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Darobactin synthase DarE forms a unique bicyclic scaffold in bacteria. This radical S-adenosylmethionine enzyme utilizes an unusual oxygen insertion from water, creating a new class of peptides called daropeptides.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Microbiology

Background:

  • Darobactin is a potent antibiotic against Gram-negative bacteria.
  • It possesses a unique bicyclic structure formed by ether and C-C crosslinks between Trp and Lys residues.

Purpose of the Study:

  • To investigate the in vivo and in vitro activity of darobactin synthase DarE.
  • To elucidate the mechanism by which DarE forms the bicyclic scaffold of darobactin.
  • To explore the diversity of darobactin-like biosynthetic gene clusters.

Main Methods:

  • Characterization of DarE as a radical S-adenosylmethionine (rSAM) enzyme.
  • In vitro enzymatic assays using purified DarE.
  • Isotopic labeling experiments using H2(18)O.
  • Genome mining analysis of darobactin-like gene clusters.

Main Results:

  • DarE is solely responsible for forming the bicyclic scaffold of darobactin.
  • DarE catalyzes an unusual oxygen insertion from water into the peptide backbone.
  • Genome mining revealed diverse darobactin-like gene clusters, some encoding monocyclic products.
  • A new family of ether-containing RiPPs, termed daropeptides, was proposed.

Conclusions:

  • DarE employs a novel rSAM-dependent mechanism involving oxygen insertion from water.
  • This mechanism leads to the formation of the unique bicyclic structure of darobactin.
  • The discovery of daropeptides expands the known repertoire of RiPPs and their biosynthetic pathways.