Carboxysomes are bacterial microcompartments (BMCs) consisting of polyhedral protein shells filled with the enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)—the predominant enzyme in carbon fixation and the rate limiting enzyme in the Calvin cycle—and carbonic anhydrase. Carboxysomes are thought to have evolved as a consequence of the increase in oxygen concentration in the ancient atmosphere; this is because oxygen is a competing substrate to carbon dioxide in the RuBisCO reaction. To overcome the inefficiency of RuBisCO, carboxysomes concentrate carbon dioxide inside the shell by means of co-localized carbonic anhydrase activity, which produces carbon dioxide from the bicarbonate that diffuses into the carboxysome. The resulting concentration of carbon dioxide near RuBisCO decreases the proportion of ribulose-1,5-bisphosphate oxygenation and thereby avoids costly photorespiratory reactions. The surrounding shell provides a barrier to carbon dioxide loss, helping to increase its concentration around RuBisCO. Carboxysomes are an essential part of the carbon dioxide-concentrating mechanism (CCM). Carboxysomes are the best studied example of bacterial microcompartments, the term for functionally diverse organelles that are alike in having a protein shell. Discovery Polyhedral bodies were discovered by transmission electron microscopy in the cyanobacterium Phormidium uncinatum in 1956. These were later observed in other cyanobacteria and in some chemotrophic bacteria that fix carbon dioxide—many of them are sulfur oxidizers or nitrogen fixers (for example, Halothiobacillus, Acidithiobacillus, Nitrobacter and Nitrococcus; all belonging to Pseudomonadota). The polyhedral bodies were first purified from Thiobacillus neapolitanus (now Halothiobacillus neapolitanus) in 1973 and shown to contain RuBisCO, held within a rigid outer covering. The authors proposed that since these appeared to be organelles involved in carbon dioxide fixation, they should be called carboxysomes. Architecture Structurally, carboxysomes are icosahedral, or quasi-icosahedral. Electron cryo-tomography studies have confirmed the approximately icosahedral geometry of the carboxysome, and have imaged protein molecules inside (presumed to be RuBisCO), arranged in a few concentric layers. The non-icosahedral faceted shapes of some carboxysomes can naturally be explained within the elastic theory of heterogeneous thin shells. The carboxysome has an outer shell composed of a few thousand protein subunits, which encapsulates a CO2-producing enzyme (carbonic anhydrase) and a carbon-fixing enzyme (RuBisCO). Proteins known to form the shell have been structurally characterized by X-ray crystallography. The proteins that constitute the majority of the shell form cyclical hexamers or pseudo-hexamers and belong to the BMC protein family. Small pores perforate many different types of BMC-H hexamers, and may serve as the route for diffusion of small substrates (e.g.