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

Alexandre Duprey, Eduardo A. Groisman

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.

Introduction

All living cells supercoil their DNA. The resulting changes in DNA structure enable compaction of the DNA so that it fits within the limited space of a bacterial cell or eukaryotic organelle [1]. DNA supercoiling is necessary for transcription in prokaryotes [2,3] and eukaryotes [4], recombination in bacteriophages [5,6] and eukaryotic viruses, including HIV [7], and chromosome segregation [8]. Because some of the enzymes governing bacterial DNA supercoiling are essential, their pharmacological inhibition is an efficient antibacterial strategy [9,10].

Materials and methods

Bacterial strains, plasmids and growth conditions
Strains, plasmids and primers are described in S1 Table.

Mutations were created by λred recombination [60]. Plasmid pSIM6 was used to supply λred in all cases. After PCR verification of the strains, mutations were moved into a clean genetic background using P22-mediated transduction in the case of S. Typhimurium [61] and P1-mediated transduction in the case of E. coli.

Strains AAD35, AAD46 and AAD85 were built by λred recombination using pKD4, pKD3 and pKD4 as templates, respectively, and primer pairs 16608/16609, 16651/16652, 16834/16835, respectively.

Strain AAD58 was built by P22 transduction using a lysate prepared in strain AAD46 to infect strain JY979.

Strain AAD181 was built by P22 transduction using a lysate prepared in strain AAD35 to infect strain AAD58.

Discussion

We have now established that different polyamines activate the DNA gyrases from S. Typhimurium and E. coli. The different response of these DNA gyrases to the polyamines putrescine and spermidine dictates the distinct basal global DNA supercoiling set point of the two species. We determined that environmental Mg2+ regulates DNA supercoiling in S. Typhimurium, but not in E. coli, by altering putrescine abundance. Our findings reveal a novel physiological role for polyamines, which play critical functions in all domains of life [48]. Moreover, they help explain why DNA is less negatively supercoiled in S. Typhimurium than in E. coli when these bacteria experience the same growth condition. And they suggest potential targets for antibacterial agents to inhibit the essential process of DNA supercoiling.

Citation: Duprey A, Groisman EA (2020) DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines. PLoS Genet 16(10): e1009085. https://doi.org/10.1371/journal.pgen.1009085

Editor: Diarmaid Hughes, Uppsala University, SWEDEN

Received: March 16, 2020; Accepted: August 27, 2020; Published: October 30, 2020.

Copyright: © 2020 Duprey, Groisman. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the manuscript and its Supporting Information files.

Funding: This work was supported by grant AI120558 from the National Institutes of Health to EAG. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

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