PMID:18039766

Citation	Durfee, T, Hansen, AM, Zhi, H, Blattner, FR and Jin, DJ (2008) Transcription profiling of the stringent response in Escherichia coli. J. Bacteriol. 190:1084-96
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 relADelta251 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 relADelta251 mutant response is both delayed and limited in scope. We show that in addition to the down-regulation 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.
Links	PubMed PMC2223561 Online version:10.1128/JB.01092-07
Keywords	Escherichia coli K12/genetics; Escherichia coli K12/growth & development; Escherichia coli K12/metabolism; Escherichia coli K12/physiology; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Heat-Shock Response; Ligases/genetics; Serine/analogs & derivatives; Serine/pharmacology; Transcription, Genetic
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
ECOLI:USPA		GO:0015968: stringent response	ECO:0000270:		P		In paragraph 5 of section "MG1655 response to SHX treatment at 10 min.", uspA is reported to be up-regulated in the first 5 min. of stringent response from amino acid starvation. Data shown in Supp. Table 1.	complete CACAO 2372

References

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