• FNR;
  • Oxygen sensing;
  • Transcription regulation;
  • Hydrogenase;
  • Sigma factor;
  • Carnitine metabolism;
  • CaiF


The hypA-E operon is involved in the maturation of all three NiFe hydrogenases in Escherichia coli. Two hyp promoters have been described; a σ54-dependent promoter upstream of hypA, and a σ70-dependent promoter (PhypA) within the hypA coding region. Here it is shown that the oxygen-responsive transcription factor FNR regulates PhypA under anaerobic conditions only. PhypA does not possess a canonical FNR recognition sequence, but two FNR half-sites are present. Studies using PhypA::lacZ fusions carrying lesions in one or both FNR half-sites indicated that although some residual anaerobic activity was retained by the promoter containing only the downstream FNR half-site, both half-sites are required for maximal PhypA activity in vivo. In vitro gel retardation analysis suggested that the primary interaction occurs at the downstream FNR half-site. Possible explanations for these observations and the implications for other FNR-regulated promoters are discussed.