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Investigating the Antimicrobial Potential of Thalassomonas

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Investigating the Antimicrobial Potential of Thalassomonas Investigating the antimicrobial potential of Thalassomonas actiniarum By Fazlin Pheiffer A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) Department of Biotechnology, University of the Western Cape Supervisor: Prof Marla Trindade Co-supervisor: Dr Leonardo van Zyl 2020 http://etd.uwc.ac.za/ Declaration Declaration I, Fazlin Pheiffer, hereby declare that ‘Investigating the antimicrobial potential of Thalassomonas actiniarum’ is my own work, that it has not been submitted for any degree or examination in any other university, and that all the sources I have used or quoted have been indicated and acknowledged by complete references. Date: 16 March 2021 Signed: i http://etd.uwc.ac.za/ Abstract Abstract The World Health Organisation predicts that by the year 2050, 10 million people could die annually as a result of infections caused by multidrug resistant bacteria. Individuals with compromised immune systems, caused by underlying disease such as HIV, MTB and COVID-19, are at a greater risk. Antibacterial resistance is a global concern that demands the discovery of novel drugs. Natural products, used since ancient times to treat diseases, are the most successful source of new drug candidates with bioactivities including antibiotic, antifungal, anticancer, antiviral, immunosuppressive, anti-inflammatory and biofilm inhibition. Marine bioprospecting has contributed significantly to the discovery of novel bioactive NPs with unique structures and biological activities, superior to that of compounds from terrestrial origin. Marine invertebrate symbionts are particularly promising sources of marine NPs as the competition between microorganisms associated with invertebrates for space and nutrients is the driving force behind the production of antibiotics, which also constitute pharmaceutically relevant natural products. In this study, the sea anemone-associated marine bacterium T. actiniarum was investigated for antibacterial activity against 4 indicator strains. Antibacterial activity was observed from a compound in the molecular size range 50kDa-100kDa against all indicator strains. Notably, the bioactivity profile and estimated molecular size of the active compound was similar to TVP1, a putative prophage-encoded hypothetical protein with lytic activity produced by T. viridans, the closest relative of T. actiniarum. The T. actiniarum homologue, TAP1 showed 78.14% similarity to TVP1, leading to the hypothesis that the strains produce a similar antibacterial protein. Therefore, the initial aim of this study was to heterologously express the putative prophage- encoded hypothetical proteins TVP1 and TAP1 and assess their antibacterial activity. Following expression of the proteins and subsequent antibacterial assays, neither TVP1 nor TAP1 showed antibacterial activity suggesting that these proteins were likely mis-identified as being responsible for the observed bioactivity from these two strains. Furthermore, transmission electron microscopy revealed that T. actiniarum produces particles that resemble tailocins, observed in a fraction containing compounds in the molecular size range >100kDa. Although not the focus of this study, investigating the antibacterial activity of these particles may further demonstrate the expansive bioactive potential of this strain. ii http://etd.uwc.ac.za/ Abstract A bioassay guided isolation approach was then used to isolate the high molecular weight antibacterial compound (50kDa-100kDa) from T. actiniarum fermentations. With common protein isolation, purification and detection methods failing to provide insight into the nature of the antibacterial compound, we hypothesized that the active agent is not proteinaceous in nature and may be a high molecular weight exopolysaccharide. Extraction and antibacterial screening of the exopolysaccharide fraction from T. actiniarum showed antibacterial activity as well as lytic activity when subjected to a zymography assay using Pseudomonas putida whole cells as a substrate. Additionally, the biosynthetic pathways for the production of poly-β-1, 6-N-acetyl- glucosamine (PNAG), an exopolysaccharide involved in biofilm formation and chondroitin sulfate, a known and industrially important glycosaminoglycan with antibacterial and anti- inflammatory activity was identified and the mechanism may be novel. Genome mining identified a variety of novel secondary metabolite gene clusters which could potentially encode other novel bioactivities. Therefore a bioassay guided isolation, focused on the small (<3kDa) molecules, was pursued. Secondary metabolites were extracted, fractionated and screened for biofilm inhibition, antibacterial and