THE CARBOXYSOMES (POLYHEDRAL BODIES) OF AUTOTROPHIC PROKARYGTES
Authors: CODD G. A. , MARSDEN W. J. N. 
Published: January 2008

1. Polyhedral bodies are present in several groups of autotrophic bacteria that assimilate inorganic carbon via the Calvin cycle, including members of the colourless sulphur‐ oxidizing bacteria, ammonia‐ and nitrite‐oxidizing bacteria and all cyanobacteria (blue‐green algae) examined. Other groups of Calvin‐cycle bacteria lack the inclusions, which have not been found in the purple photosynthetic bacteria, or in the hydrogen bacteria, with one exception in each case. Polyhedral bodies also occur in the chlorophyll b‐containing photosynthetic symbiotic prokaryote, Prochloron, and in several cyanelles. The inclusion bodies have not been found in prokaryotes that cannot fix carbon dioxide via the Calvin cycle, or in eukaryotes.

2. Polyhedral bodies have been isolated from a colourless sulphur bacterium (Thiobacillus neapolitanus), two nitrifying bacteria (Nitrobacter agilis and Nitrosomonas sp.) and two cyanobacteria (Anabaena cylindrica and Chlorogloeopsis fritschii). Ribulose 1,5‐bisphosphate carboxylase/oxygenase (RuBisCO), the carbon dioxide‐fixing enzyme of the Calvin cycle, has been found in the polyhedral bodies in each case, confirming that these inclusions in autotrophic bacteria be re‐termed carboxysomes.

3. Knowledge of carboxysome composition has been constrained by difficulties in carboxysome isolation, although effective methods, including cell disruption in low‐ionic‐strength buffers followed by density‐gradient centrifugation through silicon polymers, or sucrose, followed be preparative agarose electrophoresis, are now available.

4. Analysis of isolated T. neapolitanus, N. agilis and C. fritschii carboxysomes by dissociating sodium dodecyl sulphate‐polyacrylamide gel electrophoresis has revealed the presence of 7–15 polypeptides, the most abundant being the large and small subunits of RuBisCO. Two polypeptides of the T. neapolitanus carboxysomes have been ascribed to the carboxysome membrane (shell), although the identity of other polypeptides is unknown.

5. DNA of unknown function has been reported in carboxysomes isolated from two Nitrobacter species and may be present in the organelles from T. neapolitanus.

6. RuBisCO occurs in both the carboxysomes and in soluble form in the cytoplasm of carboxysome‐containing bacteria. Structural, kinetic, regulatory and immunological comparisons have demonstrated full or near identity between the cytoplasmic and carboxysomal forms of the enzyme. As with RuBisCO from chloroplasts and from almost all non‐carboxysome‐containing bacteria, the cytoplasmic and carboxysomal RuBisCOs each consist of eight large plus eight small subunits. All RuBisCOs are bifunctional enzymes, oxygen acting as a competitive inhibitor of carboxylation, and carbon dioxide acting competitively to inhibit the apparently wasteful oxygenase reaction. Carbon dioxide and oxygen fixation occur at the same site on the large subunit. Despite extensive study, the function of the small subunits is unknown. All RuBisCOs can exist in an inactive and active form, activation proceeding by an ordered reversible binding of carbon dioxide, followed by a divalent metal cation, to the large subunit, at sites distinct from the catalytic site. Identity of the activation and catalytic sites at lysine residues 201 and 175, respectively, on the RuBisCO large subunit in organisms as phylogenetically diverse as spinach and Rhodospirillum rubrum suggests a uniform mechanism of RuBisCO regulation throughout the Calvin cycle autotrophs.

7. Carboxysome function is unknown, although several possibilities exist. A role for the organelles in autotrophy has been assumed and studies on carboxysome function have centred on relations between the organelles and RuBisCO. Carboxysomes may serve as active sites of carbon dioxide fixation, act as CO2‐concentrating compartments for RuBisCO, protect RuBisCO from adverse effects such as inhibition by oxygen and degradation by proteases, and/or act as general protein‐storage bodies. Evidence and argument for and against each of these possibilities is presented from whole‐cell and enzyme studies with sulphur bacteria and cyanobacteria, including specialist and nutritionally versatile strains.

8. The need for further knowledge of carboxysome composition, particularly including the structure and properties of the protein shell, to permit further understanding of carboxysome function is emphasized.