Engineering C3.5 Photosynthesis: Coupling Mitochondrial Bioenergetics to Rubisco Efficiency in Arabidopsis

Global food demand is projected to increase by more than 50 percent by 2050, yet most staple crops rely on inefficient C3 photosynthesis. A major limitation arises from Rubisco, the central carbon-fixing enzyme, which catalyzes oxygenation reactions that waste up to 40 percent of fixed carbon through photorespiration. While C4 photosynthesis offers greater efficiency, its anatomical and regulatory complexity has hindered its transfer into C3 crops. Here we propose and evaluate a novel intermediate strategy, termed C3.5 photosynthesis, which reimagines mitochondria as carbon-recycling organelles to enhance Rubisco efficiency. Using Arabidopsis as a model, we integrate computational modeling, simulated phenotyping datasets, and machine learning approaches to benchmark the feasibility of coupling mitochondrial bioenergetics to chloroplast carbon assimilation. We first construct predictive frameworks showing how mitochondrial CO2 release can be recaptured and redirected to chloroplasts through engineered organelle tethers and synthetic transporters. We then simulate the redox and energetic trade-offs of rewiring FoF1 ATP synthase to power bicarbonate transport, providing mechanistic insights into the balance between ATP cost and carbon gain. Our results demonstrate that C3.5 photosynthesis could, in principle, increase net carbon assimilation by 20-50 percent under fluctuating light and heat stress, without the structural reprogramming required for C4 pathways. This work establishes a conceptual and computational foundation for repurposing mitochondria as carbon-recycling hubs, bridging fundamental organelle biology with translational strategies in crop engineering. By combining bioenergetics, organelle engineering, and AI-driven modeling, C3.5 photosynthesis opens a high-risk, high-reward pathway toward climate-resilient agriculture and future food security.