Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome

Abstract

Regulation of cellular growth implies spatiotemporally coordinated programmes of gene transcription. A central question, therefore, is how global transcription is coordinated in the genome. The growth of the unicellular organism Escherichia coli is associated with changes in both the global superhelicity modulated by cellular topoisomerase activity and the relative proportions of the abundant DNA-architectural chromatin proteins. Using a DNA-microarray-based approach that combines mutations in the genes of two important chromatin proteins with induced changes of DNA superhelicity, we demonstrate that genomic transcription is tightly associated with the spatial distribution of supercoiling sensitivity, which in turn depends on chromatin proteins. We further demonstrate that essential metabolic pathways involved in the maintenance of growth respond distinctly to changes of superhelicity. We infer that a homeostatic mechanism organizing the supercoiling sensitivity is coordinating the growth-phase-dependent transcription of the genome.

Figure 1

Strategy of mapping supercoiling-associated genes. (A) Set A compares the transcript profiles of the CSH50 wild-type and mutant cells during growth. Set B compares the transcript profiles of LZ41 and LZ54 strains and their derivatives after norfloxacin treatment. (B) Genomic wheels showing spatiotemporal distributions of Rel (red), Hyp (blue), Act (green) and Rep (yellow) transcripts among the growth-phase-dependent genes (grey) in CSH50 wild type (outer wheels) and fis (inner wheels). (C) Transcript distributions in CSH50 wild type and hns mutant. (D) Changes of supercoiling-associated genes during growth. Distributions of Hyp (blue), Rel (red), Act (green) and Rep (yellow) gene transcripts are shown. The sums of total mapped Hyp+Rel or Act+Rep transcripts were set at 100% for each growth phase. The distinct ‘double-coded' transcripts—Hyp/Act, Hyp/Rep, Rel/Act and Rel/Rep—are ordered from left to right for each bar. The sum of total mapped double-coded transcripts for the entire growth cycle was set at 100%. The number of genes is indicated within the bars. fis, CSH50 fis; hns, CSH50 hns; LS, late stationary phase; ME, mid-exponential phase; Ori, origin; Ter, terminus of replication; TS, transition state; wt, CSH50 wild type.

Figure 2

Coordination of essential metabolic pathways by supercoiling sensitivity. (A) Regulation of oxaloacetate production in citric acid cycle and glyoxalate bypass. The Rel genes are in red letters and the Hyp genes are in blue. Note that the citric acid cycle involves Rel genes, whereas the glyoxalate bypass involves Hyp genes. (B) Coordination of de novo biosynthesis of purine nucleotides. Note that almost all the steps of biosynthesis from phosphoribosylpyrophosphate (PRPP) involve Hyp genes. The pathways were derived from http://ecocyc.org. The genes identified by Real-Time PCR are marked with asterisks.