DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

Abstract

Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination. The topological state of DNA also influences its affinity for some DNA binding proteins, especially in DNA sequences that have a high A + T base content. The underwinding of DNA by the ATP-dependent topoisomerase DNA gyrase creates a continuum between metabolic flux, DNA topology and gene expression that underpins the global response of the genome to changes in the intracellular and external environments. These connections describe a fundamental and generalised mechanism affecting global gene expression that underlies the specific control of transcription operating through conventional transcription factors. This mechanism also provides a basal level of control for genes acquired by horizontal DNA transfer, assisting microbial evolution, including the evolution of pathogenic bacteria.

Keywords: DNA supercoiling; DNA topoisomerases; Gene regulation; Transcription.

Fig. 1

Transcription-induced DNA supercoiling resolved by DNA gyrase and DNA topoisomerase I. Genes A and B are transcribed convergently by RNA polymerase (red). The extent of each gene and its direction of transcription are shown by horizontal green arrows. RNA polymerases cannot rotate around the DNA as they track along the template and the template is also unable to rotate. This results in the creation and accumulation of overwound (positively supercoiled) DNA ahead of the polymerases and underwound (negatively supercoiled) DNA behind. The positive supercoils are removed by DNA gyrase in a reaction that is dependent on ATP hydrolysis. This dependency connects DNA gyrase activity to the metabolic status of the bacterium. The negative supercoils are removed by DNA topoisomerase I through an ATP-independent mechanism; the ATP-dependent DNA topoisomerase IV can also relax negative supercoils

Fig. 2

The leu-500 paradox. The Gibbs free energy of supercoiling (ΔG_SC) values (Y-axis), obtained using reporter plasmid supercoiling measurements, are represented for five strains of Salmonella Typhimurium by the five horizontal red lines (Richardson et al. 1984). The wild-type strain is shown on the left, followed by the four strains harbouring the leu-500 promoter mutation. The Leu phenotypes of the strains are given above the horizontal red lines as either Leu⁺ or Leu⁻. The presence (TopA⁺) or absence (TopA⁻) of active DNA topoisomerase I is indicated below the red line for each strain. The Leu⁻ TopA⁺ strain (leu-500 strain 1) has a ΔG_SC value that is identical to that of the wild type Salmonella Typhimurium strain with its full complement of functioning topoisomerases. The leu-500 strain 2 is Leu⁺ TopA⁻ strain and has an elevated ΔG_SC value because the loss of topoisomerase I results in a globally more negatively supercoiled genome. Strains with a Tos phenotype have topoisomerase one suppressor (tos) mutations. These mutations are typically defects in the negative supercoiling activity of gyrase that return ΔG_SC to values that are close to wild type (leu-500 strain 3) or to a lower-than-wild-type value (leu-500 strain 4). If increased negative supercoiling suppresses the leu-500 mutation, then increasing this globally by elimination of the topA gene should create a Leu⁺ phenotype, and this is, indeed, observed (leu-500 strain 2). Paradoxically, no overall correlation exists between ΔG_SC and Leu phenotype in the four strains. Instead, a Leu⁺ phenotype correlates with the absence of DNA topoisomerase I (TopA⁻)

Fig. 3

The ilvIH-leuO-leuABCD promoter relay. The segment of the Salmonella Typhimurium chromosome between ilvIH and leuABCD is shown. This genetic arrangement is conserved in E. coli. Activation of the leu-500 mutant promoter in a topA strain is achieved in cis by a promoter-to-promoter DNA supercoiling relay involving promoters P_ilvIH, P_leuO and P_leu-500 (Wu et al. 1995). There is also a positive role for the LysR-like transcription factor, LeuO, encoded by the leuO gene. LeuO prevents encroachment by the H-NS nucleoid-associated transcription-silencing protein from the region of A + T-rich DNA into the promoter P_leu-500. Although the DNA sequence of the corresponding region in E. coli is different, the average A + T content is the same (Haughn et al. 1986) and the promoter relay is conserved in both species (Chen et al. 2005). Another DNA binding protein, the leucine-responsive regulatory protein, Lrp, contributes by stimulating transcription of P_ilvIH (Wang et al. 1993)