Genome Mining Coupled with OSMAC-Based Cultivation Reveal Differential Production of Surugamide A by the Marine Sponge Isolate Streptomyces sp. SM17 When Compared to Its Terrestrial Relative S. albidoflavus J1074

Abstract

Much recent interest has arisen in investigating Streptomyces isolates derived from the marine environment in the search for new bioactive compounds, particularly those found in association with marine invertebrates, such as sponges. Among these new compounds recently identified from marine Streptomyces isolates are the octapeptidic surugamides, which have been shown to possess anticancer and antifungal activities. By employing genome mining followed by an one strain many compounds (OSMAC)-based approach, we have identified the previously unreported capability of a marine sponge-derived isolate, namely Streptomyces sp. SM17, to produce surugamide A. Phylogenomics analyses provided novel insights on the distribution and conservation of the surugamides biosynthetic gene cluster (sur BGC) and suggested a closer relatedness between marine-derived sur BGCs than their terrestrially derived counterparts. Subsequent analysis showed differential production of surugamide A when comparing the closely related marine and terrestrial isolates, namely Streptomyces sp. SM17 and Streptomyces albidoflavus J1074. SM17 produced higher levels of surugamide A than S. albidoflavus J1074 under all conditions tested, and in particular producing >13-fold higher levels when grown in YD and 3-fold higher levels in SYP-NaCl medium. In addition, surugamide A production was repressed in TSB and YD medium, suggesting that carbon catabolite repression (CCR) may influence the production of surugamides in these strains.

Keywords: OSMAC; Streptomyces; albidoflavus phylogroup; genome mining; marine sponge-associated bacteria; phylogenomics; secondary metabolites; surugamide A; surugamides.

Figure 1

Phylogenetic tree of the concatenated sequences of the 16S rRNA and the housekeeping genes atpD, gyrB, recA, rpoB, and trpB, from the Streptomyces sp. SM17 together with 30 Streptomyces isolates for which complete genome sequences were available in the GenBank database. Analysis was performed using MrBayes, with a posterior probability cut-off of 95%. 1) albidoflavus phylogroup. 2) Clade including the neighbour isolate Streptomyces koyangensis strain VK-A60T. The strains SM17 and J1074 are indicated with asterisks.

Figure 2

Venn diagram representing the presence/absence of groups of orthologous genes in the organisms belonging to the albidoflavus phylogroup.

Figure 3

Biosynthetic gene clusters (BGCs) similarity clustering using BiG-SCAPE. Singletons, i.e., BGCs without significant similarity with the BGCs from the minimum information about a biosynthetic gene cluster (MiBIG) database or with the BGCs predicted in other genomes, are not represented.

Figure 4

Venn diagram representing BGCs presence/absence in the genomes of the members of the albidoflavus phylogroup, determined using antiSMASH and BiG-SCAPE.

Figure 5

Consensus phylogenetic tree of the sur BGC region of the S. albidoflavus LHW3101 reference sur BGC sequence, plus five Streptomyces isolates determined to have sur BGC homologs, generated using MrBayes and Mega X, with a 95% posterior probability cut-off. Aquatic saline environment-derived isolates are highlighted in cyan.

Figure 6

Gene synteny of the sur BGC region, including the reference sur BGC nucleotide sequence (LHW3101) and each of the albidoflavus phylogroup genomes. Arrows at different positions represent genes transcribed in different reading frames.

Figure 7

Structure of surugamide A isolated from SM17 grown in TSB, SYP-NaCl, and YD medium with annotated ¹H NMR spectrum obtained in CD₃OD at 500 MHz.