High-Density Microarray-Mediated Gene Expression Profiling of Escherichia coli

ABSTRACT A nearly complete collection of 4,290 Escherichia coliopen reading frames was amplified and arrayed in high density on glass slides. To exploit this reagent, conditions for RNA isolation fromE. coli cells, cDNA production with attendant fluorescent dye incorporation, DNA-DNA hybridization, and hybrid quantitation have been established. A brief isopropyl-β-d-thiogalactopyranoside (IPTG) treatment elevated lacZ, lacY, and lacAtranscript content about 30-fold; in contrast, most other transcript titers remained unchanged. Distinct RNA expression patterns betweenE. coli cultures in the exponential and transitional phases of growth were catalogued, as were differences associated with culturing in minimal and rich media. The relative abundance of each transcript was estimated by using hybridization of a genomic DNA-derived, fluorescently labeled probe as a correction factor. This inventory provided a quantitative view of the steady-state level of each mRNA species. Genes the expression of which was detected by this method were enumerated, and results were compared with the current understanding of E. coli physiology.