Abstract
BackgroundThe present study represents a genome-wide transcriptomic analysis of the response of the model streptomycete Streptomyces coelicolor A3(2) M145 to fermentor culture in Modified Evans Media limited, respectively, for nitrogen, phosphate and carbon undertaken as part of the ActinoGEN consortium to provide a publicly available reference microarray dataset.FindingsA microarray dataset using samples from two replicate cultures for each nutrient limitation was generated. In this report our analysis has focused on the genes which are significantly differentially expressed, as determined by Rank Products Analysis, between samples from matched time points correlated by growth phase for the three pairs of differently limited culture datasets. With a few exceptions, genes are only significantly differentially expressed between the N6/N7 time points and their corresponding time points in the C and P-limited cultures, with the vast majority of the differentially expressed genes being more highly expressed in the N-limited cultures. Our analysis of these genes indicated expression of several members of the GlnR regulon are induced upon nitrogen limitation, as assayed for by [NH4+] measurements, and we are able to identify several additional genes not present in the GlnR regulon whose expression is induced in response to nitrogen limitation. We also note SCO3327 which encodes a small protein (32 amino acid residues) unusually rich in the basic amino acids lysine (31.25%) and arginine (25%) is significantly differentially expressed in the nitrogen limited cultures. Additionally, we investigate the expression of known members of the GlnR regulon and the relationship between gene organization and expression for the SCO2486-SCO2487 and SCO5583-SCO5585 operons.ConclusionsWe provide a list of genes whose expression is differentially expressed in low nitrogen culture conditions, including a putative nitrogen storage protein encoded by SCO3327. Our list includes several genes whose expression patterns are similar to up-regulated members of the GlnR regulon and are induced in response to nitrogen limitation. These genes represent likely targets for future studies into the nitrogen starvation response in Streptomyces coelicolor.
Highlights
It has long been known that the carbon (C), nitrogen (N) and phosphate (P) ratios of Streptomyces media require optimization for secondary metabolite biosynthesis [1,2]
Our list includes several genes whose expression patterns are similar to up-regulated members of the GlnR regulon and are induced in response to nitrogen limitation
More recent studies have extended the GlnR regulon to encompass further genes involved in nitrogen metabolism i.e. the glutamine dehydrogenase gene, the nitrate reductase gene and urease gamma subunit, in addition to other genes whose involvement in the nitrogen starvation response is unclear [15]
Summary
It has long been known that the carbon (C), nitrogen (N) and phosphate (P) ratios of Streptomyces media require optimization for secondary metabolite biosynthesis [1,2]. It is likely that the nitrogen and phosphate transcriptional regulatory networks are linked as it has been shown that PhoP represses transcription from the glnR, glnA, glnII and amtB promoters, which possess PhoP binding sites [17]. This interaction was first suggested by microarray data [18] and to extend these studies and enhance our understanding of the interactions of different nutrient specific regulatory networks the present study was conceived under the aegis of the European ActinoGEN consortium. The present study represents a genome-wide transcriptomic analysis of the response of the model streptomycete Streptomyces coelicolor A3(2) M145 to fermentor culture in Modified Evans Media limited, respectively, for nitrogen, phosphate and carbon undertaken as part of the ActinoGEN consortium to provide a publicly available reference microarray dataset
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