Formate accumulation due to DNA release in aerobic cultivations of Escherichia coli

Abstract

Three different aerobic fed-batch processes of Escherichia coli were studied, two for the production of a recombinant protein and one process with a wild-type E. coli strain. In all three processes, an accumulation of formate could be observed in the latter part of the process. Analysis of the concentration of DNA in the medium revealed that the release of DNA coincided with the accumulation of formate. It was found that increasing concentrations of DNA correlated in almost linearly increasing concentrations of formate. Formate accumulation is caused by mixed acid fermentation, although no oxygen limitation was measured with the DO electrode. It is proposed that extracellular DNA restrained mass transfer between the bulk medium and the cell. To investigate if the DNA accumulation caused formate production, DNA was removed by continuous feeding of a DNA binding polymer to the medium. The addition of the polymer decreased the content of free DNA in the broth and the formate was reassimilated. Furthermore, additional DNA early in the process resulted in early formate accumulation.

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

“…D50.1 h 21 ); this is not unheard of, and formate has been measured previously in oxic and microaerophilic E. coli cultures (Alexeeva et al, 2000;Castan & Enfors, 2002;De Maeseneire et al, 2006). The primary formate synthesis route in E. coli is pyruvate formate lyase, although it is theoretically possible formate could be produced from tetrahydrofolate metabolism.…”

“…Therefore, bulk-phase oxygen mass transfer limitation is not thought to be responsible for the formate secretion. Alternatively, it has been suggested that an extracellular polymer such as DNA could interfere with oxygen mass transfer at the cell membrane (Castan & Enfors, 2002 did not produce appreciable amounts of acetate which is typically associated with oxygen-limited E. coli growth (Alexeeva et al, 2000). The previously discussed nutrient investment versus cellular function metabolic tradeoff theory represents another possible hypothesis.…”

Physiological and Proteomic Analysis of Escherichia coli Iron-Limited Chemostat Growth

“…4d). While often associated with anaerobic growth, the secretion of formate under aerobic conditions has been reported previously (62,63). The measured biomass and by-products accounted for ϳ80% of the iron-limited cultures' carbon and electrons at D of 0.1 h Ϫ1 (see Table S2 in the supplemental material).…”

Fast dynamic response of the fermentative metabolism of Escherichia coli to aerobic and anaerobic glucose pulses

“…The specific production rate of formate in the chemostat was 0.0002 mmol/ g h. Other authors have also reported the production of formate by E. coli in fully aerobic cultures (Castan and Enfors, 2002;Lara et al, 2006a,b;Sandoval-Basurto et al, 2005). The exact mechanism for this phenomenon is not yet known, but authors have related formate accumulation to DNA release into the media, probably due to cell rupture (Castan and Enfors, 2002). It should be noted that the pfl gene, that codes for the enzyme responsible for formate production from pyruvate (pyruvate-formate lyase, PFL), is reported to be expressed only under anaerobic conditions.…”