Adaptation of anaerobic cultures of Escherichia coli K‐12 in response to environmental trimethylamine‐N‐oxide

Abstract

SummarySystematic analyses of transcriptional and metabolic changes occurring when E scherichia coli K‐12 switches from fermentative growth to anaerobic respiratory growth with trimethylamine‐N‐oxide (TMAO) as the terminal electron acceptor revealed: (i) the induction of torCAD, but not genes encoding alternative TMAO reductases; (ii) transient expression of frmRAB, encoding formaldehyde dehydrogenase; and (iii) downregulation of copper resistance genes. Simultaneous inference of 167 transcription factor (TF) activities implied that transcriptional re‐programming was mediated by 20 TFs, including the transient inactivation of the two‐component system ArcBA; a prediction validated by direct measurement of phosphorylated ArcA. Induction of frmRAB, detection of dimethylamine in culture medium and formaldehyde production when cell‐free extracts were incubated with TMAO suggested the presence of TMAO demethylase activity. Accordingly, the viability of an frmRAB mutant was compromised upon exposure to TMAO. Downregulation of genes involved in copper resistance could be accounted for by TMAO inhibition of Cu(II) reduction. The simplest interpretation of the data is that during adaptation to the presence of environmental TMAO, anaerobic fermentative cultures of E . coli respond by activating the TorTSR regulatory system with consequent induction of TMAO reductase activity, resulting in net oxidation of menaquinone and inhibition of Cu(II) reduction, responses that are sensed by ArcBA and CusRS respectively.

Generating a Metal-responsive Transcriptional Regulator to Test What Confers Metal Sensing in Cells

“…FrmA has formaldehyde dehydrogenase activity, and the operon was subsequently shown to respond to exogenous formaldehyde ( 30 , 33 ). This operon is de-repressed during anaerobic respiration using trimethylamine N -oxide as the terminal electron acceptor where endogenous formaldehyde is generated as a by-product of trimethylamine N -oxide demethylation ( 34 ). CO-releasing molecules and chloride treatments also trigger expression of the frm operon ( 35 , 36 ).…”

The Effectors and Sensory Sites of Formaldehyde-responsive Regulator FrmR and Metal-sensing Variant

“…Formaldehyde is produced by the alternative heme degradation pathway (IsdG and IsdI) in Staphylococcus aureus to acquire iron ( 13 , 14 ). The recent detection of trimethylamine N -oxide (TMAO) 3 demethylase activity in cell extracts suggests that this activity may be an endogenous source of formaldehyde in Escherichia coli ( 15 ). Demethylation of nucleic acids and production of methylglyoxal from glyceraldehyde 3-phosphate and dihydroxyacetone phosphate during glycolysis represent more widespread physiological sources of formaldehyde ( 16 – 18 ).…”

The mechanism of a formaldehyde-sensing transcriptional regulator

“…The starting point for the work reported here was the observation that formaldehyde is generated when the model bacterium Escherichia coli adapts to the presence of the alternative electron acceptor trimethylamine- N -oxide9. An inability to respond (by induction of the frmRAB operon) to this endogenous formaldehyde challenge resulted in growth inhibition, rather than growth promotion, when anaerobic E. coli cultures were provided with trimethylamine- N -oxide9.…”

“…An inability to respond (by induction of the frmRAB operon) to this endogenous formaldehyde challenge resulted in growth inhibition, rather than growth promotion, when anaerobic E. coli cultures were provided with trimethylamine- N -oxide9. The frmRAB operon codes for: a regulator, FrmR ( Ec FrmR); a formaldehyde dehydrogenase, FrmA; and an S -formylglutathione hydrolase, FrmB10.…”

“…1b). The differences between Sty FrmR and Ec FrmR along with the biological imperative to mount an effective response to endogenous sources of formaldehyde, as evidenced by the observation that the frmRAB operon was essential for adaptation of E. coli to growth on trimethylamine- N -oxide, prompted an investigation of the Ec FrmR protein9. This is worthy of investigation because, although the activities of detoxifying enzymes, such as FrmA and FrmB, have been established, the mechanism(s) used by regulatory proteins to perceive and respond to formaldehyde are poorly understood.…”