Discovery of novel antibiotics from actinomycetes by integrated metabolomics & genomics approaches

Wu, Changsheng (2016)

Doctoral Thesis

 

The explosive increase in infections by pathogens is a major problem in the clinic today. The theme of this thesis was to find novel antibiotics from actinomycetes. Next-generation sequencing revealed that the biosynthetic potential of actinomycetes had been grossly underestimated. In this thesis, different antibiotics-eliciting strategies, including microbial cocultivation, streptomycin-resistant mutation, overexpression of pathway-specific activator, variation of culture conditions, were utilized to enforce fluctuations in the production of bioactive compounds in actinomycetes, after which, NMR-based metabolic profiling was used to facilitate uncovering those elicited molecules. This pipeline allowed the discovery of new antibiotics involving various chemical skeletons, such as 7-prenylisatin, methoxylated isocoumarins, endophenazines, and C-glycosylpyranonaphthoquinones. On the other hand, genome-mining methodology enabled the discovery of a group of endophenasides and leucanicidin in Kitasatospora sp. MBT66, whereby the rhamnosylation of both scaffold are executed by a same promiscuous glycosyltransferase. Last but not least, a novel antibiotic termed lugdunomycin with unprecedented chemical scaffold, as well as a number of new angucycline-type antibiotics, were characterized from Streptomyces sp. QL37. The biosynthetic pathway of lugdunomycin was deciphered by genetic knockout and OSMAC (One Strain MAny Compound) strategy. In summary, this thesis explores an interface of genomics and metabolomics to accelerate new antibiotics discovery.

 

• Antibiotics
• Actinomycetes
• NMR
• Metabolomics
• Genomics
• Biosynthesis
• Biotransformation
• Lugdunomycin
• Gene cluster

• All authors: Wu, Changsheng
• Supervisor: Wezel, G.P. van
• Co-supervisor: Choi, Y.H.
• Committee: Spaink, H.P.; Hooykaas, P.J.J.; Overkleeft, H.S.; Piel, J.; Kuipers, O.P.
• Qualification: Doctor (dr.)
• Awarding Institution: Institute of Biology (IBL), Science, Leiden University
• Date: 2016-10-26
• Sponsorship: China Scholarship Council