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Microorganisms. 2019 Mar 15;7(3). pii: E81. doi: 10.3390/microorganisms7030081.

Supercoil Levels in E. coli and Salmonella Chromosomes Are Regulated by the C-Terminal 35⁻38 Amino Acids of GyrA.

Author information

1
Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA. nikolay.rovinskiy@aol.com.
2
Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA. agbleke@fas.harvard.edu.
3
Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA. ochesnokov@fau.edu.
4
Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA. nphiggin@uab.edu.

Abstract

Prokaryotes have an essential gene-gyrase-that catalyzes negative supercoiling of plasmid and chromosomal DNA. Negative supercoils influence DNA replication, transcription, homologous recombination, site-specific recombination, genetic transposition and sister chromosome segregation. Although E. coli and Salmonella Typhimurium are close relatives with a conserved set of essential genes, E. coli DNA has a supercoil density 15% higher than Salmonella, and E. coli cannot grow at the supercoil density maintained by wild type (WT) Salmonella. E. coli is addicted to high supercoiling levels for efficient chromosomal folding. In vitro experiments were performed with four gyrase isoforms of the tetrameric enzyme (GyrA₂:GyrB₂). E. coli gyrase was more processive and faster than the Salmonella enzyme, but Salmonella strains with chromosomal swaps of E. coli GyrA lost 40% of the chromosomal supercoil density. Reciprocal experiments in E. coli showed chromosomal dysfunction for strains harboring Salmonella GyrA. One GyrA segment responsible for dis-regulation was uncovered by constructing and testing GyrA chimeras in vivo. The six pinwheel elements and the C-terminal 35⁻38 acidic residues of GyrA controlled WT chromosome-wide supercoiling density in both species. A model of enzyme processivity modulated by competition between DNA and the GyrA acidic tail for access to β-pinwheel elements is presented.

KEYWORDS:

DNA gyrase is an enzyme with two protein subunits; DNA topology is investigated that involves two types of DNA coiling; GyrA and GyrB that catalyzes (−) supercoiling at the expense of ATP hydrolysis; RNA polymerase (RNAP); gamma delta (γδ) resolvase is a site-specific recombinase from the γδ transposon the that utilizes (−) supercoils to delete a DNA sequence that is flanked by 100 bp Res sites; gyrase processivity refers to the number of reaction cycles one enzyme carries out in a single DNA binding event; the E. coli and Salmonella condensin is a multi-protein complex composed of three proteins, MukB, MukE, and MukF that compacts chromosomal DNA; the GyrA C-terminal domain (CTD) includes a long DNA binding section that has 6 pinwheel elements plus a short 35–38 amino acid terminus called the tail; the Q10 rule states that reaction rates double for every 10° C increase in temperature; the first type is right-handed coils that Watson/Crick DNA strands adopt by winding around each other every 10.6 base pairs, the second type involves coiling of the double strands around each other in either a left handed (−) or right handed (+) direction

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