Single-bacterial genomics validates rich and varied specialized metabolism of uncultivated Entotheonella sponge symbionts

Abstract

Marine sponges are prolific sources of unique bioactive natural products. The sponge is represented by several distinct variants with largely nonoverlapping chemistry. For the Japanese chemotype Y harboring diverse complex polyketides and peptides, we previously provided genomic and functional evidence that a single symbiont, the filamentous, multicellular organism " Entotheonella factor," produces almost all of these compounds. To obtain further insights into the chemistry of "Entotheonella," we investigated another phylotype, " Entotheonella serta," present in the WA sponge chemotype, a source of theonellamide- and misakinolide-type compounds. Unexpectedly, considering the lower chemical diversity, sequencing of individual bacterial filaments revealed an even larger number of biosynthetic gene regions than for E. factor, with virtually no overlap. These included genes for misakinolide and theonellamide biosynthesis, the latter assigned by comparative genomic and metabolic analysis of a chemotype from Israel, and by biochemical studies. The data suggest that both compound families, which were among the earliest model substances to study bacterial producers in sponges, originate from the same bacterium in WA. They also add evidence that metabolic richness and variability could be a more general feature of Entotheonella symbionts.

Characterization of an Orphan Type III Polyketide Synthase Conserved in Uncultivated “Entotheonella” Sponge Symbionts

“…In contrast, the symbiont “ Ca . Entotheonella serta” is a source of natural products in chemically distinct sponges T. swinhoei WA and WB (white interior) –. It is likely that many natural products of “Entotheonella” are involved in host defense, which is a role often suspected or shown for toxic compounds of sessile invertebrates …”

“…The “Entotheonella” genomes known to date contain large sets of orphan biosynthetic gene clusters (BGCs) that are mostly unique to one particular “Entotheonella” variant and lack characterized products –. Herein, we examine the BGCs that are conserved among “Entotheonella” and might contribute functions of broader importance to these poorly understood symbionts .…”

Chemical Ecology of Marine Sponges: New Opportunities through “-Omics”

“…As previously discussed, marine sponges harbor complex microbiomes that are being cataloged on a global scale (Thomas et al 2016;Moitinho-Silva et al 2017a). Many sponge-derived natural products are now known to be biosynthesized by spongeassociated microorganisms (Wilson et al 2014;Ueoka et al 2015;Agarwal et al 2017;Mori et al 2018;Morita and Schmidt 2018), with prominent examples discussed below. The biosynthetic capacity of these oftentimes uncultivable members of the sponge microbiome can be revealed by metagenomic and single-cell DNA sequencing.…”

“…2). These filaments were originally thought to be d-proteobacteria (Bewley et al 1996;Schmidt et al 1998Schmidt et al , 2000, but cell sorting, multiple displacement amplification of genomic DNA from individual cells, and DNA sequencing supported their placement into the independent candidate phylum "Tectomicrobia"; their phylogenetic status has been further refined as more member genomes are assembled from sponge microbiomes (Wilson et al 2014;Lackner et al 2017;Mori et al 2018). Prominent examples of natural products for which the biosynthetic genes have been determined include the extensively modified, ribosomally synthesized peptidic polytheonamides (Freeman et al 2012(Freeman et al , 2016, and the polyketide onnamides (Piel et al 2004), among several other natural products (Wilson et al 2014).…”

“From Large-Scale Collections to the Potential Use of Genomic Techniques for Supply of Drug Candidates”

“…The aim then would be to have these genetic elements expressed in heterologous hosts, but to date, this has not been reported. However, the following papers, all from the Piel group (from 2013 to 2018) give an idea of where this field may be headed in the near future (Wilson and Piel, 2013;Freeman et al, 2016Freeman et al, , 2017Mori et al, 2018;Morinaka et al, 2018).…”