Fig. 1: A multicompartment reaction-diffusion model describes the Chlamydomonas PCCM.

a, Cartoon of a Chlamydomonas chloroplast with known PCCM components. HCO₃⁻ is transported across the chloroplast membrane by LCIA and across the thylakoid membranes by BST1–3 (referred to as BST henceforth for simplicity). In the acidic thylakoid lumen, a carbonic anhydrase CAH3 converts HCO₃⁻ into CO₂, which diffuses into the pyrenoid matrix where the CO₂-fixing enzyme Rubisco (Rbc) is localized. CO₂ leakage out of the matrix and the chloroplast can be impeded by potential diffusion barriers—a starch sheath and stacks of thylakoids—and by conversion to HCO₃⁻ by a CO₂-recapturing complex LCIB/LCIC (referred to as LCIB henceforth for simplicity) in the basic chloroplast stroma. b, A schematic of the modelled PCCM, which considers intracompartment diffusion and intercompartment exchange of CO₂ and HCO₃⁻, as well as their interconversion, as indicated in the inset. Colour code as in a. The model is spherically symmetric and consists of a central pyrenoid matrix surrounded by a stroma. Thylakoids run through the matrix and stroma; their volume and surface area correspond to a reticulated network at the centre of the matrix extended by cylinders running radially outward. c, Concentration profiles of CO₂ and HCO₃⁻ in the thylakoid (dashed curves) and in the matrix/stroma (solid curves) for the baseline PCCM model that lacks LCIA activity and diffusion barriers. Dotted grey line indicates the effective Rubisco K_m for CO₂ (Methods). Colour code as in a. d, Net fluxes of inorganic carbon between the indicated compartments. The width of arrows is proportional to flux; the area of circles is proportional to the average molecular concentration in the corresponding regions. The black dashed loop denotes the major futile cycle of inorganic carbon in the chloroplast. Colour code as in a. For c and d, LCIA^C-mediated chloroplast membrane permeability to HCO₃⁻ \(\kappa _{{{{\mathrm{chlor}}}}}^{H^ - }\) = 10⁻⁸ m s⁻¹, BST-mediated thylakoid membrane permeability to HCO₃⁻ \(\kappa _{{{{\mathrm{thy}}}}}^{H^ - }\) = 10⁻² m s⁻¹, LCIB rate V_LCIB = 10³ s⁻¹ and CAH3 rate V_CAH3 = 10⁴ s⁻¹ (Methods). Other model parameters are estimated from experiments (Supplementary Table 2).