Mechanism of CcdA-Mediated Rejuvenation of DNA Gyrase

Structure. 2020 May 5;28(5):562-572.e4. doi: 10.1016/j.str.2020.03.006. Epub 2020 Apr 14.

Abstract

Most biological processes involve formation of transient complexes where binding of a ligand allosterically modulates function. The ccd toxin-antitoxin system is involved in plasmid maintenance and bacterial persistence. The CcdA antitoxin accelerates dissociation of CcdB from its complex with DNA gyrase, binds and neutralizes CcdB, but the mechanistic details are unclear. Using a series of experimental and computational approaches, we demonstrate the formation of transient ternary and quaternary CcdA:CcdB:gyrase complexes and delineate the molecular steps involved in the rejuvenation process. Binding of region 61-72 of CcdA to CcdB induces the vital structural and dynamic changes required to facilitate dissociation from gyrase, region 50-60 enhances the dissociation process through additional allosteric effects, and segment 37-49 prevents gyrase rebinding. This study provides insights into molecular mechanisms responsible for recovery of CcdB-poisoned cells from a persister-like state. Similar methodology can be used to characterize other important transient, macromolecular complexes.

Keywords: CcdA-CcdB; computational analysis; gyrase; normal mode analysis; perturbation response scanning; rejuvenation; toxin-antitoxin.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Bacterial Toxins / chemistry
  • Bacterial Toxins / genetics
  • Bacterial Toxins / metabolism
  • Binding Sites
  • Cysteine / genetics
  • DNA Gyrase / chemistry*
  • DNA Gyrase / genetics
  • DNA Gyrase / metabolism*
  • Fluorescence Resonance Energy Transfer
  • Models, Molecular
  • Multiprotein Complexes / chemistry
  • Multiprotein Complexes / metabolism
  • Mutation
  • Surface Plasmon Resonance

Substances

  • Bacterial Proteins
  • Bacterial Toxins
  • CcdA protein, Bacteria
  • CcdB protein, Plasmid F
  • Multiprotein Complexes
  • DNA Gyrase
  • Cysteine