Structure of Nanotubes Formed From Bacterial Microcompartment Shell Proteins

Abstract

Bacterial microcompartments (BMCs) are self-assembling polyhedral organelles found in bacteria, composed of a protein shell and an enzymatic core. The shell is made of disk-shaped shell proteins which exhibit a bilateral asymmetry, due to a concave and convex surface, and can either be hexamers, pseudo-hexameric trimers or pentamers. The hexameric Citrobacter freundii PduA, from the propane-1,2-diol utilisation (Pdu) BMC, has been previously shown to form protein nanotubes of ~20nm diameter. Here, it is shown that the dominant trimeric shell protein, Lactobacillus reuteri PduB, also forms protein nanotubes of dimensions similar to those of a BMC (40 to 140 nm). Moreover, PduA and PduB are also able to form composite nanotubes under various ratios, but of intermediate dimensions. The ability to assemble nanotubes of differing diameters has great potential in biotechnological applications, as the dimensions could be subtly tweaked for different purposes. For all nanotube types, computational approaches were used to predict the subunit orientation to be concave external, which was subsequently demonstrated experimentally in all cases. Moreover, using a mathematical approach, a helical arrangement of the PduA hexamers was predicted within their nanotubes, paving the foundation for understanding the assembly process of these assemblies. The assembly of a nanotube can be thought of an artefact of the BMC assembly process in the absence of other shell proteins. Thus, an understanding of the nanotube assembly process can also provide insight in the context of BMCs.