Metabolic and evolutionary origin of actin-binding polyketides from diverse organisms

The as-yet uncultured filamentous bacteria "Candidatus Entotheonella factor" and "Candidatus Entotheonella gemina" live associated with the marine sponge Theonella swinhoei Y, the source of numerous unusual bioactive natural products. Belonging to the proposed candidate phylum "Tectomicrobia," Candidatus Entotheonella members are only distantly related to any cultivated organism. The Ca. E. factor has been identified as the source of almost all polyketide and modified peptides families reported from the sponge host, and both Ca. Entotheonella phylotypes contain numerous additional genes for as-yet unknown metabolites. Here, we provide insights into the biology of these remarkable bacteria using genomic, (meta)proteomic, and chemical methods. The data suggest a metabolic model of Ca. Entotheonella as facultative anaerobic, organotrophic organisms with the ability to use methanol as an energy source. The symbionts appear to be auxotrophic for some vitamins, but have the potential to produce most amino acids as well as rare cofactors like coenzyme F 420 . The latter likely accounts for the strong autofluorescence of Ca. Entotheonella filaments. A large expansion of protein families involved in regulation and conversion of organic molecules indicates roles in host-bacterial interaction. In addition, a massive overrepresentation of members of the luciferase-like monooxygenase superfamily points toward an important role of these proteins in Ca. Entotheonella. Furthermore, we performed mass spectrometric imaging combined with fluorescence in situ hybridization to localize Ca. Entotheonella and some of the bioactive natural products in the sponge tissue. These metabolic insights into a new candidate phylum offer hints on the targeted cultivation of the chemically most prolific microorganisms known from microbial dark matter.

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“…distinct Japanese sponge T. swinhoei WA, is the producer of the actin-binding polyketide misakinolide (19). Additional Ca.…”

Section: Significancementioning

confidence: 99%

Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges

Lackner

Peters

Helfrich

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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126

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“…As a relevant contrast, several elegant studies show how closely related pathways diverge by swapping functional motifs (55)(56)(57)(58)(59). In these studies, the proteins are not as closely related to each other as those described here so that multiple mutations may be involved in creating functional swaps.…”

Section: Discussionmentioning

confidence: 75%

Origin of Chemical Diversity in Prochloron-Tunicate Symbiosis

Lin

Torres

Tianero

et al. 2016

Appl Environ Microbiol

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Diversity-generating metabolism leads to the evolution of many different chemicals in living organisms. Here, by examining a marine symbiosis, we provide a precise evolutionary model of how nature generates a family of novel chemicals, the cyanobactins. We show that tunicates and their symbiotic Prochloron cyanobacteria share congruent phylogenies, indicating that Prochloron phylogeny is related to host phylogeny and not to external habitat or geography. We observe that Prochloron exchanges discrete functional genetic modules for cyanobactin secondary metabolite biosynthesis in an otherwise conserved genetic background. The module exchange leads to gain or loss of discrete chemical functional groups. Because the underlying enzymes exhibit broad substrate tolerance, discrete exchange of substrates and enzymes between Prochloron strains leads to the rapid generation of chemical novelty. These results have implications in choosing biochemical pathways and enzymes for engineered or combinatorial biosynthesis. IMPORTANCEWhile most biosynthetic pathways lead to one or a few products, a subset of pathways are diversity generating and are capable of producing thousands to millions of derivatives. This property is highly useful in biotechnology since it enables biochemical or synthetic biological methods to create desired chemicals. A fundamental question has been how nature itself creates this chemical diversity. Here, by examining the symbiosis between coral reef animals and bacteria, we describe the genetic basis of chemical variation with unprecedented precision. New compounds from the cyanobactin family are created by either varying the substrate or importing needed enzymatic functions from other organisms or via both mechanisms. This natural process matches successful laboratory strategies to engineer the biosynthesis of new chemicals and teaches a new strategy to direct biosynthesis. S econdary metabolites are specialized molecules that are often directed outward at other organisms (1, 2). For example, under the sea, soft-bodied animals defend themselves using a diverse array of specialized chemicals, which are required for their survival (3, 4). Symbiotic bacteria, and not the host animal, synthesize many secondary metabolites (5), providing a link between symbiosis, chemistry, the survival of the animal and bacterial associates, and effects on predators and other organisms on coral reefs (6-8). The chemicals underlying these interactions are structurally diverse, comprising families of related compounds that are useful in drug discovery. Slight changes to chemical structure can drastically alter function, yet many marine natural products families are extremely diverse. Compounds such as marine animal defensive chemicals are critical to interactions between organisms (3) so that structural changes have consequences that potentially ripple through the environment. An open question has been, given these many constraints, how can chemical diversity arise?The evolution of novel chemistry likely relies in part...

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“…17 In this sponge, 'Entotheonella serta' TSWA1 is the source of the homodimeric polyketide actin inhibitor misakinolide A. 18 Here, using an enriched 'Entotheonella' cell fraction prepared from T. swinhoei WA, PCR analysis with primers specific for adenylation (A) domain-encoding regions of nonribosomal peptide synthetase (NRPS) genes revealed the presence of homologous genes. These were closely related to those of the keramamide (ker) biosynthetic genes previously identified in 'E.…”

Section: Resultsmentioning

confidence: 99%

“…In another study of the WA chemotype, the polyketide misakinolide A was assigned to the symbiont 'E. serta' TSWA1 by single-cell genome sequencing; 18 however, analysis of that sequence data did not reveal the presence of keramamide genes, suggesting that these compounds are likely to be produced by either a different 'Entotheonella' phylotype or another symbiotic bacterium found in the sponge.…”

Section: Discussionmentioning

confidence: 99%

An Unusual Flavin-Dependent Halogenase from the Metagenome of the Marine Sponge Theonella swinhoei WA

et al. 2017

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Metabolic and evolutionary origin of actin-binding polyketides from diverse organisms

Cited by 119 publications

References 59 publications

Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges

Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges

Origin of Chemical Diversity in Prochloron-Tunicate Symbiosis

An Unusual Flavin-Dependent Halogenase from the Metagenome of the Marine Sponge Theonella swinhoei WA

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