Genomic approaches to metabolite exploitation from Xenorhabdus/Photorhabdus
Keywords: drug discovery, bioprospecting, compound library, antibiotics, fungicide, MRSA, filariasis, multiple-target bioactivity testing, genome mining, Xenorhabdus, Photorhabdus, exploitation, IPR
The majority of compounds used to treat disease come from a single group of organisms, the actinomycetes. This over-reliance on a single organism to produce the world's drugs is a major problem for the development of compounds with alternative modes of action which can overcome and delay the onset of drug and parasite resistance. To address this problem we will form an international multi-disciplinary group of experts to bioprospect for biologically active natural products.
The central aim of GAMEXP is to start rapidly deriving novel drugs from non-actinomycete sources.
We will isolate novel strains of the proven but not well-explored drug producers Xenorhabdus and Photorhabdus. These bacteria will be isolated from insect pathogenic nematodes and characterized taxonomically and strains will be analyzed for the production of novel compounds. This library of compounds will then be tested against a broad set of targets including bacteria, fungi, protozoans, nematodes, insects, and mammalian cell cultures. The five most productive bacterial strains will then be fully sequenced and used to construct genomic libraries. These libraries will be used to generate recombinant clones in heterologous hosts, enabling fast and efficient biotechnological production of the bioactive compounds. To ensure efficient interactions and comparability of results, especially regarding the bioactivity data, training sessions will be organized with seminars and hands on experience for each of the groups at a central site. Robust patent structures will ensure efficient technology transfer to our industrial partners and overall coordination of the scientific and training programs will be overseen.
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Up to 80% of all compounds used in medicine are either natural products or compounds derived or inspired thereof. Although this sounds very positive, only a few pharmaceutical companies still isolate and develop natural products into drugs. Despite the fact that there are several reasons for doing so as a company (shareholder value, increasing costs, low market value of compounds), we desperately need new drugs to fight against neglected diseases or multiresistant bacteria/fungi/protozoa. Therefore the rationale behind GAMEXP is to use bacteria like Xenorhabdus/Photorhabdus as a source for bioactive natural products. Xenorhabdus/Photorhabdus are already known to be natural product producers (Figure 1) but only a few strains have been analyzed. Previous work regarding these bacteria was mostly centered around the insecticidal activity of these bacteria (Figure 2) and their symbiotic relationship with insect-pathogenic nematodes of the genus Heterorhabditis or Steinernema.
One aim of GAMEXP is the generation of a large strain collection of Xenorhabdus/Photorhabdus strains, which are underrepresented in public strain collections. These strains will be cultivated at a small scale and extracts of these cultures will be tested for bioactivity. The most active strains will be cultivated at a large scale for isolation of pure compounds which will again be tested. The central aim of GAMEXP will be to obtain 50-100 Xenorhabdus/Photorhabdus-specific compounds in quantities to allow broad testing. In parallel, the genome of those strains showing the production of the most promising compounds (with the best bioactivity), will be sequenced. Moreover, cosmid or BAC libraries will be constructed for the heterologous production of the interesting compounds. Additionally, these cosmid/BAC clones will be subjected to a screening program termed Rapid Virulence Annotation (RVA) which can also reveal genes involved in virulence not associated with the previously identified compounds. The key to this project will be the broad and parallel screening process using several different well established model systems (bacteria, fungi, protozoa, cell lines, nematodes, insects). This will result in a wealth of relevant information regarding the extracts or the pure compounds which can then be used to test interesting compounds directly against several neglected diseases related to our non-pathogenic model organisms.
Besides the generation of a Xenorhabdus/Photorhabdus strain collection and Xenorhabdus/Photorhabdus-specific compound library, the goal of this project is to connect a compound library with early data on the biological activity of the compounds and the biosynthesis gene clusters required for their biosynthesis. This would make the compound library much more interesting to pharmaceutical companies as it would already provide them with a wealth of information.
As the whole project is based on a screening program no direct applications can be proposed. Ideally, very interesting compounds against one or more of the target diseases will inspire the development of structurally related drugs that will make it into the clinic. As this usually is a very rare event which takes at least 10 years and requires large pharmaceutical companies as partners, the work conducted within GAMEXP should act as a catalyst to other groups working on natural products in order to fully explore the potential of Xenorhabdus/Photorhabdus bacteria. However, the compound library generated within this project should be accessed by interested partners (pharmaceutical or biotech companies) via the formation of a small biotech company after the duration of GAMEXP. Moreover, the compound library should be tested against plant pathogenic bacteria, fungi, nematodes, and insects as they are derived directly from a related environment. At the end, one or two compounds or derivatives thereof might not end up in the clinic but as a crop protectant and thereby benefit human life.