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Area of Science:

  • Microbial genomics
  • Natural product biosynthesis
  • Evolutionary biology

Background:

  • Bacterial genomes contain many orphan biosynthetic gene clusters (BGCs) for metabolites with unknown functions.
  • The diversity and horizontal transfer of BGCs raise questions about their activity, benefit, or parasitic nature.
  • Salinispora bacteria were previously known to utilize desferrioxamine siderophores for iron acquisition.

Purpose of the Study:

  • To investigate the evolutionary dynamics of siderophore biosynthesis in Salinispora bacteria.
  • To describe a newly identified group of peptidic siderophores, salinichelins.
  • To understand the selective pressures driving the retention or loss of BGCs.

Main Methods:

  • Phylogenetic analysis of siderophore biosynthesis gene clusters.
  • Comparative genomics of Salinispora strains.
  • Evolutionary history reconstruction.

Main Results:

  • A new family of peptidic siderophores, salinichelins, was identified in a subset of Salinispora strains.
  • These strains had lost the genes for desferrioxamine biosynthesis.
  • The acquisition of salinichelins coincided with the loss of desferrioxamine pathways, an event that occurred independently at least three times.
  • High selective pressure exists against retaining functionally redundant gene clusters.

Conclusions:

  • Functional redundancy can lead to the replacement of established metabolic pathways with new ones.
  • Bacterial genomes may shed BGCs that are no longer essential due to pathway replacement.
  • Evolutionary processes actively prune superfluous gene clusters, indicating selection against non-beneficial genetic elements.