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Investigating the Potential for Environmental Perception and Adaptation in the Amoebaflagellate Naegleria Gruberi

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Investigating the Potential for Environmental Perception and Adaptation in the Amoebaflagellate Naegleria Gruberi University of Huddersfield Repository Sykes, Connor Investigating the potential for environmental perception and adaptation in the amoebaflagellate Naegleria gruberi Original Citation Sykes, Connor (2019) Investigating the potential for environmental perception and adaptation in the amoebaflagellate Naegleria gruberi. Masters thesis, University of Huddersfield. This version is available at http://eprints.hud.ac.uk/id/eprint/34975/ The University Repository is a digital collection of the research output of the University, available on Open Access. Copyright and Moral Rights for the items on this site are retained by the individual author and/or other copyright owners. Users may access full items free of charge; copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational or not-for-profit purposes without prior permission or charge, provided: • The authors, title and full bibliographic details is credited in any copy; • A hyperlink and/or URL is included for the original metadata page; and • The content is not changed in any way. For more information, including our policy and submission procedure, please contact the Repository Team at: [email protected]. http://eprints.hud.ac.uk/ C.Sykes U1363969 Master of Science by Research Investigating the potential for environmental perception and adaptation in the amoebaflagellate Naegleria gruberi Connor Sykes U1363969 A thesis submitted to the University of Huddersfield in partial fulfilment of the requirements for the degree of Master of Science by Research. Division of Biological Sciences & Nutrition, School of Applied Sciences, University of Huddersfield January 2019 1 C.Sykes U1363969 Master of Science by Research Acknowledgements First and foremost, I would like to express my deepest gratitude to my research supervisors, Professor Michael Ginger and Dr. Jane Harmer, who have supported me throughout the entirety of the MSc year and kept their cool when I was losing mine. Without their continuing guidance and dedicated involvement, this year of work and subsequent manuscript would have never come to fruition. In addition, I would like to thank all of those who worked within the MLG lab, especially Asma, Kim and Kayleigh, for their help and comradery, especially on the days when nothing went to plan! Finally, I would like to profoundly thank my wonderful family, particularly my mother and father, I don’t know how you have managed to put up with me for so long, but it’s finally done! Mum, you’re an absolute star and you have the patience of a saint. I want you to know you are amazing, and that I love you to the moon and back! Dad, I don’t think I could count the number of times you have ferried me to or from somewhere with utmost urgency, I can’t thank you enough for all of the support over the past year. Elliott, you have always been my best friend, through thick and thin, and you always manage to make everything better in times of dire stress. I couldn’t have done it without you broski. And finally, to Sophie, my gorgeous girl who has stood by me the entire way, offering late-night proofreading and all of the encouragement I could ever ask for and more. I love you truly and deeply, and can’t wait for us to begin our next chapter once this MSc is done. This thesis stands as a testament to each of you, Thank you. 2 C.Sykes U1363969 Master of Science by Research Abstract The construction and function of flagella in eukaryotes is often vital to feeding, survival and reproduction. The last 15 years has seen a realisation that some eukaryotes, which contain the majority of eukaryotic biodiversity, possess flagella that play a function as sensory antennae. There are ongoing attempts to elucidate these sensory mechanisms, which allow cells to perceive and respond to external stimuli. This is also important in a medical context, as many cells throughout the human body build cilia as a motile or sensory apparatus, which if defective, can result in genetic syndromes known as ciliopathies. Ciliopathies have been shown to predispose individuals to chronic health conditions, including cancer, obesity and diabetes. The predatory amoeba Naegleria gruberi is capable of a transformation, in which the cell differentiates into a motile flagellate cell. This occurs via assembly of two flagella and a microtubule- based cytoskeleton de novo, in response to environmental cues such as nutriment deficit. With the advent of whole genome sequencing, the genome of N. gruberi has been decoded, revealing an intriguingly large repertoire of metabolic pathway and sensory signaling proteins. RNA microarray