Genome-wide analysis of lipoprotein expression in Escherichia coli MG1655

Abstract

To gain insight into the cell envelope of Escherichia coli grown under aerobic and anaerobic conditions, lipoproteins were examined by using functional genomics. The mRNA expression levels of each of these genes under three growth conditions--aerobic, anaerobic, and anaerobic with nitrate--were examined by using both Affymetrix GeneChip E. coli antisense genome arrays and real-time PCR (RT-PCR). Many genes showed significant changes in expression level. The RT-PCR results were in very good agreement with the microarray data. The results of this study represent the first insights into the possible roles of unknown lipoprotein genes and broaden our understanding of the composition of the cell envelope under different environmental conditions. Additionally, these data serve as a test set for the refinement of high-throughput bioinformatic and global gene expression methods.

FIG. 1.

Scatter plot comparative analysis of microarray and RT-PCR data. The signal intensities of 61 genes which were designated “present” under all three growth conditions in the microarray data set were compared to the signal intensities generated by RT-PCR. Each datum point represents the log₂ ratio of the signal intensity determined for one growth condition to the signal intensity determined for another growth condition, as determined by both RT-PCR and microarray analyses. (a) Ratios for anaerobically (An) versus aerobically (Ae) grown cells; (b) ratios for anaerobic-plus-nitrate (NO₃) versus aerobic cells.