Calyculin biogenesis from a pyrophosphate protoxin produced by a sponge symbiont

Wakimoto, Toshiyuki; Egami, Yoko; Nakashima, Yu; Wakimoto, Yukihiko; Mori, Takeo; Awakawa, Takayoshi; Ito, Takuya; Kenmoku, Hiromichi; Asakawa, Yoshinori; Piel, Jörn; Abe, Ikuro

doi:10.1038/nchembio.1573

Cited by 117 publications

(154 citation statements)

References 58 publications

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“…Additional Ca. Entotheonella variants were also detected by PCR in a wide range of other sponge species (15) and were connected to natural product biosynthesis in the sponge Discodermia calyx (20,21). These data and the previous Ca.…”

Section: Significancesupporting

confidence: 68%

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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124

126

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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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Section: Significancesupporting

confidence: 68%

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.

Self Cite

124

126

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“…A previously unknown ECH and an adjacent ACP were found in a separate locus (bryTU), and these are predicted to act in the dehydration of the new side chain and as a carrier for the malonate ␤-branch, respectively. These genes are homologous to corresponding genes in other trans-AT PKS pathways, with the closest homologs to bryT and bryU being batD (batumin/kalimantacin pathway [51], 53% amino acid identity) and calX (calyculin pathway [52], 45% amino acid identity), respectively. Interestingly, all bry mRNA transcripts were detected through metatranscriptomics, except bryS, a methyltransferase previously thought to carry out the O-methylation of ␤-branches (6).…”

Section: Photorhabdus/ Xenorhabdusmentioning

confidence: 99%

Lack of Overt Genome Reduction in the Bryostatin-Producing Bryozoan Symbiont “Candidatus Endobugula sertula”

Miller

Vanee

Fong

et al. 2016

Appl Environ Microbiol

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The uncultured bacterial symbiont "Candidatus Endobugula sertula" is known to produce cytotoxic compounds called bryostatins, which protect the larvae of its host, Bugula neritina. The symbiont has never been successfully cultured, and it was thought that its genome might be significantly reduced. Here, we took a shotgun metagenomics and metatranscriptomics approach to assemble and characterize the genome of "Ca. Endobugula sertula." We found that it had specific metabolic deficiencies in the biosynthesis of certain amino acids but few other signs of genome degradation, such as small size, abundant pseudogenes, and low coding density. We also identified homologs to genes associated with insect pathogenesis in other gammaproteobacteria, and these genes may be involved in host-symbiont interactions and vertical transmission. Metatranscriptomics revealed that these genes were highly expressed in a reproductive host, along with bry genes for the biosynthesis of bryostatins. We identified two new putative bry genes fragmented from the main bry operon, accounting for previously missing enzymatic functions in the pathway. We also determined that a gene previously assigned to the pathway, bryS, is not expressed in reproductive tissue, suggesting that it is not involved in the production of bryostatins. Our findings suggest that "Ca. Endobugula sertula" may be able to live outside the host if its metabolic deficiencies are alleviated by medium components, which is consistent with recent findings that it may be possible for "Ca. Endobugula sertula" to be transmitted horizontally. IMPORTANCEThe bryostatins are potent protein kinase C activators that have been evaluated in clinical trials for a number of indications, including cancer and Alzheimer's disease. There is, therefore, considerable interest in securing a renewable supply of these compounds, which is currently only possible through aquaculture of Bugula neritina and total chemical synthesis. However, these approaches are labor-intensive and low-yielding and thus preclude the use of bryostatins as a viable therapeutic agent. Our genome assembly and transcriptome analysis for "Ca. Endobugula sertula" shed light on the metabolism of this symbiont, potentially aiding isolation and culturing efforts. Our identification of additional bry genes may also facilitate efforts to express the complete pathway heterologously. Marine invertebrates, such as tunicates and sponges, are known to harbor symbiotic communities of bacteria. Because these animals are sessile and have limited physical defenses, their microbiomes are thought to serve defensive functions, and bacterial symbionts in these invertebrates have been implicated in the production of many bioactive small molecules (1, 2). Such small molecules can possess therapeutically relevant activities, so there is great interest in studying the biosynthetic potential and symbiotic functions of these defensive microorganisms (1, 2). However, most symbionts (and most environmental bacteria in general [1,3,4]) are difficul...

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“…It should be emphasized that not only were the compounds produced, but they were in fact ribosomal products that were then tailored by a novel series of enzymes expressed by the same microbe, not as previously thought to be produced by non-ribosomal protein synthesis. Interestingly the protein phosphatase inhibitor calyculin A (18) was also produced by this sponge, with data now published by Wakimoto et al 42 demonstrating that it too was a product of the same uncultivated microbe.…”

Section: Brazilian Paederus Beetles and Marine Sponge Metabolitesmentioning

confidence: 57%

The Influence of Brazilian Biodiversity on Searching for Human Use Pharmaceuticals

Newman¹

2016

J. Braz. Chem. Soc.

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This relatively short review will cover the history of some potential drug entities whose beginnings were from Brazilian flora and fauna that led to scientific findings many years later that could not even have been thought of at the time of their initial discovery. The first two are the discoveries of the effects of peptidic toxins from the highly poisonous snake Bothrops jararaca upon the control of bradykinins that led to the angiotensin converting enzyme inhibitors, and the identification of pederin from the blister beetle Paederus species that 50 plus years later led to brand new discoveries as the source of many marine sponge metabolites. All occurred well before the Convention on Biological Diversity (CBD), in 1992. Then come discussions on lapachol and its congeners and then the potential for the investigation of microbes that are associated with insects, plants and marine invertebrates and their control of the syntheses of novel metabolites with pharmaceutical potential. The review finishes with comments on the biodiversity programs that São Paulo State has put in place and how they are materially aiding in investigations of Brazilian flora and fauna but under conditions that are CBD-compliant.

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Calyculin biogenesis from a pyrophosphate protoxin produced by a sponge symbiont

Cited by 117 publications

References 58 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

Lack of Overt Genome Reduction in the Bryostatin-Producing Bryozoan Symbiont “Candidatus Endobugula sertula”

The Influence of Brazilian Biodiversity on Searching for Human Use Pharmaceuticals

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