DNA target sequence and FNR-dependent gene expression

FNR proteins are global transcription regulators that respond to fluctuations in environmental oxygen. They recognise a DNA target consisting of an inverted repeat, TTGA-TN(1)N(2)N(3)N(4)ATCAA (where N1-4 represents a non-conserved tetrad, NCT). Analysis of 68 known and predicted FNR sites from the Escherichia coli K12 genome revealed a bias toward A or T at positions N-2 and N-3 of the NCT. The effect of the NCT sequence on FNR-dependent transcription in vivo was assessed using a series of class II and class I model promoters with different NCT sequences. Changing the NCT sequence did not affect basal activity but altered anaerobic induction by as much as an order of magnitude. Thus, the NCT sequence is a fundamental component in setting the dynamic range of the FNR switch. (C) 2003 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved.