NsrR from Streptomyces coelicolor Is a Nitric Oxide-sensing [4Fe-4S] Cluster Protein with a Specialized Regulatory Function

Crack, Jason C.; Munnoch, John; Dodd, Erin L.; Knowles, Felicity; Al‐Bassam, Mahmoud M.; Kamali, Saeed; Holland, Ashley A.; Cramer, Stephen P.; Hamilton, Chris J.; Johnson, Michael K.; Thomson, Andrew J.; Hutchings, Matthew I.; Brun, Nick E. Le

doi:10.1074/jbc.m115.643072

Cited by 81 publications

(184 citation statements)

References 61 publications

(104 reference statements)

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“…Electron paramagnetic resonance and resonance Raman spectroscopies demonstrated that NO interaction with iron in the [4Fe-4S] cluster causes dinitrosylation of iron, leading to the dissociation of NsrR from the nasD promoter DNA (11). The direct modification of the [4Fe-4S] cluster by NO has also been reported with an NsrR ortholog (12).…”

mentioning

confidence: 90%

Genome-Wide Analysis of ResD, NsrR, and Fur Binding in Bacillus subtilis during Anaerobic Fermentative Growth by In Vivo Footprinting

et al. 2017

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Upon oxygen limitation, the Bacillus subtilis ResE sensor kinase and its cognate ResD response regulator play primary roles in the transcriptional activation of genes functioning in anaerobic respiration. The nitric oxide (NO)-sensitive NsrR repressor controls transcription to support nitrate respiration. In addition, the ferric uptake repressor (Fur) can modulate transcription under anaerobic conditions. However, whether these controls are direct or indirect has been investigated only in a gene-specific manner. To gain a genomic view of anaerobic gene regulation, we determined the genome-wide in vivo DNA binding of ResD, NsrR, and Fur transcription factors (TFs) using in situ DNase I footprinting combined with chromatin affinity precipitation sequencing (ChAP-seq; genome footprinting by high-throughput sequencing [GeF-seq]). A significant number of sites were targets of ResD and NsrR, and a majority of them were also bound by Fur. The binding of multiple TFs to overlapping targets affected each individual TF's binding, which led to combinatorial transcriptional control. ResD bound to both the promoters and the coding regions of genes under its positive control. Other genes showing enrichment of ResD at only the promoter regions are targets of direct ResD-dependent repression or antirepression. The results support previous findings of ResD as an RNA polymerase (RNAP)-binding protein and indicated that ResD can associate with the transcription elongation complex. The data set allowed us to reexamine consensus sequence motifs of Fur, ResD, and NsrR and uncovered evidence that multiple TGW (where W is A or T) sequences surrounded by an A-and T-rich sequence are often found at sites where all three TFs competitively bind.IMPORTANCE Bacteria encounter oxygen fluctuation in their natural environment as well as in host organisms. Hence, understanding how bacteria respond to oxygen limitation will impact environmental and human health. ResD, NsrR, and Fur control transcription under anaerobic conditions. This work using in situ DNase I footprinting uncovered the genome-wide binding profile of the three transcription factors (TFs). Binding of the TFs is often competitive or cooperative depending on the promoters and the presence of other TFs, indicating that transcriptional regulation by multiple TFs is much more complex than we originally thought. The results from this study provide a more complete picture of anaerobic gene regulation governed by ResD, NsrR, and Fur and contribute to our further understanding of anaerobic physiology.

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Genome-Wide Analysis of ResD, NsrR, and Fur Binding in Bacillus subtilis during Anaerobic Fermentative Growth by In Vivo Footprinting

et al. 2017

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“…This is useful, particularly for protein identification, and for characterisation of post-translational covalent modifications, but it does not provide information about non-covalently bound cofactors. However, the coupling of soft electrospray ionisation (ESI) with solution and ionization conditions under which proteins remain folded has provided important new insights into non-covalent interactions for a range of biomolecules [69][70][71][72], including several Fe-S cluster proteins, where the cluster bound forms of the protein was detected [58,73,74]. Early studies reported the use of ESI and ion cyclotron resonance MS to study [4Fe-4S] ferredoxins [73].…”

Section: Electrospray Ionisation Mass Spectrometrymentioning

confidence: 99%

“…More recently, improvements in the resolution offered by Time Of Flight (TOF) mass analysers enables the cheaper ESI-TOF instruments to provide information about the type of cluster bound by Fe-S proteins. Although ionisation conditions require optimisation on a protein to protein basis, characterisation of two Fe-S regulatory proteins has been reported recently [58,74] and clearly this technique has potential for studying the reactivity of these clusters, including with NO.…”

Section: Electrospray Ionisation Mass Spectrometrymentioning

confidence: 99%

“…Furthermore, histidine coordination of a [2Fe-2S] cluster is characterised by the presence of two bands in the 250 -305 cm -1 low frequency region, compared to only one broad band in the spectrum of a similar cluster with all Cys coordination, or with one Ser, Asp or Arg residue in place of one Cys [54][55][56][57]. Because several Fe-S cluster regulatory proteins have non-all Cys cluster coordination, RR is potentially useful for their characterisation [58]. Unfortunately, despite the utility of RR for studies of Fe-S proteins, it has not been applied to studies of Fe-S nitrosylation reactions.…”

Section: Resonance Raman Spectroscopymentioning

confidence: 99%

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13. Reactivity of iron-sulfur clusters with nitric oxide

Dodd¹,

Crack²,

Thomson³

et al. 2017

Characterization, Properties and Applications

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“…NsrR is an NO-sensitive repressor from the Rrf2 family that contains an [Fe-S] cluster. The cluster is likely to be [4Fe-4S], and reaction with NO is accompanied by a decrease in DNA binding affinity and de-repression of NsrR-regulated promoters (Bodenmiller & Spiro, 2006;Tucker et al, 2008;Yukl et al, 2008;Crack et al, 2015). The previously characterized NsrR regulon includes genes encoding the NO-scavenging flavohaemoglobin (hmp), the RIC (repair of iron centres) protein that participates in the repair of NO-damaged [Fe-S] clusters (ytfE), the respiratory nitrite reductase Nrf that is also an NO reductase (nrfABCDEFG), genes involved in motility ( fliA) and aromatic amine metabolism (tynA, feaB), and genes of unknown function, for example ygbA, yccM and yeaR-yoaG (Bodenmiller & Spiro, 2006;Filenko et al, 2007;Lin et al, 2007;Rankin et al, 2008;Partridge et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

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

Chhabra

Spiro

2015

Microbiology

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NsrR from Streptomyces coelicolor Is a Nitric Oxide-sensing [4Fe-4S] Cluster Protein with a Specialized Regulatory Function

Cited by 81 publications

References 61 publications

Genome-Wide Analysis of ResD, NsrR, and Fur Binding in Bacillus subtilis during Anaerobic Fermentative Growth by In Vivo Footprinting

Genome-Wide Analysis of ResD, NsrR, and Fur Binding in Bacillus subtilis during Anaerobic Fermentative Growth by In Vivo Footprinting

13. Reactivity of iron-sulfur clusters with nitric oxide

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

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