Inefficient translation of nsrR constrains behaviour of the NsrR regulon in Escherichia coli

The NsrR protein of Escherichia coli is a transcriptional repressor that contains an [Fe-S] cluster that is the binding site for nitric oxide (NO). Reaction of NsrR with NO leads to de-repression of its target genes, which include those encoding an NO scavenging flavohaemoglobin and the RIC (repair of iron centres) protein involved in the repair of NO-damaged [Fe-S] clusters. The nsrR gene is promoter proximal in a transcription unit with rnr, encoding the cold shock-inducible RNase R. Here, we show that nsrR is expressed from a strong promoter, but that its translation is extremely inefficient, leading to a low cellular NsrR concentration. Conversion of the nsrR start codon from the wild-type GUG to AUG increased the efficiency of translation (which, nevertheless, remained extremely low) and had measurable effects on the expression of some NsrR-regulated genes. We conclude that NsrR abundance in the cell is such that promoters with low-affinity NsrR binding sites may partially escape NsrRmediated repression. Expression profiling confirmed that genes regulated by NsrR (whether directly or indirectly) tend to express lower mRNA levels when the nsrR start codon is AUG than when it is GUG. Transcriptomics data implicated the pyruvate oxidase gene poxB as a novel NsrR target, which we confirmed and showed to be due to read-through transcription from the upstream hcp-hcr genes. We also present evidence to suggest that NsrR is a regulator of the sufABCDSE genes, which encode the components of an [Fe-S] cluster biogenesis and repair system.