Abstract
Streptomyces are a genus of Actinobacteria capable of producing structurally diverse natural products. Here we report the isolation and characterization of a biosynthetically talented Streptomyces (Streptomyces sp. SD85) from tropical mangrove sediments. Whole-genome sequencing revealed that Streptomyces sp. SD85 harbors at least 52 biosynthetic gene clusters (BGCs), which constitute 21.2% of the 8.6-Mb genome. When cultivated under lab conditions, Streptomyces sp. SD85 produces sceliphrolactam, a 26-membered polyene macrolactam with unknown biosynthetic origin. Genome mining yielded a putative sceliphrolactam BGC (sce) that encodes a type I modular polyketide synthase (PKS) system, several β-amino acid starter biosynthetic enzymes, transporters, and transcriptional regulators. Using the CRISPR/Cas9–based gene knockout method, we demonstrated that the sce BGC is essential for sceliphrolactam biosynthesis. Unexpectedly, the PKS system encoded by sce is short of one module required for assembling the 26-membered macrolactam skeleton according to the collinearity rule. With experimental data disfavoring the involvement of a trans-PKS module, the biosynthesis of sceliphrolactam seems to be best rationalized by invoking a mechanism whereby the PKS system employs an iterative module to catalyze two successive chain extensions with different outcomes. The potential violation of the collinearity rule makes the mechanism distinct from those of other polyene macrolactams.
Highlights
Actinobacteria are a phylum of Gram-positive bacteria renowned for the capability to produce secondary metabolites
SD85 is one of the Actinobacteria strains that we isolated from sediment samples collected from the mangrove forest of Sungei Buloh Wetland Reserve, Singapore
The structure for one of the “unknown” compounds was established using HRMS and NMR spectroscopy (Figs S4–S10, Table S1). This compound, which was isolated from the mycelium, turned out to be sceliphrolactam (m/z = 482.2532 [M + H]+, calcd for C28H35NO6, 482.2542 [M + H]+), which is a 3-amino-2-methylpropionate-containing polyene macrolactam that was isolated recently from a wasp-associated Streptomyces strain[11]
Summary
Zhen Jie Low[1], Li Mei Pang[1], Yichen Ding[3,2], Qing Wei Cheang[1], Kim Le Mai Hoang[5], Hoa Thi Tran[1], Jinming Li6, Xue-Wei Liu5,Yoganathan Kanagasundaram[4], LiangYang 1,3 & Zhao-Xun Liang 1. Accumulating genomic sequencing data reveals that even some of the best-studied Actinobacteria strains harbor many cryptic secondary biosynthetic gene clusters[1,2]. There is a structurally distinct group of macrolactams containing a polyene skeleton and a nitrogen-containing moiety derived from L-glutamate via a β-amino acid starter unit (Fig. 1). Genome sequencing and gene inactivation experiments allowed us to identify the putative sceliphrolactam BGC to reveal the enzymes involved in the synthesis of the macrolactam scaffold and starter moiety, and a potentially iterative mechanism in the biosynthesis of the macrolactam polyene scaffold
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