Automated genome mining predicts combinatorial diversity and taxonomic distribution of peptide metallophore structures

Abstract

Microbial competition for trace metals shapes their communities and interactions with humans and plants. Many bacteria scavenge trace metals with metallophores, small molecules that chelate environmental metal ions and transport them back into the cell. Our incomplete knowledge of metallophores diversity stymies our ability to fight infectious diseases and harness beneficial microbiome interactions. The majority of known metallophores are non-ribosomal peptides (NRPs), which feature metal-chelating moieties rarely found in other classes of natural products. NRP metallophore production may be predicted by genome mining, where genomes are scanned for homologs of known biosynthetic gene clusters (BGCs). However, accurately detecting NRP metallophore biosynthesis currently requires expert manual inspection. Here, we introduce automated identification of NRP metallophore BGCs through a comprehensive detection algorithm, newly implemented in antiSMASH. Custom-designed profile hidden Markov models detect genes encoding the biosynthesis of most known NRP metallophore chelating moieties (2,3-dihydroxybenzoate, hydroxamates, salicylate, {beta}-hydroxyamino acids, graminine, Dmaq, and the pyoverdine chromophore), achieving 97% precision and 78% recall against manual curation. We leveraged the algorithm, in combination with transporter gene detection, to detect NRP metallophore BGCs in 15,562 representative bacterial genomes and predict that 25% of all non-ribosomal peptide synthetases encode metallophore production. BiG-SCAPE clustering of 2,562 NRP metallophore BGCs revealed that significant diversity remains unexplored, including new combinations of chelating groups. Additionally, we find that Cyanobacteria are severely understudied and should be the focus of more metallophore isolation efforts. The inclusion of NRP metallophore detection in antiSMASH version 7 will aid non-expert researchers and facilitate large-scale investigations into metallophore biology.