Transcription Profiling of the Stringent Response in Escherichia coli

Abstract

The bacterial stringent response serves as a paradigm for understanding global regulatory processes. It can be triggered by nutrient downshifts or starvation and is characterized by a rapid RelA-dependent increase in the alarmone (p)ppGpp. One hallmark of the response is the switch from maximum-growth-promoting to biosynthesis-related gene expression. However, the global transcription patterns accompanying the stringent response in Escherichia coli have not been analyzed comprehensively. Here, we present a time series of gene expression profiles for two serine hydroxymate-treated cultures: (i) MG1655, a wild-type E. coli K-12 strain, and (ii) an isogenic relA⌬251 derivative defective in the stringent response. The stringent response in MG1655 develops in a hierarchical manner, ultimately involving almost 500 differentially expressed genes, while the relA⌬251 mutant response is both delayed and limited in scope. We show that in addition to the downregulation of stable RNA-encoding genes, flagellar and chemotaxis gene expression is also under stringent control. Reduced transcription of these systems, as well as metabolic and transporter-encoding genes, constitutes much of the down-regulated expression pattern. Conversely, a significantly larger number of genes are up-regulated. Under the conditions used, induction of amino acid biosynthetic genes is limited to the leader sequences of attenuator-regulated operons. Instead, up-regulated genes with known functions, including both regulators (e.g., rpoE, rpoH, and rpoS) and effectors, are largely involved in stress responses. However, one-half of the up-regulated genes have unknown functions. How these results are correlated with the various effects of (p)ppGpp (in particular, RNA polymerase redistribution) is discussed.

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

“…(Fig. 3C and Table S3) were fully consistent with the known effects of ppGpp, which changes gene expression in patterns different from those we observe for the adaptive mutations (30,31) and which is generally observed to increase pausing and decrease elongation rate (12,13) (opposite to that observed for the adaptive mutant RNAPs). Therefore we have ruled out the possibility that the mutations are adaptive simply because they mimic the effects of ppGpp.…”

Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA

“…Recent genome-wide expression studies have reported that at least five and as many as 40 r-protein transcripts decrease following amino acid limitation (22,23). However, as in the earlier studies, conclusions about the mechanistic basis for the decrease in r-protein mRNA levels were constrained by reports that r-protein transcripts had lifetimes of only a few seconds when they were translationally repressed (24,25).…”

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

“…However, amino acid starvation triggers a major re-orchestration of the genome-wide transcription pattern 9,17,18 which results in a change in the cellular concentration of most RNA species shortly after the onset of starvation (refs. 18-20 and our manuscript in preparation). Therefore, there is no endogenous reference transcript which is known to be suitable for comparing the cellular levels of tRNA (or any other RNA species) during amino acid starvation to the levels during steady-state growth.…”