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.
Durfee
Tim
T
Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA. durf@genome.wisc.edu
Hansen
Anne-Marie
AM
Zhi
Huijun
H
Blattner
Frederick R
FR
Jin
Ding Jun
DJ
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