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

Chhabra, Shivani; Spiro, Stephen

doi:10.1099/mic.0.000151

Cited by 10 publications

(5 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The connection between YtfE and the repair of Fe-S cluster proteins is most likely indirect; through the alleviation of NsrR-mediated repression of the Suf Fe-S cluster biogenesis system (sufABCDSE), which is the principal route for production of Fe-S clusters under stress conditions, as well as genes encoding proteins that function to counter nitrosative stress (Figure 9). 14,83 We also note that the catalytic activity of aconitase and fumarase are reversibly/competitively inhibited by nitrite. 84 Concluding Remarks.…”

Section: T H I S C O N T E N T Imentioning

confidence: 73%

The Di-Iron Protein YtfE Is a Nitric Oxide-Generating Nitrite Reductase Involved in the Management of Nitrosative Stress

et al. 2022

View full text Add to dashboard Cite

Previously characterized nitrite reductases fall into three classes: siroheme-containing enzymes (NirBD), cytochrome c hemoproteins (NrfA and NirS), and copper-containing enzymes (NirK). We show here that the di-iron protein YtfE represents a physiologically relevant new class of nitrite reductases. Several functions have been previously proposed for YtfE, including donating iron for the repair of iron–sulfur clusters that have been damaged by nitrosative stress, releasing nitric oxide (NO) from nitrosylated iron, and reducing NO to nitrous oxide (N 2 O). Here, in vivo reporter assays confirmed that Escherichia coli YtfE increased cytoplasmic NO production from nitrite. Spectroscopic and mass spectrometric investigations revealed that the di-iron site of YtfE exists in a mixture of forms, including nitrosylated and nitrite-bound, when isolated from nitrite-supplemented, but not nitrate-supplemented, cultures. Addition of nitrite to di-ferrous YtfE resulted in nitrosylated YtfE and the release of NO. Kinetics of nitrite reduction were dependent on the nature of the reductant; the lowest K m , measured for the di-ferrous form, was ∼90 μM, well within the intracellular nitrite concentration range. The vicinal di-cysteine motif, located in the N-terminal domain of YtfE, was shown to function in the delivery of electrons to the di-iron center. Notably, YtfE exhibited very low NO reductase activity and was only able to act as an iron donor for reconstitution of apo-ferredoxin under conditions that damaged its di-iron center. Thus, YtfE is a high-affinity, low-capacity nitrite reductase that we propose functions to relieve nitrosative stress by acting in combination with the co-regulated NO-consuming enzymes Hmp and Hcp.

show abstract

Section: T H I S C O N T E N T Imentioning

confidence: 73%

The Di-Iron Protein YtfE Is a Nitric Oxide-Generating Nitrite Reductase Involved in the Management of Nitrosative Stress

et al. 2022

View full text Add to dashboard Cite

show abstract

“…However, ChIP-Seq and EMSAs show that RsrR can bind to target genes whether they contain class 1 or class 2 sites. This differs from E. coli NsrR which binds only weakly to target sites containing putative half sites (class 2)28. To gain more information about RsrR recognition sequences and the positions of these binding sites at target promoters we combined differential RNA-seq (dRNA-seq, accession number GSE81104), which maps the start sites of all expressed transcripts, with ChIP-exo (accession number GSE80818) which uses Lambda exonuclease to trim excess DNA away from ChIP complexes leaving only the DNA which is actually bound and protected by RsrR.…”

Section: Resultsmentioning

confidence: 91%

Characterization of a putative NsrR homologue in Streptomyces venezuelae reveals a new member of the Rrf2 superfamily

Munnoch

Martinez

Svistunenko

et al. 2016

Sci Rep

View full text Add to dashboard Cite

Members of the Rrf2 superfamily of transcription factors are widespread in bacteria but their functions are largely unexplored. The few that have been characterized in detail sense nitric oxide (NsrR), iron limitation (RirA), cysteine availability (CymR) and the iron sulfur (Fe-S) cluster status of the cell (IscR). In this study we combined ChIP- and dRNA-seq with in vitro biochemistry to characterize a putative NsrR homologue in Streptomyces venezuelae. ChIP-seq analysis revealed that rather than regulating the nitrosative stress response like Streptomyces coelicolor NsrR, Sven6563 binds to a conserved motif at a different, much larger set of genes with a diverse range of functions, including a number of regulators, genes required for glutamine synthesis, NADH/NAD(P)H metabolism, as well as general DNA/RNA and amino acid/protein turn over. Our biochemical experiments further show that Sven6563 has a [2Fe-2S] cluster and that the switch between oxidized and reduced cluster controls its DNA binding activity in vitro. To our knowledge, both the sensing domain and the putative target genes are novel for an Rrf2 protein, suggesting Sven6563 represents a new member of the Rrf2 superfamily. Given the redox sensitivity of its Fe-S cluster we have tentatively named the protein RsrR for Redox sensitive response Regulator.

show abstract

“…Very recently, it has been demonstrated that although nsrR is expressed from a strong promoter, the translational efficiency of this regulator is extremely inefficient, leading to low cellular NsrR protein levels. Therefore, it has been proposed that promoters with low-affinity NsrRbinding sites may partially escape NsrR-mediated repression (Chhabra & Spiro, 2015). Microarray analyses revealed that NsrR represses 9 operons encoding 20 genes in E. coli, including hmp, and the well-studied nrfA promoter (Filenko et al, 2007).…”

Section: Regulatory Proteinsmentioning

confidence: 99%

Nitrous Oxide Metabolism in Nitrate-Reducing Bacteria

Torres

Simon

Rowley

et al. 2016

Advances in Bacterial Electron Transport Systems and Their Regulation

View full text Add to dashboard Cite

Nitrous oxide (N2O) is an important greenhouse gas (GHG) with substantial global warming potential and also contributes to ozone depletion through photochemical nitric oxide (NO) production in the stratosphere. The negative effects of N2O on climate and stratospheric ozone make N2O mitigation an international challenge. More than 60% of global N2O emissions are emitted from agricultural soils mainly due to the application of synthetic nitrogen-containing fertilizers. Thus, mitigation strategies must be developed which increase (or at least do not negatively impact) on agricultural efficiency whilst decrease the levels of N2O released. This aim is particularly important in the context of the ever expanding population and subsequent increased burden on the food chain. More than two-thirds of N2O emissions from soils can be attributed to bacterial and fungal denitrification and nitrification processes. In ammonia-oxidizing bacteria, N2O is formed through the oxidation of hydroxylamine to nitrite. In denitrifiers, nitrate is reduced to N2 via nitrite, NO and N2O production. In addition to denitrification, respiratory nitrate ammonification (also termed dissimilatory nitrate reduction to ammonium) is another important nitrate-reducing mechanism in soil, responsible for the loss of nitrate and production of N2O from reduction of NO that is formed as a by-product of the reduction process. This review will synthesize our current understanding of the environmental, regulatory and biochemical control of N2O emissions by nitrate-reducing bacteria and point to new solutions for agricultural GHG mitigation.

show abstract

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

Cited by 10 publications

References 52 publications

The Di-Iron Protein YtfE Is a Nitric Oxide-Generating Nitrite Reductase Involved in the Management of Nitrosative Stress

The Di-Iron Protein YtfE Is a Nitric Oxide-Generating Nitrite Reductase Involved in the Management of Nitrosative Stress

Characterization of a putative NsrR homologue in Streptomyces venezuelae reveals a new member of the Rrf2 superfamily

Nitrous Oxide Metabolism in Nitrate-Reducing Bacteria

Contact Info

Product

Resources

About