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DNA Topoisomerases02:02

DNA Topoisomerases

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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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Rapid, DNA-induced interface swapping by DNA gyrase.

Thomas R M Germe1, Natassja G Bush1, Victoria M Baskerville1

  • 1Department Biochemistry & Metabolism, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.

Elife
|June 10, 2024
PubMed
Summary
This summary is machine-generated.

DNA gyrase, a bacterial enzyme, can rapidly swap DNA-cleaving interfaces between two active complexes. This interface swapping, essential for DNA replication and transcription, occurs without ATP and may explain non-homologous recombination.

Keywords:
DNA gyraseE. coliantibacterialsbiochemistrychemical biologyenzymologygenome dynamicsmolecular biophysicsstructural biologytopoisomerase

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • DNA gyrase is a type IIA topoisomerase crucial for bacterial DNA replication and transcription.
  • It introduces negative supercoiling by creating and repairing double-strand breaks (DSBs) in DNA.
  • The active complex is a heterotetramer of GyrA and GyrB subunits.

Purpose of the Study:

  • To investigate the stability and dynamics of DNA gyrase's DNA-cleaving interfaces.
  • To explore novel mechanisms of DNA manipulation by DNA gyrase beyond supercoil conversion.

Main Methods:

  • In vitro experiments observing DNA gyrase activity in solution.
  • Analysis of DNA binding, bending, and cleavage dynamics.
  • Investigation of factors influencing interface exchange, including DNA structure and subunit stoichiometry.

Main Results:

  • DNA gyrase exhibits rapid interface swapping (IS) between two active heterotetramers within minutes.
  • DNA bending by gyrase is critical for cleavage and favors IS; DNA wrapping and excess GyrB also promote IS.
  • Interface swapping occurs without ATP, in the presence of fluoroquinolones, and can occur in gyrase heterodimers.

Conclusions:

  • DNA gyrase possesses a previously unrecognized dynamic capability for interface swapping.
  • This mechanism provides an alternative explanation for DNA double-strand passage reactions.
  • Interface swapping raises possibilities for non-homologous recombination mediated solely by gyrase activity.