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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.
Highlights
Cellular organization has long been considered to be much simpler in bacteria than in eukaryotic cells
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
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 propanediol utilizing (Pdu) MCP
Summary
Cellular organization has long been considered to be much simpler in bacteria than in eukaryotic cells. Electron microscopy and higher resolution structural studies have demonstrated that some bacteria can form polyhedral capsid-like bodies that are 80 to 150 nm in diameter [6,7]; reviewed in [8,9,10,11]. These polyhedral inclusions, known as bacterial microcompartments, are widely distributed across nearly 20% of known bacterial strains [9,12,13]. MCPs fulfill diverse roles: enhancement of metabolic flux in their hosted enzymatic pathway [14], confinement of toxic or volatile intermediates [15,16,17] and shielding of interior enzymes from reactions with reactive or competing molecules [18]
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