Transcription profiling of the stringent response in Escherichia coli.
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.
Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA. durf@genome.wisc.edu
Tim
T
Durfee
Anne-Marie
AM
Hansen
Huijun
H
Zhi
Frederick R
FR
Blattner
Ding Jun
DJ
Jin
D048168:Escherichia coli K12 / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism / Q000502:physiology; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D018869:Heat-Shock Response; D008025:Ligases / Q000235:genetics; D012694:Serine / Q000031:analogs & derivatives* / Q000494:pharmacology; D014158:Transcription, Genetic
D029968:Escherichia coli Proteins; C028002:serine hydroxamate; D012694:Serine; D008025:Ligases; C028812:guanosine 3',5'-polyphosphate synthetases