Genome Mining and Metabolic Profiling Uncover Polycyclic Tetramate Macrolactams from Streptomyces koyangensis SCSIO 5802

Abstract

We have previously shown deep-sea-derived Streptomyces koyangensis SCSIO 5802 to produce two types of active secondary metabolites, abyssomicins and candicidins. Here, we report the complete genome sequence of S. koyangensis SCSIO 5802 employing bioinformatics to highlight its potential to produce at least 21 categories of natural products. In order to mine novel natural products, the production of two polycyclic tetramate macrolactams (PTMs), the known 10-epi-HSAF (1) and a new compound, koyanamide A (2), was stimulated via inactivation of the abyssomicin and candicidin biosynthetic machineries. Detailed bioinformatics analyses revealed a PKS/NRPS gene cluster, containing 6 open reading frames (ORFs) and spanning ~16 kb of contiguous genomic DNA, as the putative PTM biosynthetic gene cluster (BGC) (termed herein sko). We furthermore demonstrate, via gene disruption experiments, that the sko cluster encodes the biosynthesis of 10-epi-HSAF and koyanamide A. Finally, we propose a plausible biosynthetic pathway to 10-epi-HSAF and koyanamide A. In total, this study demonstrates an effective approach to cryptic BGC activation enabling the discovery of new bioactive metabolites; genome mining and metabolic profiling methods play key roles in this strategy.

Critical analysis of polycyclic tetramate macrolactam biosynthetic cluster phylogeny and functional diversity

“…Accordingly, we used a phylogenyguided degenerate oligonucleotide design strategy (see Methods, Table S3) and the resulting primers were validated against a panel of PTM + bacteria having diverse FtdB sequences (Fig S7 We found all tested group 1 strains produced highly similar PTM profiles (Fig 5A, EFG04254.1 was cloned to constitutive-expression vector pJMD3 and tested for its ability to rescue ftdF-dependent mass features in JV180 DftdADftdF (in parallel with a FtdF JV180 control). After analyzing the complemented strains (JV2997 and JV3010, respectively), we found both CYP450 genes were functional in restoring production of 1 However, this cannot completely explain the differences in product profiles; the B-3009 double mutant produces several other PTM-like mass features (18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30) to obtain these strains were Humic-acid Vitamin (HV), Arginine Glycerol-Salts(AGS),…”

Taxonomic Characterization, Antiviral Activity and Induction of Three New Kenalactams in Nocardiopsis sp. CG3

“…The amino acids are the origin of the secondary amine (-NH-) of the amide function within the macrolactam cycle [ 53 ] . The genes encoding macrolactam molecules, such as several secondary metabolites, are usually organized into cryptic genes and are regulated by an inducible operon [ 54 ].…”

Marine natural products

“…45 Two antibiotic dixiamycins 138 and 139 from Streptomyces olivaceus displayed activities against seven bacterial strains ranging from potent to no antibacterial activity. 46 Other Streptomyces strains yielded antaroide 140 , a new nine-membered macrolide that was shown to inhibit melanin biosynthesis in murine melanoma cells, 47 two antibacterial pyrrolobenzodiazepine derivatives 141 and 142 , 48 a new polycyclic tetramate macrolactam, koyanamide A 143 , 49 a new butenolide derivative 144 , featuring an octyl substitution at the γ-position, 50 two angucyclinone derivatives, gephyyamycin 145 and cysrabelomycin 146 , 51 and TMKS8A 147 , a new antibacterial chlorinated α-lapachone derivative, that was identified from the culture extract of a Streptomyces strain that was obtained from a sea slug. 52 Marinoterpins A–C 148 , 149 and 150 were isolated from the culture broth extracts of two actinomycetes associated with the family Streptomycetaceae and represent new chemical motifs as they combine quinoline- N -oxides with linear sesterterpenoid side chains.…”

“…two antibacterial pyrrolobenzodiazepine derivatives 141 and 142,48 a new polycyclic tetramate macrolactam, koyanamide A 143,49 a new butenolide derivative 144, featuring an octyl substitution at the g-position,50 two angucyclinone derivatives, gephyyamycin 145 and cysrabelomycin 146,51 and TMKS8A 147, a new antibacterial chlorinated a-lapachone derivative, that was identied from the culture extract of a Streptomyces strain that was obtained from a sea slug 52. Marinoterpins A-C 148, 149 and 150 were isolated from the culture broth extracts of two actinomycetes associated with the family Streptomycetaceae and represent new chemical motifs as they combine quinoline-N-oxides with linear sesterterpenoid side chains 53.…”