The Protein Network of the Pseudomonas aeruginosa Denitrification Apparatus.

Abstract

Oxidative phosphorylation using multiple component, membrane-associated protein complexes is the most effective way for a cell to generate energy. Here, we systematically investigated the multiple protein-protein interactions of the denitrification apparatus of the pathogenic bacterium Pseudomonas aeruginosa. During denitrification, nitrate (Nar), nitrite (Nir), nitric-oxide (Nor) and nitrous-oxide (Nos) reductases catalyze the reaction cascade of NO(3-) → NO(2-) → NO → N2O → N2. Genetic experiments suggested that the nitric-oxide reductase NorBC and the regulatory protein NosR are the nucleus of the denitrification protein network. We utilized membrane interactomics in combination with electron microscopy co-localization studies to elucidate the corresponding protein-protein interactions. The integral membrane proteins NorC, NorB and NosR form the core assembly platform that binds the nitrate reductase NarGHI and the periplasmic nitrite reductase NirS via its maturation factor NirF. The periplasmic nitrous-oxide reductase, NosZ, is linked via NosR. The nitrate transporter, NarK2, the nitrate regulatory system, NarXL, various nitrite reductase maturation proteins, NirEJMNQ, and the Nos assembly lipoproteins, NosFL, were also found to be attached. A number of proteins associated with energy generation, including electron donating dehydrogenases, the complete ATP synthase, almost all enzymes of the TCA cycle, and the SEC system of protein transport, among many other proteins, were found to interact with the denitrification proteins. This deduced nitrate respirasome is presumably only one part of an extensive cytoplasmic membrane-anchored protein network connecting cytoplasmic, inner membrane and periplasmic proteins, to mediate key activities occurring at the barrier/interface between the cytoplasm and the external environment.