RNA-Seq Analysis Reveals a Six-Gene SoxR Regulon in Streptomyces coelicolor

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.

Enzyme-constrained models and omics analysis of Streptomyces coelicolor reveal metabolic changes that enhance heterologous production

“…Indeed, when looking at the genes associated with ScbR (Li et al, 2015), AfsR (Lee et al, 2002) and AdpA (Wolański et al, 2011), a clear difference in expression profiles of M145 and M1152 can be observed ( Figure 6B, S8A and S8B), while this is not the case for genes associated with ArgR (Fig S8C). Cluster 4 is enriched for genes that are related to the redox regulated transcription factor SoxR (Naseer et al, 2014), and a similar pattern is observed for the entire SoxR regulon, (Figure 6C). SoxR is known to react directly to the presence of actinorhodin (Dela Cruz et al, 2010;Shin et al, 2011), and indeed, in M145 this group of genes follows the production profile of actinorhodin, while expression remains low in M1152.…”

“…SoxR is known to react directly to the presence of actinorhodin (Dela Cruz et al, 2010;Shin et al, 2011), and indeed, in M145 this group of genes follows the production profile of actinorhodin, while expression remains low in M1152. The SoxR regulon contains flavin and quinone reductases (Dela Cruz et al, 2010;Naseer et al, 2014), and it is suggested that these proteins reduce ATP generation by reducing the proton motive force (Esnault et al, 2017). This is supported by the RNA-seq data where the ATP-synthase gene cluster (SCO5366-SCO5374) is upregulated almost 2-fold in M1152 compared to M145, most prominently in the stationary phase (Figure S9A).…”

Transcription Factors That Defend Bacteria Against Reactive Oxygen Species

“…Strikingly, only enterics employ SoxS; in all the other bacteria SoxR directly controls the expression of all regulon members. Just as striking is the fact that in these non-enterics the SoxR regulon is quite different from that of E. coli : it typically comprises only a handful of genes of unclear function (80), and these generally do not include sodA or other genes that might confer resistance to O 2 − (13, 14, 50, 80, 99). The implication is that the physiological purpose of SoxR in non-enterics is quite different from its purpose in E. coli .…”

Factors affecting redox potential and differential sensitivity of SoxR to redox‐active compounds

“…For example, in Escherichia coli, where it was first found and named as a superoxide-sensor SoxR (Greenberg et al, 1990;Tsaneva and Weiss, 1990), its sole known direct target is the adjacent gene soxS whose product induces transcription of about 100 genes that function in anti-oxidative and anti-superoxide response, as well as in diminishing the concentration of RACs by pumping them out or altering envelope permeability (Wu and Weiss, 1991;Nunoshiba et al, 1992;Ma et al, 1995;Pomposiello et al, 2001;Lee et al, 2009). In comparison, SoxRs from non-enteric bacteria such as pseudomonads and streptomycetes activate several target genes whose primary function appears defense against the toxicity of inducing compounds, without involving anti-superoxide activity such as superoxide dismutase (Palma et al, 2005;Dietrich et al, 2008;Shin et al, 2011;Naseer et al, 2014).…”