Specific and global networks of gene regulation in Streptomyces coelicolor

Streptomycetes produce a plethora of secondary metabolites, including antibiotics, and undergo a complex developmental cycle. The GC-rich species, Streptomyces coelicolor is used by many laboratories as a model for studying gene regulation, morphological development, cellular physiology and microbial signalling. A genome-wide view of many factors that control S. coelicolor gene expression at the level of transcription initiation and beyond was obtained successfully from a combination of RNA-sequencing approaches. For instance, sites of transcription initiation, vegetative promoters, leaderless mRNAs, sites involved in the processing and degradation of rRNA, tRNA and mRNA, and small RNAs, including those that may be involved in attenuation-like switching mechanisms, were successfully detected. Many of the small RNAs identified in this study are novel. Overall, our approaches show the ability to identify new layers of transcriptional complexity associated with several key regulators of secondary metabolism and morphological development in S. coelicolor. Here we were able to show that AtrA activates the transcription of ssgR, the gene product of which is in turn required for the transcription of ssgA, the best-studied SALP, which has a crucial role in septation and the morphology aerial hyphae. AtrA also binds to the promoter region of leuA2, which encodes α-isopropylmalate that directly utilise acetyl-CoA. Interestingly, crude extract from M1146 strain (Δact, Δred, Δcpk, and Δcda) was found to inhibit the DNA-binding activity of AtrA; however, the specificity of the small molecule(s) interaction with AtrA should be investigated. Addition of the 3 x FLAG tag™ to the N-terminus of AtrA does not hinder its ability to substitute functionally for untagged AtrA in S. coelicolor and can be used for the mapping of AtrA binding sites by ChIP-sequencing. Taken together the above suggest that AtrA has a direct role in morphological development and coordinating the utilisation of acetyl-CoA for primary and secondary metabolism.