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Sulfur and Nitrogen Limitation in Escherichia coli K-12: Specific Homeostatic Responses

Prasad Gyaneshwar,^1, Oleg Paliy,^1, Jon McAuliffe,² David L. Popham,³ Michael I. Jordan,^2,4 and Sydney Kustu^1*

Department of Plant & Microbial Biology,¹ Department of Statistics,² Division of Computer Science, University of California, Berkeley, California,⁴ Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia³

Received 19 July 2004/ Accepted 13 October 2004

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.

Present address: Biotechnology Institute, University of Minnesota, St. Paul, MN 55108.

Present address: Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH 45435.

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