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

PLoS computational biology (2015-02-04)
Julien Jorda, Yu Liu, Thomas A Bobik, Todd O Yeates
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.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Ethanolamine, purified by redistillation, ≥99.5%
Sigma-Aldrich
Ethanolamine, ACS reagent, ≥99.0%
Sigma-Aldrich
Ethanolamine, ≥98%
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Ethanolamine, liquid, BioReagent, suitable for cell culture, ≥98%
Supelco
Ethanolamine, analytical standard
Sigma-Aldrich
Ethanolamine, puriss. p.a., ACS reagent, ≥99.0% (GC/NT)
Sigma-Aldrich
Ethanolamine, ≥99%
Supelco
Aucubin, analytical standard
SAFC
Ethanolamine
Aucubin, primary reference standard
Trolamine impurity A, European Pharmacopoeia (EP) Reference Standard