Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment

Abstract

Bacterial microcompartments (MCPs) are protein-bound organelles that carry out diverse metabolic pathways in a wide range of bacteria. These supramolecular assemblies consist of a thin outer protein shell, reminiscent of a viral capsid, which encapsulates sequentially acting enzymes. The most complex MCP elucidated so far is the propanediol utilizing (Pdu) microcompartment. It contains the reactions for degrading 1,2-propanediol. While several experimental studies on the Pdu system have provided hints about its organization, a clear picture of how all the individual components interact has not emerged yet. Here we use co-evolution-based methods, involving pairwise comparisons of protein phylogenetic trees, to predict the protein-protein interaction (PPI) network governing the assembly of the Pdu MCP. We propose a model of the Pdu interactome, from which selected PPIs are further inspected via computational docking simulations. We find that shell protein PduA is able to serve as a “universal hub” for targeting an array of enzymes presenting special N-terminal extensions, namely PduC, D, E, L and P. The varied N-terminal peptides are predicted to bind in the same cleft on the presumptive luminal face of the PduA hexamer. We also propose that PduV, a protein of unknown function with remote homology to the Ras-like GTPase superfamily, is likely to localize outside the MCP, interacting with the protruding β-barrel of the hexameric PduU shell protein. Preliminary experiments involving a bacterial two-hybrid assay are presented that corroborate the existence of a PduU-PduV interaction. This first systematic computational study aimed at characterizing the interactome of a bacterial microcompartment provides fresh insight into the organization of the Pdu MCP.

Author Summary

Many bacteria produce giant proteinaceous structures within their cells, which they use to carry out special metabolic reactions in their interior. Much has been learned recently about the individual components—shell proteins and encapsulated enzymes—that assemble together, thousands of subunits in all, to make these bacterial microcompartments or MCPs. However, in order to carry out their biological functions, these systems must be highly organized through specific protein-protein interactions, and such a higher level understanding of organization in MCP systems is lacking. In this study, we use genomic data and phylogenetic analysis to predict the network of interactions between the approximately 20 different kinds of proteins and enzymes present in the Pdu MCP. Then, we use computational docking to examine a subset of those that are predicted to involve enzymes bound to the interior surface of the shell proteins, and show that the results are consistent with recent experimental data. We further provide new experimental evidence for one of the predicted protein-protein interactions. This study expands our understanding of a complex system of proteins serving as a metabolic organelle in bacterial cells, and provides a foundation for further experimental investigations.