Expression of the Escherichia coli yfiD gene responds to intracellular pH and reduces the accumulation of acidic metabolic end products

Abstract

The YfiD protein of Escherichia coli has been reported to be an acid-inducible protein.Here it is shown that expression of a yfiD ::lac reporter fusion is enhanced up to 35-fold during acidic growth. The anaerobic transcription factor FNR was confirmed as the major regulator of yfiD expression, and ArcA was found to enhance anaerobic yfiD expression, probably by displacing a repressing FNR dimer in the N935 region of the promoter. Moreover, the pyruvate sensor PdhR was shown to act as a minor anaerobic repressor of yfiD expression. On the basis of its strong homology to the C-terminal region of pyruvate formate-lyase (PFL) it was predicted that YfiD would be a radicalcontaining enzyme. The YfiD radical was found to be introduced by the PFLactivase enzyme, but unlike PFL, AdhE did not deactivate radicalized YfiD. The extent of radical activation of YfiD was enhanced by low intracellular pH, and thus it was concluded that both yfiD expression and YfiD activity are affected by growth at low pH. The yfiD mutant strain JRG4033 excreted increased levels of organic acids compared to the parental strain when grown in chemostat culture under oxygen-starved conditions, consistent with the acid-inducibility of yfiD expression and the recently reported ability of YfiD to rescue the activity of oxygenolytically cleaved PFL.

The Acetate Switch

“…Consistent with this hypothesis, growth in the presence of pyruvate or under microaerobic conditions elevates the level of YfiD (50,290), while the pyruvate-sensitive regulator PdhR and the oxygen-sensitive global regulators FNR and ArcA control yfiD transcription (290,476). Cells also up-regulate YfiD when exposed to low pH (50,476) or to the organic acids propionate (50), benzoate (476), or acetate (240). Up-regulation also oc-curs in cells that express the heterologous FNR protein HlyX (161) or a heterologous acetyl-CoA-draining pathway (175).…”

“…It has been proposed that YfiD acts as a substitute glycyl radical domain used by oxygen-stressed cells to repair oxygeninduced damage to the glycyl radical of PFL (461). Consistent with this hypothesis, growth in the presence of pyruvate or under microaerobic conditions elevates the level of YfiD (50,290), while the pyruvate-sensitive regulator PdhR and the oxygen-sensitive global regulators FNR and ArcA control yfiD transcription (290,476). Cells also up-regulate YfiD when exposed to low pH (50,476) or to the organic acids propionate (50), benzoate (476), or acetate (240).…”

Inactivation of E. coli pyruvate formate-lyase: Role of AdhE and small molecules

“…Yet in hundreds of experiments in our laboratory, no evidence for AdhE-catalyzed PFL deactivation can be found. Our results are, however, consistent with a recent report on YfiD, a PFL homolog in E. coli that can be activated to generate a glycyl radical by PFL-AE, but cannot be deactivated by AdhE [29]. Lack of deactivation of PFL by AdhE.…”

A Genome-Wide View of theEscherichia coliBasS–BasR Two-component System Implicated in Iron-responses

“…23) The expression level of yfiD is enhanced during growth at pH 4.4 and upon the addition of propionate at pH 6. (6) The tdc operon is implicated in the expression of anaerobically-induced threonine/serine permease.…”