The YfiD protein contributes to the pyruvate formate‐lyase flux in an Escherichia coli arcA mutant strain

Abstract

The product of yfiD gene is similar to pyruvate formate-lyase (PFL) activase and it has been reported to activate PFL by replacing the glycyl radical domain. To quantitate the effect of YfiD on the cell metabolism in microaerobic cultures, glucose-limited chemostat cultures were conducted with Escherichia coli yfiD mutant and yfiDarcA mutant strains. The microaerobic condition was controlled by purging the culture media with 2.5% O(2) in N(2). The intracellular metabolic flux distributions in these cultures were estimated based on C-13 labeling experiments. By comparing with the flux distributions in wild-type E. coli and the arcA mutant, it was shown that YfiD contributes to about 18% of the PFL flux in the arcA mutant, but it did not contribute to the PFL flux in wild-type E. coli. It was also shown that the cell used both PFL and pyruvate dehydrogenase (PDH) to supplement the acetyl-coenzyme A (AcCoA) pool under microaerobic conditions. The flux through PDH was about 22-30% of the total flux toward AcCoA in the wild-type, the yfiD mutant and yfiDarcA mutant strains. Relatively higher lactate production was seen in the yfiDarcA mutant than the other strains, which was due to the lower total flux through PFL and PDH toward AcCoA in this strain.

Analysis of the Proteome of Intracellular Shigella flexneri Reveals Pathways Important for Intracellular Growth

“…These data suggest that mixed-acid fermentation, and metabolism of pyruvate in particular, is required for optimal growth of S. flexneri in the host cell cytoplasm. YfiD, which activates PflB, is also elevated in the intracellular bacteria (Table 3), which would increase flux through this pathway (74).…”

Metabolic Flux Analysis of Escherichia coli creB and arcA Mutants Reveals Shared Control of Carbon Catabolism under Microaerobic Growth Conditions

“…15% was observed. In addition, it should be noted that conversion of Pyr into acetyl-CoA may also occur through the reactions catalyzed by TdcE (56) or modulated by YfiD, particularly in a ⌬arcA background (77).…”

“…Although the acetylCoA pool was mainly supplemented by the reaction through Pfl, both Pfl and PDH were active under the 2.5% O 2 -in-N 2 condition used in the present study. Since the formate formed by Pfl would not be decomposed at neutral pH (77), the Pfl flux would correlate with the extracellular formate fluxes. Small differences observed in this correlation could be attributed to the activity of formate-hydrogen lyase, which catalyzes the conversion of formate into CO 2 and H 2 (9).…”

Physiological, biomass elemental composition and proteomic analyses of Escherichia coli ammonium-limited chemostat growth, and comparison with iron- and glucose-limited chemostat growth

“…Operation of pyruvate formate lyase under oxic conditions might be possible if the damaged portion of the enzyme were repaired continually. YfiD is thought to replace the oxygen-damaged portion of pyruvate formate lyase (Wagner et al, 2001;Zhu et al, 2007) creating a theoretical mechanism that could permit pyruvate formate lyase to function under oxic conditions. The repair protein is small (127 aa), and a damaged protein could be replaced many times and still require fewer resources than a single PDHc.…”