Genome Mining for Microbial Siderophores: Improving Structural Predictions
- Author(s): Reitz, Zachary L
- Advisor(s): Butler, Alison
- et al.
Nearly all life requires iron; however, under aerobic conditions, Fe(III) is nearly insoluble. To meet their metabolic needs, many bacteria synthesize siderophores: small-molecule, high-affinity Fe(III) chelators. The discovery of new siderophores has been streamlined by genome mining, where bacterial genomes of interest are scanned for siderophore biosynthetic gene clusters (BGCs). This dissertation is focused on the development of new bioinformatics tools to improve siderophore structural predictions, as well as the application of those tools towards traditional natural product isolation.
Some peptidic siderophores contain the chelating ligand β-hydroxyaspartate (β-OHAsp), which provides bidentate OO′ coordination to Fe(III). Current genome mining methods cannot reliably predict which aspartate residues will be hydroxylated, nor the resulting stereochemistry, leaving structural ambiguities which must be rectified experimentally. Through coupling BGCs with verified structures, the origin of the β-OHAsp diastereomers in siderophores is reported. Two functional subtypes of nonheme Fe(II)/α-ketoglutarate–dependent aspartyl β-hydroxylases were identified in siderophore BGCs. Each aspartyl β-hydroxylase subtype effects distinct diastereoselectivity. A previously undescribed, noncanonical member of the nonribosomal peptide synthetase (NRPS) condensation domain superfamily is identified, named the interface domain, which is proposed to position the β-hydroxylase and the NRPS-bound amino acid prior to hydroxylation. Through mapping characterized β-OHAsp diastereomers to the phylogenetic tree of siderophore β-hydroxylases, methods to predict β-OHAsp stereochemistry in silico are realized.
The DHB-CAA-Ser family of triscatechol siderophores each contain a different cationic amino acid (CAA = D-Arg, D-Lys, or L-Orn), hinting at the existence of their diastereomers with L-Arg, L-Lys, and D-Orn. With no knowledge of which bacteria, if any, are capable of their production, a novel high-throughput genome mining workflow was developed, the Catechol Siderophore Cluster Analysis (CatSCAn). Over 11,000 bacterial genomes were scanned for siderophore BGCs, revealing about 1% potentially capable of the biosynthesis of the combinatoric suite of DHB-CAA-Ser siderophores with L- and D-CAA. The NRPS from Marinomonas sp. TW1 was found to be unusually promiscuous, producing a relatively rare example of a suite of siderophores with D-Arg, D-Orn, and L-Orn amino acids.
CatSCAn produced a rich dataset of putative BGCs that may be coupled with structurally- characterized siderophores to study the chemistry and biology of triscatechol siderophores. A detailed analysis of BGCs highlighted key features within siderophore pathways. Mapping known and predicted siderophores onto a phylogenetic tree of NRPS proteins reveals repeated changes in CAA stereochemistry and identity within the DHB-CAA-Ser family. Parsimony suggests that the ancestor of all DHB-CAA-Ser siderophores was trivanchrobactin, (DHB-DArg-Ser)3. A model of DHB-CAA-Ser siderophore evolution is presented where enzyme promiscuity allows for the biosynthesis of new siderophores.
Genome mining for VibH homologs reveals several species of Acinetobacter with a gene cluster that putatively encodes the biosynthesis of catechol siderophores with an amine core. A. bouvetii DSM 14964 produces three novel biscatechol siderophores: propanochelin, butanochelin, and pentanochelin. This strain has a relaxed specificity for the amine substrate, allowing for the biosynthesis of a variety of non-natural siderophore analogs by precursor directed biosynthesis. Of potential synthetic utility, A. bouvetii DSM 14964 condenses 2,3-dihydroxybenzoic acid (2,3-DHB) to allylamine and propargylamine, producing catecholic compounds which bind iron(III) and may be further modified via thiol–ene or azide–alkyne click chemistry.