Rubisco condensate formation by CcmM in β-carboxysome biogenesis

Cells use compartmentalization of enzymes as a strategy to regulate metabolic pathways and increase their efficiency¹. The α- and β-carboxysomes of cyanobacteria contain ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)-a complex of eight large (RbcL) and eight small (RbcS) subunits-and carbonic anhydrase^2-4. As HCO₃^- can diffuse through the proteinaceous carboxysome shell but CO₂ cannot⁵, carbonic anhydrase generates high concentrations of CO₂ for carbon fixation by Rubisco⁶. The shell also prevents access to reducing agents, generating an oxidizing environment^7-9. The formation of β-carboxysomes involves the aggregation of Rubisco by the protein CcmM¹⁰, which exists in two forms: full-length CcmM (M58 in Synechococcus elongatus PCC7942), which contains a carbonic anhydrase-like domain⁸ followed by three Rubisco small subunit-like (SSUL) modules connected by flexible linkers; and M35, which lacks the carbonic anhydrase-like domain¹¹. It has long been speculated that the SSUL modules interact with Rubisco by replacing RbcS^2-4. Here we have reconstituted the Rubisco-CcmM complex and solved its structure. Contrary to expectation, the SSUL modules do not replace RbcS, but bind close to the equatorial region of Rubisco between RbcL dimers, linking Rubisco molecules and inducing phase separation into a liquid-like matrix. Disulfide bond formation in SSUL increases the network flexibility and is required for carboxysome function in vivo. Notably, the formation of the liquid-like condensate of Rubisco is mediated by dynamic interactions with the SSUL domains, rather than by low-complexity sequences, which typically mediate liquid-liquid phase separation in eukaryotes^12,13. Indeed, within the pyrenoids of eukaryotic algae, the functional homologues of carboxysomes, Rubisco adopts a liquid-like state by interacting with the intrinsically disordered protein EPYC1¹⁴. Understanding carboxysome biogenesis will be important for efforts to engineer CO₂-concentrating mechanisms in plants^15-19.