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

Abstract

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.

Redox-Sensing Under Hypochlorite Stress and Infection Conditions by the Rrf2-Family Repressor HypR inStaphylococcus aureus

“…The 12-3-12 bp inverted repeat sequence TAATTGTAACTA-N 3 -CAGTTACAATTA was detected in the hypR-merA upstream region as possible HypR binding site that overlapped with the putative −10 region. Similar inverted repeats are characteristic as full-length binding sites for other Rrf2 regulators, such as SaiR, CymR, IscR, and RsrR ( 67 , 68 , 82 , 84 ). We searched for the conservation of the putative HypR operator sequence upstream of homologous hypR-merA operons in the genomes of other Staphylococcus species.…”

“…The hypR-merA operon was most strongly upregulated under NaOCl in the transcriptome that encodes for the novel redox-sensing regulator HypR and the pyridine nucleotide disulfide reductase mercuric ion reductase (MerA). HypR belongs to the widespread Rrf2 family of transcriptional regulators that include iron/sulfur (FeS)-cluster redox sensors for nitric oxide (NsrR) ( 23 , 90 , 98 ), the iron/sulfur status of the cell (IscR) ( 82 , 83 ), iron metabolism (RirA) ( 40 ), or other signals ( 67 ). Other Rrf2 family regulators do not contain FeS clusters, such as the cysteine metabolism repressor (CymR) ( 28 , 47 , 84 ) and the redox-sensing SaiR repressor of Bacillus anthracis that controls spxA2 under disulfide stress conditions and is a close homologue of HypR ( 68 ).…”

Sensing iron availability via the fragile [4Fe–4S] cluster of the bacterial transcriptional repressor RirA

“… 17 , 20 , 21 The observation of monomeric RirA in the mass spectrum indicates that the protein monomerizes to a significant extent during ionisation, as recently observed for other dimeric iron–sulfur cluster regulators such as NsrR, RsrR and FNR. 21 , 33 , 34 …”

Dissolution of the Disparate: Co-ordinate Regulation in Antibiotic Biosynthesis

“…In streptomycetes, the production of secondary metabolites is intimately linked to the developmental transition from vegetative hyphae to aerial hyphae and the onset of sporulation [23,86]. Interestingly the S. venezuelae ∆mtrB mutant decoupled chloramphenicol production from this developmental schedule, resulting in constitutive production of the antibiotic.…”