Analysis of carboxysomes from Synechococcus PCC7942 reveals multiple rubisco complexes with carboxysomal proteins CcmM and CcaA

In cyanobacteria, the key enzyme for photosynthetic CO₂ fixation, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), is bound within proteinaceous polyhedral microcompartments called carboxysomes. Cyanobacteria with Form IB Rubisco produce β-carboxysomes whose putative shell proteins are encoded by the ccm-type genes. To date, very little is known of the protein-protein interactions that form the basis of β-carboxysome structure. In an effort to identify such interactions within the carboxysomes of the β-cyanobacterium Synechococcus sp. PCC7942, we have used polyhistidine-tagging approaches to identify at least three carboxysomal subcomplexes that contain active Rubisco. In addition to the expected L8S8 Rubisco, which is the major component of carboxysomes, we have identified two Rubisco complexes containing the putative shell protein CcmM, one of which also contains the carboxysomal carbonic anhydrase, CcaA. The complex containing CcaA consists of Rubisco and the full-length 58-kDa form of CcmM (M58), whereas the other is made up of Rubisco and a short 35-kDa form of CcmM (M35), which is probably translated independently of M58 via an internal ribosomal entry site within the ccmM gene. We also show that the high CO₂-requiring ccmM deletion mutant (ΔccmM) can achieve nearly normal growth rates at ambient CO₂ after complementation with both wild type and chimeric (His6-tagged) forms of CcmM. Although a significant amount of independent L ₈S₈ Rubisco is confined to the center of the carboxysome, we speculate that the CcmM-CcaA-Rubisco complex forms an important assembly coordination within the carboxysome shell. A speculative carboxysome structural model is presented.