title: 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.
authors: UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California, United States of America.
authors: Julien
authors: J
authors: Jorda
authors: Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America.
authors: Yu
authors: Y
authors: Liu
authors: Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America.
authors: Thomas A
authors: TA
authors: Bobik
authors: UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California, United States of America; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, United States of America.
authors: Todd O
authors: TO
authors: Yeates
mesh_terms: D001419:Bacteria / Q000166:cytology*; D001426:Bacterial Proteins / Q000378:metabolism* / Q000502:physiology; D019295:Computational Biology; D008954:Models, Biological; D008958:Models, Molecular; D015388:Organelles / Q000378:metabolism* / Q000502:physiology; D060066:Protein Interaction Maps / Q000502:physiology*
chemical_list: D001426:Bacterial Proteins
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