Scaffolding protein CcmM directs multiprotein phase separation in beta-carboxysome biogenesis

Biochemical, biophysical and structural analysis reveals how the scaffolding protein CcmM recruits the enzymes Rubisco and carbonic anhydrase into a condensate for encapsulation into carboxysomes-microcompartments in cyanobacteria that serve to optimize CO2 assimilation. Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural biotechnology. Here we analyzed the role of the scaffolding protein CcmM of the beta-cyanobacterium Synechococcus elongatus PCC 7942 in sequestrating the hexadecameric Rubisco and the tetrameric carbonic anhydrase, CcaA. We find that the trimeric CcmM, consisting of gamma CAL oligomerization domains and linked small subunit-like (SSUL) modules, plays a central role in mediation of pre-carboxysome condensate formation through multivalent, cooperative interactions. The gamma CAL domains interact with the C-terminal tails of the CcaA subunits and additionally mediate a head-to-head association of CcmM trimers. Interestingly, SSUL modules, besides their known function in recruiting Rubisco, also participate in intermolecular interactions with the gamma CAL domains, providing further valency for network formation. Our findings reveal the mechanism by which CcmM functions as a central organizer of the pre-carboxysome multiprotein matrix, concentrating the core components Rubisco and CcaA before beta-carboxysome shell formation