Genetics & Chemistry Unite: Natural Products Biosynthesis
Natural products are small molecules synthesized by bacteria, plants, fungi, and other organisms - examples are penicillins, lovastatin, quinine, and many others, targeting many disease states. Only a small minority of natural products have been characterized, and many discoveries will be made through the marriage of genetic and chemical technologies. The goal of our lab is to understand the roles and origins of natural product diversity and to use this understanding for the genetic engineering and discovery of new molecules with therapeutic potential.
The blue animal above is the marine sponge, Reniera sp. It is being eaten by a nudibranch (sea slug; white with black rings). Both the sponge and the slug that eat it contain chemicals exemplified by renieramycins (above). Making this chemical story even more complicated, it's possible that the compounds are made by bacteria living symbiotically with the sponge.
In our lab, we examine how natural products are made at the genetic and biochemical levels. By finding genes for the biosynthesis of bioactive compounds, we are able to use genetic engineering to synthesize new chemicals. As scientists studying biosynthesis learn more about how natural products are made, we will increasingly be able to make any designer molecule using genetics, swapping and manipulating genes in laboratory bacteria.
We are particularly interested in two types of organisms: marine invertebrate animals (sponges, ascidians, and others) and filamentous fungi. Both groups are famous for their production of natural products with pharmaceutical potential, and both are relatively understudied in comparison to bacteria.
This research area advances fundamental science and also provides practical outcomes. A good example of a "basic science" project with direct application to drug discovery is described below.
The Symbiosis Story: Marine Natural Products
Sponges, ascidians, and other marine animals harbor numerous bacteria that are suspected to synthesize the natural products isolated from these animals. Many of these bacterial associations are very specific to individual animal species, while some appear less specific and may even be quite casual. If bacteria make the compounds, genes for the biosynthesis can be cloned and expressed in bacteria. This technology will allow unique marine natural products to be developed into drugs and will bring the biochemical wealth of invertebrates into laboratory systems for genetic manipulation. It is also environmentally important, since bacterial symbiosis adds another depth to the complexity of marine ecosystems.
Our major effor involves the model symbiosis between the ascidian, Lissoclinum patella, and cyanobacteria, Prochloron didemni. These organisms live together throughout the tropical Pacific, and L. patella is well known among chemists because it contains unique cyclic peptides.
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| The ascidian, Lissoclinum patella; the green is a pure culture of Prochloron |
A single cell of Prochloron, which belongs to the cyanobacteria |
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| L. patella contains this cyclic peptide, which we traced to Prochloron using genetics |
There are many other related ascidian- Prochloron symbioses, including this one |
In collaboration with several researchers (links), we are sequencing the genome of P. didemni. From the draft sequence, we identified the first complete gene cluster for a marine invertebrate natural product and transferred this cluster to the laboratory bacterium, Escherichia coli. We are now modifying the genes to make new natural products and discovering new biosynthetic pathways from new ascidian symbioses. Of biological importance, we are annotating the Prochloron genome and completing a comparative analysis of symbiont-host taxonomy vs. natural product potential.
To obtain these organisms, we perform field studies in Palau, Papua New Guinea, the Red Sea, and elsewhere.
Tales of Fungi: Genes and Tools for Fungal Biosynthetic Studies
Filamentous fungi make numerous, bioactive natural products, yet in comparison to bacteria their biosynthetic pathways are relatively uncharacterized. Fungal genomes that have been sequenced often harbor many biosynthetic pathways (~40 or more), yet only a small fraction of these produce known natural products. These fungal genomes represent just a tiny fraction of the available biosynthetic diversity, since the vast majority of fungi have not even been cultured yet.
It is the goal of our lab to provide tools and data to better understand fungal biosynthetic pathways. With this increased knowledge, fungal natural product structures could be predicted from gene sequences, genes could be more rationally manipulated, and new genes from the environment could be more readily discovered. We are working with a model system, the filamentous fungus Fusarium heterosporum, which produces >2 g per L of the toxin, equisetin.
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| The filamentous fungus, Fusarium heterosporum, in culture |
Equisetin, produced by F. heterosporum, is a hybrid peptide-polyketide |
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| Light micrograph of hyphae of F. heterosporum from liquid culture |
Light micrograph of protoplasts of F. heterosporum. |
We have been working with equisetin synthetase, a hybrid polyketide synthase-nonribosomal peptide synthetase from F. heterosporum. What makes this enzyme unique in comparison to bacterial relatives is that the polyketide synthase works iteratively, while the peptide synthetase is modular. We are currently exploiting this property in the development of general tools for fungal natural product manipulation. We are also exploring the enzymology of the system and using it as a platform for natural product discovery.
