Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2).
Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2).
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DOI：
10.1186/1756-0500-4-78
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发表时间：
2011-03-23
影响因子：
1.8
通讯作者：
Smith CP
中科院分区：
文献类型：
--
作者：
Lewis RA;Shahi SK;Laing E;Bucca G;Efthimiou G;Bushell M;Smith CP
本研究代表了模型链霉菌天蓝色链霉菌A3（2）M145对改良埃文斯培养基有限公司发酵罐培养物的反应的全基因组转录组分析，分别为氮，磷酸盐和碳，作为ActinoGEN财团的一部分进行，以提供公开可用的参考微阵列数据集。使用来自每个营养限制的两个重复培养物的样品生成微阵列数据集。在本报告中，我们的分析集中在三对不同限制的培养数据集的生长期相关的匹配时间点的样品之间通过秩积分析确定的显著差异表达的基因。除了少数例外，基因仅在N6/N7时间点与其在C和P限制培养物中的相应时间点之间显著差异表达，绝大多数差异表达的基因在N限制培养物中更高表达。我们对这些基因的分析表明GlnR调节子的几个成员的表达在氮限制时被诱导，如通过[NH 4 +]测量测定的，并且我们能够鉴定GlnR调节子中不存在的几个另外的基因，其表达响应于氮限制而被诱导。我们还注意到SCO 3327编码一种小蛋白（32个氨基酸残基），其异常富含碱性氨基酸赖氨酸（31.25%）和精氨酸（25%），在氮限制培养物中显著差异表达。此外，我们研究了GlnR调节子的已知成员的表达以及SCO 2486-SCO 2487和SCO 5583-SCO 5585操纵子的基因组织和表达之间的关系。我们提供了一个在低氮培养条件下差异表达的基因列表，包括SCO 3327编码的一个假定的氮储存蛋白。我们的列表包括几个基因，其表达模式类似于GlnR调节子的上调成员，并响应于氮限制而被诱导。这些基因代表了天蓝色链霉菌氮饥饿反应未来研究的可能目标。
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. 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. 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.