Sulfur and Nitrogen Limitation inEscherichia coliK-12: Specific Homeostatic Responses

• DOI: 10.1128/jb.187.3.1074-1090.2005
• Publication Date: 2005-01-19T20:20:52Z
• Authors: Prasad Gyaneshwar; Oleg Paliy; Jon McAuliffe; David L. Popham; Michael I. Jordan; Sydney Kustu
• Keywords: DNA, Bacterial; 0301 basic medicine; 2. Zero hunger; DNA, Complementary; Escherichia coli K12; Models, Genetic; Transcription, Genetic; Nitrogen; Gene Expression Regulation, Bacterial; Peptidoglycan; 03 medical and health sciences; Cluster Analysis; Homeostasis; Genome, Bacterial; Sulfur; Oligonucleotide Array Sequence Analysis

ABSTRACTWe determined global transcriptional responses ofEscherichia coliK-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 theddpoperon 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 dipeptided-alanine-d-alanine, the substrate of the Ddp system.