Fig. 4.

Carboxysome proton concentration is modulated by CO₂ efflux. Carboxysome-free proton concentration (A and B) and carboxysome pH (C and D) indicate that a functional carboxysome compartment undergoes net acidification at limiting HCO₃⁻ and RuBP supply (SI Appendix, Fig. S4). Plotted are proton concentration and pH over a range of [HCO₃⁻] and [RuBP] for modeled carboxysomes with an internal CA, allowing for two protons to be produced per carboxylation reaction and under typical modeled CO₂ permeability within the model (10⁻⁶ m/s; solid pink lines). If CO₂ efflux were rapid and unimpeded (CO₂ permeability 1 m/s; dashed green lines), pH rapidly returns to ∼8 (black dashed line, panels C and D) as external limiting substrate supply increases. Slow CO₂ efflux (CO₂ permeability 10⁻⁹ m/s; dashed orange lines) does not allow for dissipation of protons. Efflux of CO₂ from the carboxysome contributes to pH maintenance as it represents the loss of substrate for the CA hydration reaction (CO₂ + H₂O ↔ HCO₃⁻ + H⁺), which would otherwise lead to free proton release. Each dataset was modeled with an initial [RuBP] of 5 mM for HCO₃⁻ response curves and 20 mM HCO₃⁻ in the case of RuBP response curves, and CA activity is confined only to the carboxysome compartment. All other permeabilities under these conditions are set to 10⁻⁶ m/s as for a carboxysome (Table 1). The COPASI (66) model was run in parameter scan mode, achieving steady-state values over a range of substrate concentrations. Data presented are for the tobacco Rubisco (Table 2).