title: 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 3 small middle dot5-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 -93 small middle dot5 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 radical-containing enzyme. The YfiD radical was found to be introduced by the PFL-activase 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.
authors.affiliation: The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK1.
authors.forename: Neil R
authors.initials: NR
authors.lastname: Wyborn
authors.affiliation: The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK1.
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Messenger
authors.affiliation: The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK1.
authors.forename: Robin A
authors.initials: RA
authors.lastname: Henderson
authors.affiliation: Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK2.
authors.forename: Gary
authors.initials: G
authors.lastname: Sawers
authors.affiliation: The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK1.
authors.forename: Ruth E
authors.initials: RE
authors.lastname: Roberts
authors.affiliation: The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK1.
authors.forename: Margaret M
authors.initials: MM
authors.lastname: Attwood
authors.affiliation: The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK1.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Green
mesh_terms: D000123:Acetyltransferases / Q000737:chemistry; D000332:Aerobiosis; D000693:Anaerobiosis; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002264:Carboxylic Acids / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D017930:Genes, Reporter; D006863:Hydrogen-Ion Concentration; D011401:Promoter Regions, Genetic; D011993:Recombinant Fusion Proteins / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D002264:Carboxylic Acids; D029968:Escherichia coli Proteins; D011993:Recombinant Fusion Proteins; C459789:YfiD protein, E coli; D000123:Acetyltransferases; C022560:formate C-acetyltransferase