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

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

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Abstract

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.
Original languageEnglish
Article number78
Number of pages9
JournalBMC Research Notes
Volume4
DOIs
Publication statusPublished - 23 Mar 2011

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Streptomyces coelicolor
Nitrogen
Genes
Genome
Regulon
Gene expression
Gene Expression
Microarrays
Basic Amino Acids
Bioreactors
Operon
Starvation
Cell culture
Nutrients
Lysine
Byproducts
Arginine
Proteins
Carbon
Phosphates

Keywords

  • Streptomyces coelicolor
  • nitrogen limitations
  • low nitrogen content
  • streptomyces

Cite this

Lewis, R. A., Shahi, S., 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, [78]. https://doi.org/10.1186/1756-0500-4-78
Lewis, Richard A ; Shahi, Sanjay ; Laing, Emma ; Bucca, Giselda ; Efthimiou, Georgios ; Bushell, Michael ; Smith, Colin P. / Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2). In: BMC Research Notes. 2011 ; Vol. 4.
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Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2). / Lewis, Richard A; Shahi, Sanjay; Laing, Emma; Bucca, Giselda; Efthimiou, Georgios; Bushell, Michael; Smith, Colin P.

In: BMC Research Notes, Vol. 4, 78, 23.03.2011.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2)

AU - Lewis, Richard A

AU - Shahi, Sanjay

AU - Laing, Emma

AU - Bucca, Giselda

AU - Efthimiou, Georgios

AU - Bushell, Michael

AU - Smith, Colin P

PY - 2011/3/23

Y1 - 2011/3/23

N2 - 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.

AB - 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.

KW - Streptomyces coelicolor

KW - nitrogen limitations

KW - low nitrogen content

KW - streptomyces

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U2 - 10.1186/1756-0500-4-78

DO - 10.1186/1756-0500-4-78

M3 - Article

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JO - BMC Research Notes

JF - BMC Research Notes

SN - 1756-0500

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ER -