The secreted metabolome of Streptomyces chartreusis and implications for bacterial chemistry

Abstract

are known for producing diverse secondary metabolites. Combining genomics with untargeted data-dependent tandem MS and molecular networking, we characterized the secreted metabolome of the tunicamycin producer NRRL 3882. The genome harbors 128 predicted biosynthetic gene clusters. We detected>1,000 distinct secreted metabolites in culture supernatants, only 22 of which were identified based on standards and public spectral libraries. adapts the secreted metabolome to cultivation conditions. A number of metabolites are produced iron dependently, among them 17 desferrioxamine siderophores aiding in iron acquisition. Eight previously unknown members of this long-known compound class are described. A single desferrioxamine synthesis gene cluster was detected in the genome, yet different sets of desferrioxamines are produced in different media. Additionally, a polyether ionophore, differentially produced by the calcimycin biosynthesis cluster, was discovered. This illustrates that metabolite output of a single biosynthetic machine can be exquisitely regulated not only with regard to product quantity but also with regard to product range. Compared with chemically defined medium, in complex medium, total metabolite abundance was higher, structural diversity greater, and the average molecular weight almost doubled. Tunicamycins, for example, were only produced in complex medium. Extrapolating from this study, we anticipate that the larger part of bacterial chemistry, including chemical structures, ecological functions, and pharmacological potential, is yet to be uncovered.

Aromatic polyketide biosynthesis: fidelity, evolution and engineering

“…Thus, in practice, any biosynthetic pathway will lead 40 to the accumulation of a mixture comprising the final product plus varying concentrations of 41 pathway intermediates and shunt metabolites. The composition of such a mixture will vary 42 further when alternate growth conditions are used 3 . Sometimes the 'final' product of the 43 pathway cannot even be clearly discerned.…”

“…Intrigued by these compounds, which exhibit potent 55 antibacterial activity, and as part of studies to decipher their biosynthetic pathway, we 56 employed targeted metabolomics to identify further congeners that may have been missed 57 during manual analysis of culture extracts. This led us to identify the formicapyridines (1)(2)(3)(4)(5)(6)(7)(8)(9), 58 pyridine containing polyketide alkaloids which represent additional products of the 59 are minor shunt metabolites that likely arise due to derailment of the formicamycin 70 biosynthetic pathway. Intrigued by these observations we investigated the possibility of 71 reprogramming, or evolving, the BGC such that the formicapyridines might become the 72 major products of the formicamycin BGC.…”

“…Analysis of C/H ratios and m/z data allowed us to 111 identify a group of three additional new metabolites (4-6) with mass spectra suggesting a 112 close structural relationship to the fasamycins/formicamycins; these varied only in the 113 number of methyl groups present. By searching for equivalent ions lacking chlorine atoms 114 we identified three additional congeners (1)(2)(3). Compounds 1-6 were not initially observed in 115 the UV chromatograms of the WT, and qualitative examination of the LCMS data suggested 116 titres at least 100-fold lower than for the formicamycins.…”

“…In contrast, the methyl group atom C24 shows 218 enrichment and coupling to C1. The C2 atom of [1,[2][3][4][5][6][7][8][9][10][11][12][13] C2] sodium acetate is highlighted as a 219 blue circle, the C1 atom as a black circle, and the coupled unit by a bold line. The gene product ForD shows significant sequence similarity to aromatase/cyclases 238 (ARO/CYC) such as the N-terminal domain (pfam 03364) of the archetypical tetracenomycin 239 polyketide cyclase TcmN which belongs to the Bet v1-like superfamily (cl10022) 15 .…”

“…Sigma-Aldrich or Fisher Scientific. [1,[2][3][4][5][6][7][8][9][10][11][12][13] C2] sodium acetate was purchased from 372 CORTECNET. All solvents were of HPLC grade or equivalent.…”