Siderophore Synthesis Genes Identification

FeGenie can also be used to identify siderophore synthesis genes and potential operons. Siderophores are microbially produced products (500–1200 Da) that have a preference for binding ferric iron (up to 10^–53 M) (Ehrlich and Newman, 2008 ), enabling microorganisms to obtain this largely insoluble iron form. There are over 500 identified siderophores, categorized as catecholates, hydroxamates, or hydroxycarboxylic acids (Kadi and Challis, 2009 ). Microorganisms can synthesize siderophores via the NRPS (non-ribosomal peptide synthetase) or NIS (NRPS-independent siderophore) pathways (Carroll and Moore, 2018 (link)). The NRPSs are megaenzymes that consist of modular domains (adenylation, thiolation, and condensation domains) to incorporate and sequentially link amino acids, keto acids, fatty acids, or hydroxy acids (Gulick, 2017 (link)). The NRPSs are highly selective and predictable based on the product produced, and FeGenie will identify these putative siderophore synthesis genes based on the genomic proximity of each identified gene (Table 1). In contrast, the NIS pathway consists of multiple enzymes that each have a single role in the production of a siderophore, such as aerobactin, which was the first siderophore discovered to be synthesized by this pathway (Kadi and Challis, 2009 ). The operon involved in aerobactin biosynthesis is iucABCD, and homologs of the genes iucA and iucC (which are included in FeGenie) are indicators of siderophore production via the NIS pathway (Carroll and Moore, 2018 (link)). The HMM library that represents siderophore synthesis consists of HMMs derived from the Pfam database, as well as those constructed here (Table 1). Because many different siderophore synthesis pathways share homologous genes, we developed HMMs that were sensitive to the entirety of each gene family, rather than for each individual siderophore. Supplementary Data Sheet S1 summarizes the gene families from which HMMs were built and includes gene families for siderophore export, iron uptake and transport, and heme degradation. Although FeGenie cannot predict the exact siderophore produced, FeGenie enables users to identify putative (and potentially novel) siderophore synthesis operons, which can then be confirmed by external programs, such as antiSMASH (Weber et al., 2015 (link)), a bioinformatics tool to identify biosynthetic gene clusters.