Quantifying photosynthetic metabolites permeability across bacterial microcompartments using computational microscopy

Abstract

Carboxysomes are Bacterial microcompartments, found in cyanobacteria that locally concentrate carbon dioxide (CO2) to improve the efficiency of the enzyme RuBisCO, a key step towards photosynthetic carbon fixation by the Calvin-Benson-Bassham (CBB) cycle. The carboxysome shell is made up of proteins that encapsulate RuBisCO and carbonic anhydrase. Carbonic anhydrase converts soluble bicarbonate to CO2, increasing the local concentration of CO2 for RuBisCO. In addition to CO2, other metabolites such as oxygen (O2), bicarbonate (HCO3−), 3-phosphoglyceric acid (3-PGA) and ribulose-1,5-bisphosphate (RuBP) also need to permeate through the carboxysome shell to efficiently perform CO2 fixation. Quantifying the permeability of the shell for these metabolites currently remains a challenge and one of the critical design features related to the design of synthetic bacterial microcompartments for metabolic and sustainablebioengineering applications. Leveraging a high resolution cryo-electron microscopy structure of a synthetic beta-carboxysome shell and new graphics processing unit (GPU)-resident molecular simulation engines, we determine the permeability of photosynthetic metabolites across synthetic carboxysome shell through unbiased molecular simulation at all-atom resolution. We find that the carboxysome itself is not selectively permeable to bicarbonate over carbon dioxide, as originally hypothesized. Instead, the carboxysome shell proteins form a general barrier to maintain the carbon dioxide gradient generated by carbonic anhydrase activity within the carboxysome, compensating for inefficiencies of endogenous RuBisCO, specifically slow turnover rate, and photorespiration. The results from all-atom molecular simulations presented here provide a detailed mechanistic picture, using the shell permeabilities to engineer smart synthetic bacterial microcompartments and to improve photosynthetic efficiency with a wide range of applications in sustainable, metabolic, agricultural, and biomedical engineering.