Filamentous Actinobacteria, such as Streptomyces, produce a plethora of chemically diverse bioactive metabolites that have found applications across medicine, agriculture and biotechnology. Yet,... Show moreFilamentous Actinobacteria, such as Streptomyces, produce a plethora of chemically diverse bioactive metabolites that have found applications across medicine, agriculture and biotechnology. Yet, the vast majority of the biosynthetic potential of Actinobacteria remains uncharacterised, largely because their biosynthetic gene clusters (BGCs) are poorly expressed in the laboratory, preventing the discovery of the cognate natural products. Additionally, only a narrow band of environments and a few taxonomic groups have been explored for gifted Actinobacteria. In this thesis different approaches are described, wherein we combined drug discovery with ecology, aimed at accessing the full potential of Actinobacteria. Bioactive Actinobacteria were isolated from a faecal sample of a 28,000-year-old-mammoth and their taxonomic and metabolic diversity was analysed. Furthermore, the effect of human stress hormones on the production of antibiotics by Streptomyces was investigated, resulting in the discovery of adrenaline as elicitor of siderophore production. This was later shown to be caused by the adrenaline analog catechol, which is ubiquitous in nature. Catechol also elicited the production of angucycline glycosides, well known for their therapeutic potential as anticancer and antibiotic compounds. Lastly, zebrafish were used as an in vivo model to explore the bioactive and functional potential of Actinobacteria within the animal microbiome. Show less
Streptomyces are filamentous bacteria that produce more than two-thirds of known antibiotics. Due to their multicellular lifestyle as well as their prolific production of secondary metabolites, Str...Show moreStreptomyces are filamentous bacteria that produce more than two-thirds of known antibiotics. Due to their multicellular lifestyle as well as their prolific production of secondary metabolites, Streptomyces are of unique fundamental and applied importance. However, Streptomyces have unstable genomes, an attribute that can cause genomic rearrangements and dramatically alter their phenotype. Previous studies have failed to explain this phenomenon. In this dissertation, we investigate the evolutionary functions and mechanisms of genomic instability in Streptomyces coelicolor. We first find that a subpopulation of cells generated through large genomic rearrangements becomes specialized to produce antibiotics. This results in a division of labor which benefits the entire colony, while the yield and diversity of antibiotics are maximized, despite significant fitness costs to this altruistic subpopulation. Next, we show that these altruistic mutants continue to lose fitness due to the irreversible accumulation of large deletions and deleterious mutations, coupled to an increased mutation rate. Finally, we explore the molecular consequences of large genomic rearrangements for development and antibiotic production using detailed proteomics and metabolomics analyses, which highlight key pathways that are impacted by these genomic events. Overall, this dissertation provides new insights of genomic instability in Streptomyces. Show less
Actinobacteria are Gram-positive bacteria that have a complex multicellular life cycle and are well known for their ability to produce a wide range of bioactive natural products (NPs). High... Show moreActinobacteria are Gram-positive bacteria that have a complex multicellular life cycle and are well known for their ability to produce a wide range of bioactive natural products (NPs). High throughput screening has failed to deliver the new antibiotics we so desperately need to combat multidrug-resistant pathogens. Therefore, new systematic approaches are needed to further explore the rich potential of Actinobacteria. The work described in this thesis entails systems biology approaches consisting of technologies such as proteomics, genomics, metabolomics and DNA binding studies. These were then applied to identify the biosynthetic gene clusters (BGCs) that are responsible for the production of novel antibiotics. Small molecules were thereby used as elicitors to activate the expression of cryptic BGCs in Streptomyces roseifaciens. Furthermore, S. coelicolor M1152 that was optimized for heterologous expression of antibiotics, was analysed for changes in protein expression, to understand which changes correlate to optimal antibiotic production. Finally, the role of the nucleoid associated protein SCO1839 in development and antibiotic production was studied. Chip-seq technology showed that it binds to thousands of DNA sequences on the S. coelicolor chromosome, which contain the motif GATC. I hope that this thesis contributes to utilizing multi-dimensional ‘omics approaches to answer major biological questions. Show less
Plants are colonized by an astounding number of microorganisms that can provide different life-support functions, including nutrient acquisition and protection against (a)biotic stresses like... Show morePlants are colonized by an astounding number of microorganisms that can provide different life-support functions, including nutrient acquisition and protection against (a)biotic stresses like drought or pathogen attack Here, the diversity of bacteria living inside plant root tissue was explored with a focus on Actinobacteria, and in particular Streptomyces. Streptomycetes are filamentous bacteria that are commonly found in soil. They were brought into the laboratory for their ability to produce a large diversity of natural products, including many different antibiotics. In plant-associated environments, Streptomyces can be found in the rhizosphere, the endosphere and the phyllosphere. In these niches, they receive nutrients from the plants, feasting on various biopolymers and exudates. In return, the plant may benefit from their presence by enhanced nutrient acquisition, pathogen antagonism and induced systemic resistance To date, however, plant-Streptomyces interactions are not well understood and the mechanisms underlying plant colonization and invasion by Streptomyces remain largely elusive. Also, the chemistry of plant-Streptomyces interactions is yet underexplored, leaving us with a reservoir of untapped natural products that may contribute to solving the problem of emerging antibiotic resistance. Therefore, this research was focused on the aforementioned topics. Show less