anticancer activity and activity was observed in all assays. Active fractions were dereplicated by UHPLC-QToF-MS and compounds of interest were isolated using mass guided preparative HPLC. The purity of the isolated compounds was assessed using UHPLC-QToF-MS and NMR and the structure of the target compounds elucidated. Structures that could be determined were the bile acids cholic acid and 3-oxo cholic acid and although not responsible for the observed activities, this is the first report of bile acid production for this genus. This is the first study investigating the bioactive potential of the strain and the first demonstrating that T. actiniarum is a promising source of potentially novel pharmaceutically relevant natural products depicted through both culture-dependent and culture-independent approaches. Keywords: bioactive natural products, marine natural products, heterologous expression, genome mining, exopolysaccharides, bioassay-guided fractionation iii http://etd.uwc.ac.za/ Acknowledgements Acknowledgements I would like to thank my supervisor, Professor Marla Trindade and my co- supervisor, Dr Lonnie van Zyl for this amazing opportunity and for their exceptional leadership, continuous support, motivation and encouragement. A big thank you to the NRF for funding this research. I would also like to thank everyone at IMBM, support staff and students, as completing this work would have been all the more difficult without all of you. A special thanks to Shanice, for her continuous motivation and wonderful friendship from the start of this journey, until now. I’d like to thank everyone at Marbio, UiT (The Arctic University of Norway) as well as Johan Isaksson for their assistance and input with regards to Chapter 4 of this work. Lastly, I would like to thank my family for their patience, reassurance and support. This accomplishment is yours as much as it is mine. iv http://etd.uwc.ac.za/ Dedication Dedication This work is dedicated to those who often asked me, ‘So, when are you done?’ To my son, Seth. Unknowingly, you kept me going. v http://etd.uwc.ac.za/ Abbreviations Abbreviations µ micro µg microgram µg/ml Microgram per milliliter µl microliter µm micrometer A domain adenylation domain ACP acyl carrier protein antiSMASH antibiotic and Secondary Metabolite Analysis Shell APS ammonium persulfate AT acyl transferase ATCC American Type Culture Collection ATP adenosine triphosphate BCC Burkholderia cepacia complex BGC biosynthetic gene cluster BLAST Basic Local Alignment Tool bp base pair BPI base peak intensity C domain condensation domain CFU/ml colony forming units per milliliter CLB’s colicin-like bacteriocins cm centimeter vi http://etd.uwc.ac.za/ Abbreviations CoA co-enzyme A Contig contiguous COVID-19 Coronavirus Diseases 2019 Da Dalton DH dehydratase dH2O distilled water DMSO dimethyl sulfoxide DNA deoxyribonucleic acid EDTA ethylenediaminetetraacetic acid EPS exopolysaccharide ER enoyl reductase ESKAPE Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Pseudomonas aeruginosa and Enterobacter sp. FDA Food and Drug Administration FPLC Fast Protein Liquid Chromatography g gram g/L grams per liter g/ml grams per milliliter GAG glycosaminoglycan HIV Human Immunodeficiency Virus HMW high molecular weight HPLC High Performance Liquid Chromatography HR-MS High Resolution Mass Spectrometry vii http://etd.uwc.ac.za/ Abbreviations IMBM Institute for Microbial Biotechnology and Metagenomics kDa kilodalton KR ketoreductase KS ketosynthase L liter LB Luria Broth LC-MS Liquid Chromatography Mass Spectrometry LC-NMR Liquid Chromatography Nuclear Magnetic Resonance Spectroscopy LPS lipopolysaccharide m/z mass to charge MDR multidrug resistant MERS-CoV Middle East Respiratory Syndrome Coronavirus mg/ml milligrams per milliliter MIC Minimum Inhibitory Concentration ML Machine Learning ml milliliter mm millimeter mM millimolar M Molar MS Mass Spectrometry MT methyltransferase MTS 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4- sulfophenyl)-2H-tetrazolium) viii http://etd.uwc.ac.za/ Abbreviations NCBI National Centre for Biotechnology Information NMR Nuclear Magnetic Resonance NP natural product NRP nonribosomal peptide NRPS nonribosomal peptide synthase ºC Degrees Celcius OD Optical density OSMAC One Strain Many Compounds PCP peptidyl carrier protein PG peptidoglycan PK polyketide PKS polyketide synthase ppm parts per minute PRISM PRediction Informatics for Secondary Metabolomes RNA ribonucleic acid RP reversed-phase rpm rotations per minute SDS sodium dodecyl sulphate SDS-PAGE sodium dodecyl sulphate polyacrylamide gel electrophoresis ST domain sulfotransferase TE thioesterase UHPLC ultra-high performance liquid chromatography UHPL-MS ultra-high performance liquid chromatography mass spectrometry ix http://etd.uwc.ac.za/ Abbreviations xg relative centrifugal force
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