Surveying Bacterial Microcompartment Core Enzymes to Identify Prospective Encapsulation Peptides and Principles of Core Interactions

Bacterial microcompartments (BMCs) are prokaryotic organelles composed of a quasi-icosahedral or polyhedral protein shell enclosing an enzymatic core. These encapsulated enzymatic cores perform coordinated metabolic functions, such as carbon fixation in carboxysomes and the catabolism of various substrates—including ethanolamine, propanediol, glycerol, choline, rhamnose, and fucose—in metabolosomes. While enzyme interaction networks within carboxysome cores are well characterized, those of metabolosomes remain comparatively understudied. Short, often amphipathic sequences known as encapsulation peptides (EPs) have been shown to mediate enzyme–shell interactions; however, their role in enzyme–enzyme (core–core) interactions is still poorly understood.In this study, we systematically and comparatively investigated EP-mediated interactions in five distinct, previously underexplored types of glycyl radical enzyme-associated (GRM) BMCs. We identified eleven novel core–core interactions and one shell–core interaction across these five GRM BMC types, with EPs being either fully or partially responsible for mediating interactions between core enzymes. These findings provide new insights into the mechanisms underlying BMC core assembly and might be useful for further biotechnological applications.