The three FNR (fumarate and nitrate reductase regulatory protein)-type transcription activators of Paracoccus denitrificans, NarR, NnrR and FnrP, appear to have specific tasks in gene regulation during the switch from aerobic growth to denitrification. We here set out a series of experiments to get a fundamental understanding of the mechanism underlying this specificity. In one of these, we changed the nucleotide sequence of an NnrR box, the binding site for NnrR, into one found in FnrP-regulated promoters. As a result, we observed a change in regulation of that promoter from NnrR to FnrP. In a second series, we constructed hybrid promoters of NnrR-, NarR- and FnrP-regulated promoters and analysed their expression profiles in cells grown under various growth conditions. Our results indicate that the specificity of the FNR-type regulators is determined in part by the quality of the FNR box and in part by the sequences downstream of the FNR box. The latter suggests that specific σ factors are involved in binding any of the Fnr-type regulators in P. denitrificans.

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