Data from: Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes in response to glucose starvation

How do bacteria regulate their cellular physiology in response to
starvation? Here, we present a detailed characterization of Escherichia
coli growth and starvation over a time-course lasting two weeks. We have
measured multiple cellular components, including RNA and proteins at deep
genomic coverage, as well as lipid modifications and flux through central
metabolism. Our study focuses on the physiological response of E. coli in
stationary phase as a result of being starved for glucose, not on the
genetic adaptation of E. coli to utilize alternative nutrients. In our
analysis, we have taken advantage of the temporal correlations within and
among RNA and protein abundances to identify systematic trends in gene
regulation. Specifically, we have developed a general computational
strategy for classifying expression-profile time courses into distinct
categories in an unbiased manner. We have also developed, from dynamic
models of gene expression, a framework to characterize protein degradation
patterns based on the observed temporal relationships between mRNA and
protein abundances. By comparing and contrasting our transcriptomic and
proteomic data, we have identified several broad physiological trends in
the E. coli starvation response. Strikingly, mRNAs are widely
down-regulated in response to glucose starvation, presumably as a strategy
for reducing new protein synthesis. By contrast, protein abundances
display more varied responses. The abundances of many proteins involved in
energy-intensive processes mirror the corresponding mRNA profiles while
proteins involved in nutrient metabolism remain abundant even though their
corresponding mRNAs are down-regulated.