Regulation of the Escherichia coli ydhY-T operon in the presence of alternative electron acceptors

Microbiology (Reading). 2017 Apr;163(4):584-594. doi: 10.1099/mic.0.000445. Epub 2017 Apr 18.


The Escherichia coli K-12 ydhY-T operon, coding for a predicted oxidoreductase complex, is activated under anaerobic conditions and repressed in the presence of nitrate or nitrite. Anaerobic activation is mediated by the transcription factor FNR, and nitrate/nitrite repression is mediated by NarXL and NarQP. In vitro transcription reactions revealed that the DNA upstream of ydhY-T contains sufficient information for RNA polymerase alone to initiate transcription from five locations. FNR severely inhibited synthesis of two of these transcripts (located upstream of, and within, the FNR binding site) and activated the FNR-dependent promoter previously identified in vivo. Enhanced expression of ydhY-T in an hns mutant was consistent with the location of ydhY-T within a promoter island and the FNR-independent transcription observed in vitro. FNR-dependent transcription in vitro was decreased in the presence of NarL~P. DNaseI footprinting indicated that FNR and NarL~P simultaneously bound at the ydhY-T promoter region and that NarL~P-mediated repression was due to occupation of the 7-2-7 site located downstream of the FNR-dependent promoter. Expression of ydhY-T during the anaerobic growth cycle was repressed when nitrate was present but less so in the presence of nitrite. In vivo transcription measurements indicated that the alternative electron acceptors, DMSO and fumarate, could also lower ydhY-T expression, whereas trimethylamine-N-oxide (TMAO) permitted high expression. Therefore, expression of ydhY-T is subject to complex regulation in response to electron acceptor availability that involves at least three transcription factors, FNR (anaerobic activation), NarL~P (nitrate repression) and H-NS (repression in the absence of an antagonist; e.g. FNR).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anaerobiosis / physiology
  • Bacterial Proteins / genetics*
  • DNA-Binding Proteins / genetics*
  • DNA-Directed RNA Polymerases / metabolism
  • Dimethyl Sulfoxide / pharmacology
  • Escherichia coli K12 / genetics*
  • Escherichia coli Proteins / genetics*
  • Escherichia coli Proteins / metabolism
  • Ferredoxins / genetics*
  • Fumarates / pharmacology
  • Gene Expression Regulation, Bacterial*
  • Iron-Sulfur Proteins / genetics*
  • Iron-Sulfur Proteins / metabolism
  • Methylamines / pharmacology
  • Oxidants / pharmacology*
  • Oxidoreductases / genetics
  • Promoter Regions, Genetic / genetics


  • Bacterial Proteins
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • FNR protein, E coli
  • Ferredoxins
  • Fumarates
  • H-NS protein, bacteria
  • Iron-Sulfur Proteins
  • Methylamines
  • Oxidants
  • YdhT protein, E coli
  • YdhY protein, E coli
  • NarL protein, E coli
  • Oxidoreductases
  • DNA-Directed RNA Polymerases
  • trimethyloxamine
  • Dimethyl Sulfoxide