The complexity of prokaryotic organelle construction: examples from Rhodospirillum rubrum and Clostridium autoethanogenum

Bacterial microcompartments (BMCs) are proteinaceous organelles that encapsulate specific metabolic pathways to enhance key catalytic processes and protect the cell from toxic intermediates. Carboxysomes and the 1,2-propanediol utilising and ethanolamine utilising metabolosomes have been studied extensively. However, bioinformatic analyses have revealed a host of BMCs that are yet to be experimentally investigated. This study examined the production by E. coli of previously uncharacterised shell proteins from two organisms: Rhodospirillum rubrum and Clostridium autoethanogenum. The flexible nature of microcompartment formation was revealed by the different structures formed by the R. rubrum shell proteins both in vivo in E. coli and following their isolation. In vivo, shell proteins formed swirled sheets that were unable to form compartments. However, upon isolation the components of the protein structures were able to re-assemble to form apparently closed "empty" compartments. This highlighted the complex nature of the protein interactions involved in microcompartment assembly and the effect of a changing environment upon these interactions. The production of C. autoethanogenum shell proteins in E. coli revealed a previously unobserved interaction of protein sheets with ribosomes within the cytoplasm. This phenotype was shown to involve a C-terminally extended hexameric shell protein, Caethg_3286. The function of C-terminally extended shell proteins, which are encoded in many BMC operons, is unknown at present although the structure of one, EutK, was resolved and shows a high degree of similarity to nucleic acid binding domains. The crystal structure of the BMC domain of Caethg_3286 revealed that the C-terminus is on the concave surface of the hexamer allowing the C-terminal extension to extend into the cytoplasm and interact with ribosomes. The ribosomal interaction revealed in this study and the potential nucleic acid binding capacity of another C-terminal extension may indicate a role of the C-terminal extension in the regulation of BMC formation at the level of translation.