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Systematic analyses of transcriptional and metabolic changes occurring when Escherichia coliK-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.

Summary Systematic 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.

NO plays important antimicrobial defences in innate immunity but microbes have evolved intricate NO-sensing and defence mechanisms that are now the subjects of a vast literature. In this work we have studied the major targets of NO and nitrosative damage (metal centres, thiols and others) especially using newer ‘omic’ methods for unravelling the complex repercussions of assault from NO and its chemical cousins, particularly nitrosonium (NO+) and peroxynitrite (ONOO−). Microbial defence mechanisms, many of which are critical for pathogenicity, include the activities of haemoglobins that enzymically detoxify NO (to nitrate), NO reductases and repair mechanisms (for example, those that reverse S-nitrosothiol formation). Microbial resistance to these stresses is generally inducible and many, diverse transcriptional regulators are involved – some that are secondary sensors (such as Fnr) and those that are ’dedicated’ (such as NorR, NsrR, NssR) in that their physiological function appears to be detecting primarily NO and then regulating expression of genes that encode enzymes with NO as a substrate. The best understood bacterial defence against NO is the flavohaemoglobin Hmp that catalyses the aerobic, CO-sensitive conversion of NO to the relatively innocuous nitrate anion. However, other bacterial pathogens notably Campylobacter jejuni and Mycobacterium tuberculosis possess two non-flavo-haemoglobins and some bacteria have four or more globins of unknown function. Are their functions redundant? New data on the roles of the C. jejuni globins and M. tuberculosis HbN are presented. This work was supported by the Biotechnology and Biological Sciences Research Council and the EU Commission through an FP7 grant.