studies have revealed that a large number of these proteins are developmentally regulated throughout the differentiation process, which suggests that the flagellate form of Naegleria is likely well equipped for perception of environmental conditions. This stands to reason, as the primary role of the temporary flagellate form is to find a new habitable environment before the cell expires, in order to resume amoebic growth and proliferation. Throughout the MSc a bioinformatic analysis of various serpentine receptor proteins was carried out, utilizing previously published microarray data, to categorise these proteins by expression levels and expression patterns during the differentiation process. I also studied the effects of different environmental triggers upon differentiation and encystment of N. gruberi, with the intent to elucidate how vastly different environmental conditions would influence the ameboflagellate differentiation sensory response. Finally, the purification of recombinant proteins of interest was carried out, with the aim to later localise these proteins via immunolocalization and biochemical fractionation, to assess the sensory capability of the flagellum of N. gruberi both during and after differentiation. 3 C.Sykes U1363969 Master of Science by Research Contents Acknowledgements 2 Abstract 3 Contents page 4 Abbreviations and terms 10 Contents of figures 14 Contents of tables 17 Chapter 1: Introduction 18 1.1 - The life cycle and evolution of Naegleria species 18 1.1.1 - The evolution of Naegleria 18 1.1.2 - Naegleria characterisation and morphology 19 1.1.3 - Molecular, cellular, and ecological biology of Naegleria 20 1.1.4 - N. fowleri and human infectious disease 21 1.1.5 - Naegleria amoeba-to-flagellate differentiation and life cycle 22 1.1.6 - N. gruberi as a model organism 24 1.2 - Environmental perception and intercellular signalling in eukaryotes 25 1.2.1 - G protein-coupled cell-surface receptors (GPCRs) and G proteins 25 1.2.2 - Signalling cyclases and kinases 27 1.3 - Cilia and flagella as sensory antennae 29 1.3.1 - Structure of flagella and cilia 29 1.3.2 - Sensory functions 31 1.3.3 - Ciliopathies 31 4 C.Sykes U1363969 Master of Science by Research 1.4 - 1.1 - The aims of this MSc Thesis 32 Chapter 2: Materials and Methods 33 2.1 - General lab practice 33 2.1.1 - Preparing a kanamycin stock 33 2.1.2 - Preparation of LB media 33 2.1.3 - Preparation of LB agar plates 33 2.1.4 - Preparation of amoeba saline agar plates 33 2.1.5 - Maintaining Naegleria gruberi Cultures 34 2.1.6 - Picking colonies and preparing overnight cultures 34 2.1.7 - Initial protein induction 34 2.1.8 - Preparing 1xSDS loading buffer 34 2.1.9 - Preparing 2xSDS loading buffer 35 2.1.10 - Preparing samples for running on an SDS polyacrylamide gel electrophoresis (PAGE) gel 35 2.1.11 - Preparing 5x SDS running buffer 35 2.1.12 - Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis 35 2.1.13 - Small-scale protein induction 36 2.1.14 - Large-scale protein induction 36 2.1.15 - Preparation of lysis buffer for Nickel Nitrilotriacetic acid (Ni NTA) protein purification under denaturing conditions 37 2.1.16 - Preparation of wash buffer for Ni NTA protein purification under denaturing conditions 37 2.1.17 - Preparation of elution buffer for Ni NTA protein purification under denaturing conditions 37 5 C.Sykes U1363969 Master of Science by Research 2.1.18 - Preparation of lysis buffer for Ni NTA protein purification under native conditions 38 2.1.19 - Preparation of wash buffer for Ni NTA protein purification under native conditions 38 2.1.20 - Preparation of elution buffer for Ni NTA protein purification under native conditions 38 2.1.21 - Ni NTA purification 38 2.1.22 - Preparation of AS stock 1 39 2.1.23 - Preparation of AS stock 2 39 2.1.24 - Preparation of AS solution for differentiation 39 2.2 - Differentiation 40 2.2.1 - Preparing Naegleria gruberi differentiation plates 40 2.2.2 - Observation and selection of cells 40 2.2.3 - Differentiation procedure 40 2.2.4 - Differentiation cell counting 41 2.2.5 - Sodium azide experiments 41 2.2.6 - Sodium Nitrate + Sodium Nitrite plates 41 2.2.7 - Foetal bovine serum (FBS) experiments 41 2.2.8 - Glucose experiments 41 2.2.9 - Anaerobic and microaerophilic CO2 rich environments 42 2.2.10 - TWEEN20 (polyoxyethylenesorbitan, monolaurate) experiments 42 2.2.11 - Differentiation data processing 42 2.3 - Bioinformatic Microarray Analysis 44 2.3.1 - Obtaining the microarray data 44 6 C.Sykes U1363969 Master of Science by Research 2.3.2 - Organising the microarray library 44 2.3.3 - Plotting the microarray data 45 2.4 - Analysis of proteins of interest 46 2.4.1 - Using controls 46 2.4.2 - Sorting results and further protein analysis 47 2.4.3 - Finding similar proteins to the most expressed proteins of interest 47 2.5 - Morphology of cysts formed within different
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