Novel bacterial metabolites via synthetic biology

Natural products from bacteria represent a rich source for the discovery of new drugs to treat various human diseases, including infections and cancer. However, in the recent decades efforts on finding novel bioactive natural products from bacteria using conventional screening faced a problem of frequent re-discovery of already known compounds. Recent developments in the fields of genomics, bio- and chemoinformatics, metabolic engineering, and synthetic biology opened completely new possibilities for drug discovery. Genomes of some bacteria were found to contain hundreds of genes for biosynthesis of natural products that are silent under laboratory conditions, but can be woken up to yield potentially novel bioactive compounds. Synthetic biology is a new scientific discipline that applies engineering principles in order to build de novo biological systems and organisms with pre-programmed features. SynBioBac project intends to address the challenge of waking silent natural product biosynthesis genes in bacteria by using synthetic biology principles and tools. This will be followed by purification and comprehensive characterization of novel compounds that may have a potential to be developed into human drugs for fighting infectious diseases and cancer. Correspondingly, the objectives of SynBioBac include cloning of selected biosynthesis genes, their re-engineering, development of tools for activation of these genes and biosensors for detection of produced secondary metabolites. The engineered genes will be expressed in well-characterized bacterial hosts, to allow easy purification and biological testing of novel natural products.

Bacteria-derived natural products represent a rich source for drug discovery, but many genes involved in the biosynthesis of such molecules are not expressed under laboratory conditions. The SynBioBac project was designed to unlock the potential of several actinomycete bacteria to produce novel natural products with potential medical applications using synthetic biology-inspired tools and approaches. The project's objectives included cloning of selected biosynthetic gene clusters and manipulating them with the aim of activating their expression and hence producing new natural products. To this end, several such gene clusters were cloned and subjected to manipulations using CRISPR/Cas9-based gene editing system. Introduction of native or engineered gene clusters into heterologous bacterial hosts resulted in production of several known as well as previously undescribed natural products. One of the new compounds of the meroterpenoid class displayed significant antibacterial activity while showing no cytotoxicity, suggesting that it may become a starting point for developing new antibiotics. Another project's achievement is identification of the previously undescribed genes responsible for the biosynthesis of anti-mycobacterial antibiotic acidomycin. Manipulation of one of such genes yielded new acidomycin derivatives which may prove useful in developing drugs against tuberculosis. The project's results also provided important new insights into natural product biosynthesis, which can be used in the future to engineer new bioactive molecules for drug discovery.