Regulation of nrf operon expression in pathogenic enteric bacteria: sequence divergence reveals new regulatory complexity

• Published in: Molecular microbiology 2017-05, Vol.104 (4), p.580-594
• Main Authors: Godfrey, Rita E., Lee, David J., Busby, Stephen J. W., Browning, Douglas F.
• Format: Article
• Language: English
• Subjects: Anaerobiosis; Bacteria; Base Sequence - genetics; Binding sites; Binding Sites - genetics; Cytochrome c Group - genetics; Cytochrome c Group - metabolism; Divergence; E coli; Enterobacteriaceae - metabolism; Escherichia coli - genetics; Escherichia coli K12 - genetics; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Gene expression; Gene Expression Regulation, Bacterial - genetics; Gene sequencing; Genes; Microbiology; Molecular Sequence Data; Nitrite reductase; Nitrite Reductases - genetics; Nitrite Reductases - metabolism; Nitrites; Nitrites - metabolism; Operon - genetics; Operons; Periplasmic Proteins; Promoter Regions, Genetic - genetics; Proteins; Regulatory sequences; Repressor Proteins - genetics; Repressor Proteins - metabolism; Ribonucleic acid; RNA; RNA-binding protein; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Salmonella; Transcription Factors - metabolism; Transcription Initiation Site; Transcription, Genetic - genetics
• ISSN: 0950-382X; 1365-2958
• DOI: 10.1111/mmi.13647

Summary The Escherichia coli K‐12 nrf operon encodes a periplasmic nitrite reductase, the expression of which is driven from a single promoter, pnrf. Expression from pnrf is activated by the FNR transcription factor in response to anaerobiosis and further increased in response to nitrite by the response regulator proteins, NarL and NarP. FNR‐dependent transcription is suppressed by the binding of two nucleoid associated proteins, IHF and Fis. As Fis levels increase in cells grown in rich medium, the positioning of its binding site, overlapping the promoter −10 element, ensures that pnrf is sharply repressed. Here, we investigate the expression of the nrf operon promoter from various pathogenic enteric bacteria. We show that pnrf from enterohaemorrhagic E. coli is more active than its K‐12 counterpart, exhibits substantial FNR‐independent activity and is insensitive to nutrient quality, due to an improved −10 element. We also demonstrate that the Salmonella enterica serovar Typhimurium core promoter is more active than previously thought, due to differences around the transcription start site, and that its expression is repressed by downstream sequences. We identify the CsrA RNA binding protein as being responsible for this, and show that CsrA differentially regulates the E. coli K‐12 and Salmonella nrf operons. The Escherichia coli nrf operon encodes the NrfA periplasmic nitrite reductase, which can detoxify nitric oxide and reduce nitrite to ammonium to support bacterial growth. Operon expression is driven from a single promoter and controlled by a number of global transcription factors in response to environmental conditions. Here, we examine the regulation of nrf operon promoters from various enteric pathogens and uncover the different regulatory strategies used to control the expression of this important enzyme.