under a broad range of conditions, while the 3-hydroxypropionate 4-hydroxybutyrate cycle and the 3-hydroxypropionate bicycle appear capable of generating large thermodynamic driving forces at only moderate ATP yield losses.IMPORTANCEBiotechnology can lead to cost-effective processes for capturing carbon dioxide using the natural or genetically engineered metabolic capabilities of microorganisms. However, introducing desirable genetic modifications into microbial strains without compromising their fitness (growth yield and rate) during industrial-scale cultivation remains a challenge. The approach and results presented can guide optimal pathway configurations for enhanced prokaryotic carbon fixation through metabolic engineering. By aligning strain modifications with these theoretically revealed near-optimal pathway configurations, we can optimally engineer strains of good fitness under open culture industrial-scale conditions.
Keywords: carbon metabolism; electron carrier analysis; microbial strain engineering; microbial thermodynamics; optimisation of microbial pathways; prokaryotic carbon fixation; rate-yield trade-off.