Cells are exposed to various forms of oxidative stressors such as reactive oxygen species (ROS), natural or xenobiotic redox-active compounds, or some antibiotics, which elicit the formation of ROS inside the cell. The response mechanism involves various enzymes to remove such oxidants, systems to repair and recycle damaged cell components, and to maintain optimal cell physiology (Imlay, 2008; Zuber, 2009). One form of oxidative damage that frequently occurs in proteins and small molecules is the oxidation of cysteine thiols by ROS (Kiley and Storz, 2004; Jacob et al., 2006). Cysteine thiols can also be modified by reactive nitrogen species (RNS) and thiol-reactive electrophiles (Hess et al., 2005; Rudolph and Freeman, 2009)
The presence of ROS, RNS and other thiol-reactive compounds can be sensed directly through thiol-based sensor-regulators, which modulate the expression of genes encoding functions that constitute the biological stress response (Antelmann and Helmann, 2011). The best studied examples of thiol-based sensor-regulators that respond to ROS in bacteria include H2O2-sensing OxyR in Escherichia coli, organic peroxide-sensing OhrR in Bacillus subtilis, and the anti-sigma factor RsrA that senses thiol oxidation and modulates regulator SigR activity in Streptomyces coelicolor (Paget and Buttner, 2003; D'Autreaux and Toledano, 2007; Antelmann and Helmann, 2011). In eukaryotes, thiol-based redox switches have been well exemplified in Yap1 of Saccharomyces cerevisiae and the mammalian Nrf2/Keap1 system (D'Autreaux and Toledano, 2007; Kensler et al., 2007; Brandes et al., 2009). Representative target genes of these thiol-based regulators are those that encode thiol homeostasis system such as thioredoxin (Trx), glutaredoxin (Grx) and small molecular thiol systems (regulated by OxyR, SigR/RsrA, Yap1, Nrf2/Keap1), catalases and peroxidases (by OxyR and Yap1), organic hydroperoxidase (by OhrR), detoxification of electrophiles (by SigR and Nrf2), and some proteolytic system (by OxyR, SigR, Yap1, Nrf2) (Kensler et al., 2007; den Hengst and Buttner, 2008; Imlay, 2008; Antelmann and Helmann, 2011).
A zinc-containing anti-sigma (ZAS) factor RsrA that binds an ECF (group 4) sigma factor SigR in S. coelicolor responds to diamide-induced thiol oxidation by forming disulphide bonds, releasing SigR to transcribe its target genes (Kang et al., 1999; Li et al., 2003b; Bae et al., 2004). In addition to thiol-oxidants, the presence of non-oxidative thiol-reactive compounds also induces expression of the SigR regulon, suggesting that RsrA may respond to these compounds either directly through thiolation of reactive cysteines or indirectly through changes in reduced thiol pools such as mycothiol, the functional equivalent in actinomycetes of glutathione (Newton et al., 2008; Park and Roe, 2008). To date, around 44 SigR target genes have been identified based on promoter sequence similarity, S1 mapping and microarray expression profiling (Paget et al., 1998; 2001; Park and Roe, 2008; Kallifidas et al., 2010). The products of known SigR target genes include thiol-redox proteins such as thioredoxin systems (TrxBA, TrxC), the first enzyme in mycothiol synthesis (MshA), and a glutaredoxin-like protein called mycoredoxin (Mrx). They also include proteolytic components of protein quality control (PepN, SsrA, ClpP1P2, ClpX, ClpC, Lon), cysteine production (CysM), methionine reduction (MsrA, MsrB), guanine synthesis (GuaB), ribosome-associated function (RpmE, RelA), and electrophile detoxification (Mca) (Paget et al., 2001; Park and Roe, 2008; Kallifidas et al., 2010). Therefore, perturbation of intracellular thiols, as sensed through RsrA, induces expression of gene products that contributes to protein quality control, detoxification of thiol-conjugative xenobiotics, and modulation of transcription and translation.
Because SigR/RsrA activity controls the cellular response to a variety of stressors, we expect the SigR regulon to be large and encompass additional stress response functions in S. coelicolor. Therefore, we performed chromatin immuno-precipitation on a chip (ChIP-chip) assays and discovered > 100 direct SigR target promoters transcribing > 160 genes. The comprehensive characterization of the S. coelicolor SigR regulon helped us understand in more details the global effects of and cellular response to thiol-oxidative stress. Furthermore, to identify functions that are most critical to survive thiol-oxidative stress response, we used the SigR-binding consensus sequence to predict orthologous thiol-oxidative stress regulons in other actinomycetes. The analysis revealed a core conserved regulon as well as lineage-specific adaptations.