High-density microarray-mediated gene expression profiling of Escherichia coli

A nearly complete collection of 4,290 Escherichia coli open reading frames was amplified and arrayed in high density on glass slides. To exploit this reagent, conditions for RNA isolation from E, coli cells, cDNA production w ith attendant fluorescent dye incorporation, DNA-DNA hybridization, and hyb rid quantitation have been established. A brief isopropyl-beta -D-thiogalae topyranoside (IPTG) treatment elevated lacZ, lacY, and lacA transcript cont ent about 30-fold; in contrast, most other transcript titers remained uncha nged. Distinct RNA expression patterns between E. coli cultures in the expo nential and transitional phases of growth were catalogued, as were differen ces associated with culturing in minimal and rich media. The relative abund ance of each transcript was estimated by using hybridization of a genomic D NA-derived, fluorescently labeled probe as a correction factor. This invent ory provided a quantitative view of the steady-state level of each mRNA spe cies, Genes the expression of which was detected by this method were enumer ated, and results were compared with the current understanding of E. coli p hysiology.