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Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2)

Lewis, Richard A; Shahi, Sanjay K; Laing, Emma; Bucca, Giselda; Efthimiou, Georgios; Bushell, Michael; Smith, Colin P


Richard A Lewis

Sanjay K Shahi

Emma Laing

Giselda Bucca

Michael Bushell

Colin P Smith


Background: 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. Findings. A 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. Conclusions: We 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.


Lewis, R. A., Shahi, S. K., Laing, E., Bucca, G., Efthimiou, G., Bushell, M., & Smith, C. P. (2011). Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2). BMC research notes, 4(1),

Journal Article Type Article
Acceptance Date Mar 23, 2011
Online Publication Date Mar 23, 2011
Publication Date 2011-12
Deposit Date Dec 18, 2019
Publicly Available Date Dec 24, 2019
Journal BMC Research Notes
Print ISSN 1756-0500
Electronic ISSN 1756-0500
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 4
Issue 1
Article Number 78
Keywords Nitrogen limitation; Expression category; Limited culture; Nitrate reductase gene; Nitrogen limited culture
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Copyright Statement
© 2011 Smith et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative CommonsAttribution License (, which permits unrestricted use, distribution, and reproduction inany medium, providedthe original work is properly cited.

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