Expression Analysis of Escherichia coli Growing on Minimal and Rich Media
November, 1999
DNA arrays of the entire set of Escherichia coli 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 4290 E. coli protein encoding genes
(cds) were obtained and analysis of the expression ratio data indicated that
the physiological state of the cells in the two growth conditions could be ascertained.
The cells in the rich medium grew faster, and expression of the majority of
the translation apparatus genes was significantly elevated under this growth
condition, consistent with known patterns of growth rate dependent regulation
and increased rate of protein synthesis in rapidly growing cells. The cells
grown on minimal medium showed significantly elevated expression of many genes
involved in biosynthesis of building blocks, most notably the amino acid biosynthetic
pathways. Nearly half of the known RpoS dependent genes were expressed at significantly
higher levels in minimal medium compared to rich medium, and rpoS expression
was similarly elevated. The role of RpoS regulation in these logarithmic phase
cells was suggested by the functions of the RpoS dependent genes that were induced.
The hallmark feature of E. coli cells growing on glucose minimal medium
appeared to be the formation and excretion of acetate, metabolism of the acetate,
and protection of the cells from acid stress. A hypothesis invoking RpoS and
UspA (universal 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 demonstrates
that genomic expression assays can be applied in a meaningful way to the study
of whole-bacterial cell physiology for generation of hypotheses and as a guide
for more detailed studies of particular genes of interest.
Tao et al., 1999 J. Bact., 181:6425-40
(PDF)
Minimal vs. Rich Media Experimental
Data Set (Requires Excel 4MB)
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