Function-related replacement of bacterial siderophore pathways.

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.