The variable hydroxamic acid siderophore metabolome of the marine actinomycete Salinispora tropica CNB-440

Abstract

The recently sequenced genome of the marine actinomycete Salinispora tropica CNB-440 revealed a high frequency of gene clusters which code for the biosynthesis of known and novel secondary metabolites. Of these metabolites, bioinformatics analysis predicted that S. tropica CNB-440 could potentially biosynthesize, as high affinity Fe(iii) ligands, siderophores from the hydroxamic acid desferrioxamine class (sid1 gene cluster) and the phenolate-thia(oxa)zoli(di)ne class (sid2 and sid4 gene clusters). In this work, we have used Ni(ii)-based immobilized metal ion affinity chromatography (IMAC) to pre-fractionate the hydroxamic acid siderophore metabolome of S. tropica CNB-440 from the secondary metabolome, to reveal low abundance siderophores. LC-MS measurements and electronic absorption spectra from purified extracts incubated with exogenous Fe(iii) revealed eight siderophores from the desferrioxamine class (DFOA2, DFOA1a, DFOA1b, DFOB, DFON, DFOD2, DFOE, DFOD1), which included two constitutional isomers (DFOA1a, DFOA1b), and one new siderophore (DFON), the latter which would require assembly from a combination of 1,5-diaminopentane and 1,6-diaminohexane as diamine substrates. Three additional species (m/zobs 496.14, 792.34 and 804.34) with electronic absorption spectra characteristic of complexes formed between Fe(iii) and hydroxamic acid-type siderophores were evident under some conditions. The signal at m/zobs 792.34 eluted in the hydrophobic region of the reverse-phase LC and correlated with a DFOD1 analogue with a C-terminal branched chain fatty acid ([M + K(+)](+)m/zcalc 792.35), which has been previously identified from marine sediment dwelling Micrococcus luteus KLE1011. The S. tropica CNB-440 hydroxamic acid siderophore metabolome was modulated by culture conditions (pH 7, 22 °C; pH 7, 28 °C; pH 9, 28 °C) designed to simulate the variable marine environment. An increase in temperature at constant pH value showed increased levels of DFOA2 and DFOA1, and decreased levels of DFOB and DFOE. An increase in pH value at constant temperature showed decreased levels of DFOA2 and DFOA1, and increased levels of DFOB, DFON and DFOE. These results indicate that the marine adaptation of S. tropica CNB-440 could involve its ability to select a suite of siderophores from a large number of candidates, which are optimized for the iron microenvironment.

Azido‐Desferrioxamine Siderophores as Functional Click‐Chemistry Probes Generated in Culture upon Adding a Diazo‐Transfer Reagent

“…DH was partially viable as a substrate in the biosynthesis of 1 , with substitution of one DP unit with DH (substrate denoted “N”) to give DFON 1 [001], as evidenced by a signature MS/MS fragmentation pattern. No analogues containing DPr were observed.…”

The marine actinomycete genus Salinispora: a model organism for secondary metabolite discovery

“…Bioassay-guided fractionation confirmed the production of desferrioxamines B ( 72 ) and E ( 73 ) in both species, which were formally linked to the des pathway via gene inactivation. Subsequent studies using Ni(II)-based immobilized metal ion chromatography led to the isolation of six additional desferrioxamine siderophores including the new analogue desferrioxamine N ( 74 ) 132 . A recent report also describes the isolation of the known fungal metabolite mevinolin ( 75 ) from two different S. arenicola strains 133 , which led the authors to suggest the possibility of horizontal gene transfer between fungi and bacteria.…”

Discovering the Recondite Secondary Metabolome Spectrum of Salinispora Species: A Study of Inter-Species Diversity

“…The compound salinosporamide A, isolated from S. tropica is currently in Phase 1 clinical trials in patients with multiple myeloma, lymphomas, leukaemia and solid tumours [8]. This genus has also been found to produce secondary metabolites with diverse activities, for instance arenimycin, rifamycins, staurosporine, saliniketal A and B, cyclomarazines and cyclomarins, as well as hydroxamic acid siderophores [4], [8], [9], [10].…”