DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines

Abstract

DNA supercoiling is essential for all living cells because it controls all processes involving DNA. In bacteria, global DNA supercoiling results from the opposing activities of topoisomerase I, which relaxes DNA, and DNA gyrase, which compacts DNA. These enzymes are widely conserved, sharing >91% amino acid identity between the closely related species Escherichia coli and Salmonella enterica serovar Typhimurium. Why, then, do E . coli and Salmonella exhibit different DNA supercoiling when experiencing the same conditions? We now report that this surprising difference reflects disparate activation of their DNA gyrases by the polyamine spermidine and its precursor putrescine. In vitro , Salmonella DNA gyrase activity was sensitive to changes in putrescine concentration within the physiological range, whereas activity of the E . coli enzyme was not. In vivo , putrescine activated the Salmonella DNA gyrase and spermidine the E . coli enzyme. High extracellular Mg 2+ decreased DNA supercoiling exclusively in Salmonella by reducing the putrescine concentration. Our results establish the basis for the differences in global DNA supercoiling between E . coli and Salmonella , define a signal transduction pathway regulating DNA supercoiling, and identify potential targets for antibacterial agents.

The regulation of DNA supercoiling across evolution

“…54 The Topo I enzymes also differ in that the eukaryotic Topo I is stimulated by the polyamines spermidine and spermine, 54 whereas bacterial Topo I is insensitive to spermidine and its precursor putrescine. 55 Archaea generally lack an equivalent type I topoisomerase. The dissipation of excessive supercoils is instead dependent on a type IIB enzyme-called Topo VI (Figure 2d)-that differs greatly from its bacterial and eukaryotic counterparts.…”

“…Curiously, excess Mg 2+ also causes relaxation in S. Typhimurium. 55 The latter effect results from a decrease in the concentration of polyamines, 55 which are required for DNA gyrase activity. 55,120 The in vitro activities of bacterial DNA gyrase 55 and eukaryotic Topo I 54 are polyamine dependent.…”

“…55 The latter effect results from a decrease in the concentration of polyamines, 55 which are required for DNA gyrase activity. 55,120 The in vitro activities of bacterial DNA gyrase 55 and eukaryotic Topo I 54 are polyamine dependent. In vivo, bacterial DNA supercoiling is directly correlated with the concentration of the polyamines putrescine and spermidine.…”

“…In vivo, bacterial DNA supercoiling is directly correlated with the concentration of the polyamines putrescine and spermidine. 55 Thus, DNA supercoiling is intimately connected with polyamine metabolism, import, and export. The identity of the specific polyamine controlling DNA gyrase in vivo often differs across closely related bacterial species.…”

“…For example, spermidine and putrescine are the main polyamines controlling DNA supercoiling in E. coli and S. Typhimurium, respectively. 55 Putrescine is converted into spermidine by the enzyme SpeE. 122 Thus, inactivation of the speE gene has opposite effects on E. coli and S. Typhimurium: it increases global DNA supercoiling in the former but decreases it in the latter.…”