Systems approaches for optimizing CO₂ fixation pathways

We survey recent works on designing and implementing CO₂ fixation pathways. We describe how these studies reveal a gap between a well-designed pathway and a productive strain. This gap includes phenomena that are often not accounted for in design, such as hidden enzyme energy usage and regulatory rewiring during adaptive evolution. Several systems biology tools can help overcome this gap. Kinetic models can be generated rapidly using new algorithms, and when coupled with retrobiosynthesis, can evaluate pathway dynamics and stability in the context of the native network. Quantitative and interaction proteomics reveal how the host strain adapts to novel pathways and can identify interference from native metabolites. In vivo optimization through adaptive laboratory evolution is used extensively to optimize modules or whole pathways, but requires the pathway phenotype to be linked to growth. Post-evolution characterization reveals that cells optimize pathway integration through substantial proteome reallocation.