Exploring bacterial organelle interactomes: a model of the protein-protein interaction network in the Pdu microcompartment

PLoS Comput Biol. 2015 Feb 3;11(2):e1004067. doi: 10.1371/journal.pcbi.1004067. eCollection 2015 Feb.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Bacteria / cytology*
  • Bacterial Proteins / metabolism*
  • Bacterial Proteins / physiology
  • Computational Biology
  • Models, Biological*
  • Models, Molecular
  • Organelles / metabolism*
  • Organelles / physiology
  • Protein Interaction Maps / physiology*


  • Bacterial Proteins