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.
Highlights
Trimethylamine-N-oxide (TMAO) is an osmolyte in marine organisms and is often found in anaerobic environments where it is used as a terminal electron acceptor, being reduced to trimethylamine (TMA) to support the growth of enteric bacteria (Barrett and Kwan, 1985)
Glucose-limited chemostat cultures have been used to systematically study the effects of perturbing anaerobic fermentative cultures of E. coli K-12 by addition of the terminal electron acceptor TMAO using transcript profiling, metabolite and biochemical measurements combined with probabilistic modeling of transcription factor (TF) activities to obtain a deeper understanding of the dynamics of the adaptive process
Anaerobic steady-state chemostat cultures (20 mM glucose-limited medium, dilution rate 0.2 h) of E. coli K-12 MG1655 were established, and measurement of overmetabolites present in the culture medium at steady state showed the presence of acetate, ethanol, formate, succinate, fumarate, lactate and orotate, consistent with anaerobic fermentative growth during which ∼40% of the formate was converted to CO2 and H2 by formate hydrogen-lyase (Table 1; Eq 2)
Summary
Systematic analyses of transcriptional and metabolic changes occurring when Escherichia 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. 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 Received 19 August, 2014; revised 17 November, 2014; accepted 19 November, 2014 *For correspondence. TMAO reductase activity, resulting in net oxidation of menaquinone and inhibition of Cu(II) reduction, responses that are sensed by ArcBA and CusRS respectively
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