| Summary: | Bacterial respiration generates the energy required for bacterial growth. Respiration is not only limited to oxygen but could be fuelled with nitrate in anaerobic environments. Upon signal reception bacteria adjust their respiratory pathway in short time by effectively regulating respiratory gene expression and subsequently engineering the complete removal of nitrite, nitric oxide and nitrous oxide from the cytoplasm. Comparison of anaerobic and aerobic gene expression data in continuous cultures of Paracoccus denitrificans revealed a majority of highly expressed genes were co-regulated by CPR/FNR type transcriptional regulators. Motif analysis of the upstream region showed similar patterns recognizable by FNR. P. denitrificans expresses three FNR type regulators that could potentially compete for cognate site binding. Three mutant strains of fnrP, nnrR and narR were used to investigate the transcriptional expression of genes involved in respiration. It was demonstrated that the transcriptional factor FnrP positively regulated the transcription of nar, nor and nap and repressed the expression of nos operon. NnrR positively regulated the nir and nor operons and inhibited the expression of the nar and nos operons, in the latter case due to substrate unavailability. Finally, NarR positively enhanced the expression of the nar operon during the initial stage of anaerobicity. Additionally the expression of the nir and nos operons was repressed in the ΔnarR strain suggesting that NarR may compete for the promoter binding sites and possibly repress the expression of those genes. Additionally, sub-optimal pH inhibited growth and repressed the expression of nirS, norB and nosZ resulting in detectable nitrous oxide emissions. Therefore, the transcription factors FnrP, NnrR and NarR compete for the binding sites upstream of the denitrification operons in a way that optimizes the metabolic rates of denitrification and subsequently eliminates the accumulation of toxic denitrification intermediates. Therefore a new model of regulation of denitrification in P. denitrificans is proposed and discussed.
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