| DNA microarrays provide us with powerful tools for functional genomics studies. Here used microarrays to monitor gene expression profiles of Escherichia coli under cold shock and iron-limited conditions. In the cold shock study, the temporal transcriptional dynamics of the response are revealed. A set of known cold shock genes is induced immediately when the cell temporarily ceases its growth due to low temperature. Several new cold shock-related genes are also identified. Conversely, multiple metabolic pathways are down-regulated, consistent with growth arrest during acclimation. With the help of cold shock proteins and key stress response regulators, the cell adapts to the cold environment, with transcription levels of metabolic genes significantly reduced, relative to pre-shock levels. In the iron starvation response study, we report the gene expression profiles of two E. coli strains, the non-pathogenic K12 strain MG1655, and the uropathogen CFT073 strain, under both iron-replete and iron-limiting conditions. The results demonstrate that both strains share a common transcriptional response to iron starvation, including derepression of the iron acquisition systems, inactivation of the two-component system, BasS-R, and activation of a second two-component system, EvgS-A. Moreover, many known and putative virulence-related genes are specifically induced in'CFT073. These observations shed new light on the response to iron limitation and may also suggest additional components involved in pathogenesis.;I also developed a microarray-based method for transcription start site identification in genome scale. In the pilot study, more than 150 new transcription start sites have been identified. Furthermore, the pilot study demonstrated the efficiency of this high-throughput method for transcription termination site and operon composition determination. |
