Functional genomics: Expression analysis of Escherichia coli growing on minimal and rich media

DNA arrays of the entire set of Escherichia coil genes were used to measure the genomic expression patterns of cells growing in late logarithmic phase on minimal glucose medium and on Luria broth containing glucose. Ratios of the transcript levels for all 4,290 E. coli protein-encoding genes (cds) w ere obtained, and analysis of the expression ratio data indicated that the physiological state of the cells under the two growth conditions could be a scertained. The cells in the rich medium grew faster, and expression of the majority of the translation apparatus genes was significantly elevated und er this growth condition, consistent with known patterns of growth rate-dep endent regulation and increased rate of protein synthesis in rapidly growin g cells. The cells grown on minimal medium showed significantly elevated ex pression of many genes involved in biosynthesis of building blocks, most no tably the amino acid biosynthetic pathways. Nearly half of the known RpoS-d ependent genes were expressed at significantly higher levels in minimal med ium than in rich medium, and rpoS expression was similarly elevated. The ro le of RpoS regulation in these logarithmic phase cells was suggested by the functions of the RpoS dependent genes that were induced. The hallmark feat ures of E. coli cells growing on glucose minimal medium appeared to be the formation and excretion of acetate, metabolism of the acetate, and protecti on of the cells from acid stress. A hypothesis invoking RpoS and UspA (univ ersal stress protein, also significantly elevated in minimal glucose medium ) as playing a role in coordinating these various aspects and consequences of glucose and acetate metabolism was generated. This experiment demonstrat es that genomic expression assays can be applied in a meaningful way to the study of whole-bacterial-cell physiology for the generation of hypotheses and as a guide for more detailed studies of particular genes of interest.