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25162599
RNA-Seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor.

PLoS One, 2014;9(8):e106181.

Naseer N[1], Shapiro JA[1], Chander M[1]

Affiliations

PMID: 25162599DOI: 10.1371/journal.pone.0106181

Impact factor: 3.752

Abstract
The redox-regulated transcription factor SoxR is conserved in diverse bacteria, but emerging studies suggest that this protein plays distinct physiological roles in different bacteria. SoxR regulates a global oxidative stress response (involving > 100 genes) against exogenous redox-cycling drugs in Escherichia coli and related enterics. In the antibiotic producers Streptomyces coelicolor and Pseudomonas aeruginosa, however, SoxR regulates a smaller number of genes that encode membrane transporters and proteins with homology to antibiotic-tailoring enzymes. In both S. coelicolor and P. aeruginosa, SoxR-regulated genes are expressed in stationary phase during the production of endogenously-produced redox-active antibiotics. These observations suggest that SoxR evolved to sense endogenous secondary metabolites and activate machinery to process and transport them in antibiotic-producing bacteria. Previous bioinformatics analysis that searched the genome for SoxR-binding sites in putative promoters defined a five-gene SoxR regulon in S. coelicolor including an ABC transporter, two oxidoreductases, a monooxygenase and an epimerase/dehydratase. Since this in silico screen may have missed potential SoxR-targets, we conducted a whole genome transcriptome comparison of wild type S. coelicolor and a soxR-deficient mutant in stationary phase using RNA-Seq. Our analysis revealed a sixth SoxR-regulated gene in S. coelicolor that encodes a putative quinone oxidoreductase. Knowledge of the full complement of genes regulated by SoxR will facilitate studies to elucidate the function of this regulatory molecule in antibiotic producers.
MeSH terms
Anti-Bacterial Agents; Bacterial Proteins; Base Sequence; Binding Sites; Carrier Proteins; Escherichia coli; Gene Expression Regulation, Bacterial; Genes, Regulator; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Molecular Sequence Data; Oxidation-Reduction; Oxidative Stress; Oxidoreductases; Promoter Regions, Genetic; Protein Binding; Pseudomonas aeruginosa; Racemases and Epimerases; Regulon; Sequence Alignment; Streptomyces coelicolor; Transcription Factors
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