Sulfur and nitrogen limitation in Escherichia coli K-12:: Specific homeostatic responses
Sulfur and nitrogen limitation in Escherichia coli K-12:: Specific homeostatic responses
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DOI：
10.1128/jb.187.3.1074-1090.2005
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发表时间：
2005-02-01
影响因子：
3.2
通讯作者：
Kustu, S
中科院分区：
文献类型：
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作者：
Gyaneshwar, P;Paliy, O;Kustu, S
我们确定了大肠杆菌K-12在适应批培养和营养转移培养中对硫(S)或氮(N)限制生长的全球转录反应。使用两个限制有助于区分营养特异性mRNA水平的变化和与生长速率相关的常见变化。在变化过程中，稳态和缓慢生长反应都被放大了。这使得检测这些反应更加可靠，并增加了差异表达基因的数量。我们通过几种方式分析微阵列数据：通过使用统计归一化算法确定表达变化，通过分层和k-means聚类，以及通过目视检查对齐的基因组图像。利用这些工具，我们确认了已知的由激活因子CysB和Cbl控制的全局S限制的稳态反应，并发现S限制传播到蛋氨酸代谢，FeS簇的合成和氧化应激中。此外，我们还确定了几个开放的阅读框架，它们可能对S的可用性做出特定的响应。从ddp操纵子被NtrC激活的事实可以预测，在限氮条件下，鼠蛋白层中二氨基氨基酸残基之间交联的合成增加，三肽的比例也增加。这两种作用都可能增加从二肽d -丙氨酸- d -丙氨酸（Ddp系统的底物）中清除N的能力。
We determined global transcriptional responses of Escherichia coli K-12 to sulfur (S)- or nitrogen (N)-limited growth in adapted batch cultures and cultures subjected to nutrient shifts. Using two limitations helped to distinguish between nutrient-specific changes in mRNA levels and common changes related to the growth rate. Both homeostatic and slow growth responses were amplified upon shifts. This made detection of these responses more reliable and increased the number of genes that were differentially expressed. We analyzed microarray data in several ways: by determining expression changes after use of a statistical normalization algorithm, by hierarchical and k-means clustering, and by visual inspection of aligned genome images. Using these tools, we confirmed known homeostatic responses to global S limitation, which are controlled by the activators CysB and Cbl, and found that S limitation propagated into methionine metabolism, synthesis of FeS clusters, and oxidative stress. In addition, we identified several open reading frames likely to respond specifically to S availability. As predicted from the fact that the ddp operon is activated by NtrC, synthesis of cross-links between diaminopimelate residues in the murein layer was increased under N-limiting conditions, as was the proportion of tripeptides. Both of these effects may allow increased scavenging of N from the dipeptide D-alanine-D-alanine, the substrate of the Ddp system.