Proteomic analysis of the sponge (Porifera) Aggregation Factor implicates an ancient protein domain toolkit for allorecognition and adhesion in animals

The discovery that sponges (Porifera) can fully regenerate from aggregates of dissociated cells launched them as one of the earliest experimental models to study the evolution of cell adhesion and allorecognition in animals. This process depends on an extracellular glycoprotein complex called the Aggregation Factor (AF), which is composed of proteins thought to be unique to sponges. We used label-free quantitative proteomics to identify additional AF components and interacting proteins in the classical model, Clathria prolifera, and compared them to proteins involved in cell interactions in Bilateria. Our results confirm that the MAFp3/p4 proteins are the primary components of the AF, but implicate related proteins with calx-beta and wreath domains as additional components. Using AlphaFold, we unveiled close structural similarities of AF components to protein domains in other animals, previously masked by the mutational decay of sequence similarity. The wreath domain, believed to be unique to the AF, was predicted to contain a central beta-sandwich of the same organization as the vWFD domain (also found in extracellular, gel-forming glycoproteins in other animals). Additionally, many co-purified proteins share a conserved C-terminus, containing divergent Ig and Fn3 domains predicted to serve as an AF-interaction interface. One of these proteins, MAFAP1, resembles immunoglobulin superfamily cell adhesion molecules (IgCAMs) and we hypothesize that it may function to link the AF to the surface of cells. Our results highlight the existence of an ancient toolkit of conserved protein domains regulating cell-cell and cell-ECM interactions in all animals, and likely reflect a common origin of cell adhesion and allorecognition.