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Mass-Spectrometry Based Metabolomics to Decipher Strain Specific Microcystis Cyanopeptide Profiles

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Mass-Spectrometry Based Metabolomics to Decipher Strain Specific Microcystis Cyanopeptide Profiles MASS-SPECTROMETRY BASED METABOLOMICS TO DECIPHER STRAIN SPECIFIC MICROCYSTIS CYANOPEPTIDE PROFILES by Kimberlynn Pearl McDonald A thesis submitted to the Faculty of Graduate and Postdoctoral Affairs in partial fulfillment of the requirements for the degree of Master of Science in Chemistry with Specialization in Chemical and Environmental Toxicology Carleton University Ottawa, Ontario © 2020, Kimberlynn Pearl McDonald i. Abstract Over the last one hundred years, ecosystem changes have occurred as a result of human population growth, pollution, increased temperatures, and habitat degradation. A visible change is the increase in frequency and magnitude of toxic cyanobacterial blooms. Cyanobacterial blooms release mixtures of biologically active compounds into freshwater that negatively impact human and ecosystem health as well as having socioeconomic consequences. The factors that influence cyanobacterial growth and toxin production are broadly understood. However, cyanobacteria are a prolific source of structurally diverse and strain specific mixtures of biologically active compounds. Currently, the chemistry, toxicology, environmental concentrations, and risks posed to human and ecosystem health by most cyanobacterial secondary metabolites are unknown. Advances in mass spectrometry and metabolomic techniques can aid in comprehension of complex metabolomes. Here, the use of untargeted and semi-targeted mass spectrometry-based metabolomics is used to decipher the non-ribosomal peptide natural products (cyanopeptides) from five Microcystis strains. Cyanopeptides are grouped based on shared structural features, such as the incorporation of non-proteogenic amino acids or partial amino acid sequences that generate diagnostic product ions with the MS/MS of metabolites within the same cyanopeptide group. Global natural product society (GNPS) molecular networking and diagnostic fragmentation filtering (DFF) techniques utilize the similarity in product ion spectra to visualize all variants in the different cyanopeptide groups and the production by Microcystis strains. The semi-targeted DFF technique is applied to environmental water and bloom samples for the detection of entire cyanopeptide groups. Finally, growth medium composition effects on Microcystis chemical profiles are assessed with the established metabolomic techniques. Optimal growth conditions for cyanopeptide production have been elucidated for the Microcystis strains. This will enable the i growth of target strains that produce novel compounds and common environmental contaminants on a large scale for the isolation and purification of new cyanopeptides. With tangible material of novel cyanopeptides, structural and toxicological assessments as well as quantification of environmental concentrations can be performed. ii ii. Acknowledgements I would first like to thank my supervisor, David McMullin, for providing the opportunity to develop and expand the cyanopeptide project with interdisciplinary work. Thank you to Justin Renaud for his expertise with advanced mass-spectrometry and metabolomics as well as Dr Mark Sumarah for the experience in the LRDC lab to better expand our analytical techniques. And thanks to Natasha Desrochers for her metabolomic talents and quick replies. I am grateful for the opportunity to attend the Gordon Research Conference on Phycotoxins and Mycotoxins which expanded my research interests and provided inspiration to my own work. Thank you to Dr David Miller for many projects and experiences over the course of my time at Carleton University that helped me build up my skills and critical thought processes as a scientist. Thank you to Francis Pick for the collection and detailed information for the bloom samples collected in the National Capital Region analyzed here. Thank you to the fellow graduate students for the support and encouragement throughout my time at Carleton University, from brainstorming experimental approaches to trivia night at Mike’s Place. I would also like to thank the dedicated undergraduate students that helped perform experiments and did the grunt work. Finally, thank you to my parents and sisters for the never-ending love and support through this experience. iii iii. Table of Contents i. Abstract...................................................................................................................................................... i ii. Acknowledgements ................................................................................................................................ iii iii. Table of Contents .................................................................................................................................. iv i.v. List of abbreviations: .......................................................................................................................... vii v. List of figures: ......................................................................................................................................... x v.i. List of tables: ...................................................................................................................................... xvi 1. Introduction ............................................................................................................................................. 1 1.1 Cyanobacteria ..................................................................................................................................... 1 1.2 Secondary metabolites ........................................................................................................................ 6 1.3 Cyanotoxins ...................................................................................................................................... 11 1.3.1 Neurotoxic cyanotoxins ............................................................................................................. 12 1.3.2 Hepatotoxic cyanotoxins ............................................................................................................ 14 1.4 Cyanopeptides from Microcystis species .......................................................................................... 16 1.4.1 Microcystins ............................................................................................................................... 16 1.4.2 Anabaenopeptins ........................................................................................................................ 19 1.4.3 Cyanopeptolins .......................................................................................................................... 20 1.4.4 Microginins ................................................................................................................................ 21 1.4.5 Cyanobactins .............................................................................................................................. 22 1.4.6 Aeruginosins .............................................................................................................................. 24 1.4.7 Microviridins .............................................................................................................................. 25 1.5 Metabolomics .................................................................................................................................... 26 1.5.1 High-resolution LC-MS data collection ..................................................................................... 27 1.5.2 Untargeted mass-spectrometry based metabolomics ................................................................. 29 1.5.3 Semi-targeted mass-spectrometry based metabolomics ............................................................. 31 1.6 Project aim ........................................................................................................................................ 32 2.0 Materials and Methods ....................................................................................................................... 33 2.1 General experimental procedures. ..................................................................................................... 33 2.2 Cyanobacteria strain cultivation. ....................................................................................................... 34 2.3 Monitoring the growth of Microcystis strains. .................................................................................. 37 2.4 Extraction of cyanopeptides from Microcystis cells. ........................................................................ 37 2.5 Cyanopeptide extraction from environmental samples. .................................................................... 38 2.6 Untargeted LC-HRMS/MS analysis. ................................................................................................ 39 iv 2.7 Metabolite identification. .................................................................................................................. 40 2.8 Untargeted LC-HRMS/MS data processing. .................................................................................... 42 2.9 Post-Data Acquisition Processing and Visualization. ....................................................................... 44 2.9.1 Principal component analysis and factor loading analysis. ........................................................ 44 2.9.2 Heat map analysis to depict media effects on cyanopeptide production. ................................... 45
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