Genomics approaches to exploit the biotechnological potential of marine sponge-derived Streptomyces spp. isolates

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Almeida, Eduardo L.
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Members of the Streptomyces genus are widely known for their capability in producing compounds of pharmacological, clinical, and biotechnological interest, being the source of approximately a third of all the antibiotics that have been identified to date. However, the discovery of natural products with antimicrobial activities has declined following the so-called “Golden Age of Antibiotics” (1940s-1950s), particularly due to the common re-discovery of previously known compounds. Thus, natural products discovery research has shifted towards investigating diverse environmental niches, such as marine ecosystems, mangroves, and symbiotic communities of insects and sponges, resulting in the discovery of a variety of previously unidentified compounds of pharmacological interest; including those isolated from marine-derived Streptomyces species. However, in despite of their relevance as producers of potentially novel bio-active molecules with pharmacological, clinical and biotechnological interest, marine-derived Streptomyces isolates are still rather underexplored and under-characterized, particularly those found in association with marine sponges. In the studies presented in this thesis, various state-of-the-art methodologies related to genome mining and bioinformatics-based pipelines, together with molecular and synthetic biology, were employed and proved to be extremely useful in helping to uncover the biotechnological potential of marine sponge-derived Streptomyces isolates. These studies essentially aimed at a) genetically characterizing marine sponge-derived Streptomyces spp. isolates and their potential to produce novel secondary metabolites, as shown in Chapter 2; b) to in silico identify, isolate, and quantify a secondary metabolite produced by a marine sponge-derived Streptomyces isolate, together with genetically characterizing its genome-encoded biosynthetic gene cluster (BGC), as reported in Chapter 3; and c) to perform an in silico screening of a novel polyesterase from a marine sponge-derived Streptomyces isolate, followed by heterologous protein expression in an E. coli host, as demonstrated in Chapter 4. In Chapter 2, two of the first complete genomes from marine sponge-derived Streptomyces spp. isolates were determined, namely from Streptomyces sp. SM17 and Streptomyces sp. SM18. The high-quality data provided in this study allowed for a reliable prediction of secondary metabolites biosynthetic gene clusters (BGCs) in their genomes, which determined that these isolates possess a variety of BGCs potentially encoding for the production of known compounds, and also potentially new molecules. Differential growth assessment determined that the marine isolates SM17 and SM18 grew and differentiated better in the presence of salts in the culture medium, when compared to their phylogenetically determined closely-related terrestrial relatives, namely S. albidoflavus J1074 (referred to as S. albus J1074 in Chapter 2) and S. pratensis ATCC 33331, respectively. Comparative genomics allowed for the identification of a proposed environmental niche adaptations (ENA) gene pool, which included genes related to osmotic stress defence, transcriptional regulation; symbiotic interactions; antimicrobial compound production and resistance; ABC transporters; together with horizontal gene transfer and defence-related features. These results shed new light on some of the genetic traits possessed by these marine sponge-derived isolates, and on how these might be linked to secondary metabolites production, and further highlighted their importance for the discovery of potentially novel natural products. In Chapter 3, the previously unreported capability of the Streptomyces sp. SM17 to produce surugamides has been described. Surugamides are a family of compounds that have been previously reported to possess antitumor and antifungal activities. This was performed employing genome mining, which allowed for the identification of the surugamides BGC (sur BGC) in the SM17 genome, and analytical chemistry techniques for compound isolation and quantification. Phylogenomics analyses provided novel insights with respect to the distribution and conservation of the sur BGC at a genetic level, and provided evidence that the sur BGC might have had a marine origin. Additionally, when comparing the surugamide A production capabilities of a marine isolate (strain SM17) with a terrestrial relative (strain J1074) employing a “One Strain Many Compounds” (OSMAC)-based cultivation approach, the Streptomyces sp. SM17 isolate was shown to produce higher levels of surugamide A in all the conditions tested for. These findings may provide important insights towards a better characterisation, improved production and industrial development of this family of compounds. In Chapter 4, the capability of marine sponge-derived Streptomyces spp. isolates to degrade synthetic polyesters was investigated. This was based on the fact that these microorganisms might have developed mechanisms to assimilate components of micro-plastics, which are now believed to be ubiquitous in marine ecosystems and pose as one of the top environmental problems that society faces today. Using 15 known PET hydrolases (PETases) as references, including the Ideonella sakaiensis 201-F6 PETase, in silico screening was performed to determine the presence of homologs to these reference PETase enzymes in 52 Streptomyces genome sequences (of which 29 were derived from marine ecosystems). The best candidate identified, namely the SM14est protein from the marine sponge-derived Streptomyces sp. SM14, was in silico characterised with respect to its amino acid sequence and predicted three dimensional structure, and was subsequently heterologously expressed in an E. coli host. This allowed for the confirmation of the polyesterase activity possessed by the SM14est enzyme, via a polycaprolactone (PCL) plate-clearing assay. Better characterising, identifying sources, and determining methods for improved protein expression are essential steps towards the development of biotechnological applications and industrial processes employing this family of enzymes, such as new plastic waste processing technologies.
Streptomyces , Microbiology , Biotechnology , Bioinformatics , Genetics , Genomics , Plastics , Polycaprolactone , PETases , Marine Streptomyces , Genome sequencing , Comparative genomics , Natural products , Secondary metabolites , Plastics degradation , Synthetic polyesters , Heterologous expression , Marine bacteria , Marine sponges , Marine microbiology , Marine biotechnology
Almeida, E. L. 2019. Genomics approaches to exploit the biotechnological potential of marine sponge-derived Streptomyces spp. isolates. PhD Thesis, University College Cork.
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