Fumarate dependent protein composition under aerobic and anaerobic growth conditions in Escherichia coli.

In the absence of sugars, C4-dicarboxylates (C4DC) like fumarate represent important substrates for growth of Escherichia coli. Aerobically, C4DCs are oxidized to CO2 whereas anaerobically, C4DCs are used for fumarate respiration. In order to determine the impact of fumarate under aerobic and anaerobic conditions, proteomes of E. coli W3110 grown aerobically or anaerobically with fumarate and/or the non-C4DC substrate glycerol were comparatively profiled by nanoLC-MS/MS. Membrane enrichment allowed sensitive detection of membrane proteins. A total of 1657 proteins of which 646 and 374 were assigned to the cytosol or membrane, respectively, were covered. Presence of fumarate triggered changes (≥ 2fold) to the levels of 211 and 76 proteins under aerobic and anaerobic growth, respectively. The fumarate induced changes included proteins encoded by genes regulated by the C4DC two-component system DcuS-DcuR (DctA, DcuB, FumB, FrdABC proteins) catalyzing uptake and initial catabolic steps. Many of the proteins displaying altered levels are not part of the DcuS-DcuR regulon, including proteins of citric acid cycle and associated pathways (aerobic), proteins involved in motility and chemotaxis (anaerobic), and oxidative stress. Their genes are mostly preceded by cAMP receptor protein (CRP) sites, some by DcuR-like sites. Testing of selected genes confirmed regulation by CRP and DcuS-DcuR.