Bacterial microcompartment

Bacterial microcompartments (BMCs) are organelle-like structures, consisting of a protein shell that encloses enzymes and other proteins. BMCs are typically about 40–200 nanometers in diameter and are entirely made of proteins. The shell functions like a membrane, as it is selectively permeable. Other protein-based compartments found in bacteria and archaea include encapsulin nanocompartments and gas vesicles. Bacterial microcompartments (BMCs) are organelle-like structures, consisting of a protein shell that encloses enzymes and other proteins. BMCs are typically about 40–200 nanometers in diameter and are entirely made of proteins. The shell functions like a membrane, as it is selectively permeable. Other protein-based compartments found in bacteria and archaea include encapsulin nanocompartments and gas vesicles. The first BMCs were observed in the 1950s in electron micrographs of cyanobacteria, and were later named carboxysomes after their role in carbon fixation was established. Until the 1990s, carboxysomes were thought to be an oddity confined to certain autotrophic bacteria. But then genes coding for proteins homologous to those of the carboxysome shell were identified in the pdu (propanediol utilization) and eut (ethanolamine utilization) operons. Subsequently, transmission electron micrographs of Salmonella cells grown on propanediol or ethanolamine showed the presence of polyhedral bodies similar to carboxysomes. The term metabolosome is used to refer to such catabolic BMCs (in contrast to the autotrophic carboxysome). Although the carboxysome, propanediol utilizing (PDU), and ethanolamine utilizing (EUT) BMCs encapsulate different enzymes and therefore have different functions, the genes encoding for the shell proteins are very similar. Most of the genes (coding for the shell proteins and the encapsulated enzymes) from experimentally characterized BMCs are located near one another in distinct genetic loci or operons. There are currently over 20,000 bacterial genomes sequenced, and bioinformatics methods can be used to find all BMC shell genes and to look at what other genes are in the vicinity, producing a list of potential BMCs. In 2014, a comprehensive survey identified 23 different loci encoding up to 10 functionally distinct BMCs across 23 bacterial phyla. The BMC shell appears icosahedral or quasi-icosahedral, and is formed by (pseudo)hexameric and pentameric protein subunits. The major constituents of the BMC shell are proteins containing Pfam00936 domain(s). These proteins form oligomers that are hexagonal in shape and are thought to form the facets of the shell. The BMC-H proteins, which contain a single copy of the Pfam00936 domain, are the most abundant component of the facets of the shell. The crystal structures of a number of these proteins have been determined, showing that they assemble into cyclical hexamers, typically with a small pore in the center. This opening is proposed to be involved in the selective transport of the small metabolites across the shell. A subset of shell proteins are composed of tandem (fused) copies of the Pfam00936 domain (BMC-T proteins). The structurally characterized BMC-T proteins form trimers that are pseudohexameric in shape. Some BMC-T crystal structures show that the trimers can stack in a face-to-face fashion. In such structures, one pore from one trimer is in an “open” conformation, while the other is closed – suggesting that there may be an airlock-like mechanism that modulates the permeability of some BMC shells. Another subset of BMC-T proteins contain a cluster, and may be involved in electron transport across the BMC shell. Twelve pentagonal units are necessary to cap the vertices of an icosahedral shell. Crystal structures of proteins from the EutN/CcmL family (Pfam03319) have been solved and they typically form pentamers (BMC-P). The importance of the BMC-P proteins in shell formation seems to vary among the different BMCs. It was shown that they are necessary for the formation of the shell of the PDU BMC as mutants in which the gene for the BMC-P protein was deleted cannot form shells, but not for the alpha-carboxysome: without BMC-P proteins, carboxysomes will still assemble and many are elongated; these mutant carboxysomes appear to be “leaky”. While the BMC shell is architecturally similar to many viral capsids, the shell proteins have not been found to have any structural or sequence homology to capsid proteins. Instead, structural and sequence comparisons suggest that both BMC-H (and BMC-T) and BMC-P, most likely, have evolved from bona fide cellular proteins, namely, PII signaling protein and OB-fold domain-containing protein, respectively.