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 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.

FIG. 1.

Growth curves for MG1655 (A) and the relAΔ251 derivative (B) during an SHX-mediated stringent response. The arrow indicates the time when SHX was added. Asterisks indicate times when expression profiles of each strain were determined. OD₆₀₀, optical density at 600 nm.

FIG. 2.

Differentially expressed gene sets expand hierarchically in MG1655 but are aberrant both in scope and timing in relAΔ251: Venn diagrams of overlapping up- and down-regulated gene sets (left and right diagrams, respectively) in MG1655 (A) and the relAΔ251 strain (B). Time points are indicated as follows: dotted circles, 5 min; dashed circles, 10 min; and solid circles, 30 min. The numbers indicate the numbers of core genes affected at each time point (i.e., not affected at previous time points).

FIG. 3.

P1 transcripts of rRNA operons in MG1655, but not in the relAΔ251 strain, rapidly decline during the stringent response: autoradiograph of rrn P1 primer extension products from the strains determined at the time points used for expression profiling. The ompA products, which were maintained at constant levels (as shown by array data), were used as an internal control to normalize rRNA levels. The relative amounts of rRNA synthesized from the P1 promoters were determined by comparing the normalized values at each time to the time zero control. The experiments were repeated at least twice, and similar results were obtained. WT, wild type.

FIG. 4.

Expression of attenuator-regulated amino acid biosynthetic operons is steadily up-regulated in MG1655 but shows aberrant activation in the relAΔ251 strain: histograms of signal intensities (log₂ scale) for each of the eight attenuator-regulated amino acid biosynthetic leader elements in MG1655 (A) and relAΔ251 (B). Time points are indicated as follows: open bars, zero time; light gray bars, 5 min; dark gray bars, 10 min; and black bars, 30 min.

FIG. 5.

Schematic diagram of down-regulated genes involved in flagellum synthesis and chemotaxis. For flagellum-related expression, the key master regulator, encoded by flhDC, activates expression of eight operons (indicated on the right). Chemotaxic signal transduction involves sensing by one of five chemoreceptors (shown across the inner membrane) which in complex with CheW and the CheA kinase activate the CheY response regulator via phosphorylation. CheY then influences flagellum activity through interaction with the motor. Dephosphorylation of CheY by CheZ resets the system. CheB and CheR control the methylation state of the chemoreceptors. Colored letters indicate when the gene is first down-regulated in MG1655, as follows: red, 5 min; gold, 10 min; purple, 30 min; and black, not affected. Colored asterisks indicate when the gene is first down-regulated in relAΔ251.

FIG. 6.

Schematic diagram of up- and down-regulated genes involved in central metabolism, respiration, and transport. For clarity in central metabolism, only glycolysis/gluconeogenesis and the tricarboxylic acid cycle are shown. For up- and down-regulated transporters (shown on the left and right, respectively) the arrows indicate the direction of transport. Colored letters indicate when the gene is first up- or down-regulated in MG1655, as follows: green, up-regulated at 5 min; dark blue, up-regulated at 10 min; light blue, up-regulated at 30 min; red, down-regulated at 5 min; gold, down-regulated at 10 min; purple, down-regulated at 30 min. Colored asterisks indicate when the gene is first down-regulated in relAΔ251. Abbreviations: G6P, glucose-6-phosphate; DHAP, dihydroxyacetone-phosphate; G3P, d-glyceraldehyde-3-phosphate; PEP, phosphoenolpyruvate; PYR, pyruvate; AcCoA, acetyl coenzyme A; α-KG, α-ketoglutarate; OAA, oxaloacetate; NMN, nicotinamide mononucleotide.

FIG. 7.

Affected pathways involved in fatty acid, phospholipid, and MDO synthesis. Colored letters indicate when the gene is first up- or down-regulated in MG1655, as follows: dark blue, up-regulated at 10 min; light blue, up-regulated at 30 min; gold, down-regulated at 10 min; purple, down-regulated at 30 min; black letters, not affected. Colored asterisks indicate when the gene is first affected in the relAΔ251 mutant. Alternative paths not affected at the transcript level are omitted for clarity. Abbreviations: CoA, coenzyme A; ACP, acyl carrier protein.