INVESTIGATING THE DEVELOPMENTAL ROLES FOR THE FUNCTIONAL AMYLOID SYSTEM OF STREPTOMYCES VENEZUELAE INVESTIGATING THE DEVELOPMENTAL ROLES FOR THE FUNCTIONAL AMYLOID SYSTEM OF STREPTOMYCES VENEZUELAE BY DAVID A. CRISANTE, B.SC. A Thesis Submitted to the School of Graduate Studies In Partial Fulfillment of the Requirements of the Degree of Master of Science McMaster University © Copyright by David A. Crisante Master of Science (2018) McMaster University (Biology) Hamilton Ontario TITLE: Investigating the developmental roles for the functional amyloid system of Streptomyces venezuelae AUTHOR: David Allen Crisante, B.Sc. (McMaster University) SUPERVISOR: Dr. Marie Elliot NUMBER OF PAGES: xiii, 108 ii Abstract Amyloid proteins are found in all domains of life, and have a number of defining characteristics, including considerable β-sheet secondary structure and the ability to self-assemble into large, insoluble fibers. These insoluble aggregates are often deleterious to the cell, evidenced by amyloid proteins being involved in Alzheimer’s, Parkinson’s, and Huntington’s disease. Remarkably however, some organisms have found ways to circumvent the toxicity of amyloid proteins, and instead co-opt them as beneficial aspects of their development and survival. An example of this can be seen in the bacteria genus Streptomyces. Streptomyces bacteria have a complex, multicellular life cycle that involves progressing through a number of distinct developmental stages. The reproductive phase of the life cycle requires the activity of amyloid-forming proteins known as chaplins - hydrophobic proteins that polymerize on the cell surface, ultimately promoting reproductive development. Due to limitations in other model Streptomyces, key questions regarding the function of chaplins have not yet been addressed. The emerging model species Streptomyces venezuelae is unique given its rapid growth, its ability to develop in liquid, and its potential to adopt two distinct life cycle programs. This work sought to characterize how chaplins influence these processes. We created a number of chaplin mutants, and determined that chaplins contribute to these process in mostly redundant ways, but when deleted in bulk cause significant phenotypic changes. We have also shown that the requirement of chaplins in development goes beyond what was previously understood - as their loss affects development in all classical life cycle stages, and further impacts alternative life cycle programs. To understanding how chaplins are regulated in S. venezuelae, mutagenesis screens were conducted to identify mutants with altered chaplin regulation. These yielded promising candidates for further investigation. Collectively, this work has advanced our understanding of chaplin proteins, specifically how they are regulated, and how they affect various modes of Streptomyces growth and development. iii Acknowledgements Marie – I can’t thank you enough for everything you have helped me with during the past three years. I know I still have room for scientific growth but your mentorship has had enormous influences on the way I interpret, analyze, and communicate science, and when I leave McMaster you should know that I credit you with the majority of the scientific learning I have done here. I know having your grad student come into your office and talk to you about any and all life advice he needs at the moment is probably nowhere near your job description…but I appreciated these discussions more than you may ever know, and I am grateful to have had a supervisor who cares as much as you. My committee members – Thank you for the helpful scientific advice and ensuring that my research stayed well directed. Steph – When I look back on my time doing my Master’s, my memories with you will always hold a special place in my heart. I always hated your impatience and bluntness, but I know you were like this because you cared and wanted to see me be as successful/happy/fulfilled as possible… and now that I’m older and wiser I realize that is the mark of a true friend. It sounds corny to say, but you are the first person I have ever been able to be my true self around: no holding back, no secrets, no embarrassment… completely uninhibited. And for this, I will never be able to thank you enough, and I certainly will never forget the amazing friend I had in you. I agree that our friendship was entirely solidified that night in the Phoenix – I think we entered that party as two acquaintances who enjoyed each other’s company, and left as life-long friends. Our squash matches and chats about life (typically one-sided) quickly became regular activities, and it’s remarkable how such ordinary things are now amongst my most cherished memories. Our time as the “homogenius unstoppable force” was one of the best parts about my experience in the Elliot lab. Christine – I can’t believe that when I first met you I thought “ugh we don’t have much in common, I’ll probably never be good friends with this person” - how wrong I was. We have so much in common, from our love of Starbucks, pool, people-watching, our appreciation for the perfect playlist for road trips, ice-caps (but maybe not bubble tea – why did you have to tell me that plastic fact…), and the list goes on. I honestly think you are a genius and a beautiful person inside and out, and I am proud to call you a friend. If I was ever in a bad mood, the thought of going on one of our (often) two Starbucks trips a day would cheer me up, because I enjoyed your company and our friendship that much. One of my favourite memories with you will always be the CSM conference – the whole time with you was a blast, but I’ll especially remember the party on the last night (thank god for Adrian’s help!). Savannah – Savannah, my lab mate, roommate, friend, and cousin…I’m going to miss being able to say that. I had my skepticisms when you first asked if I wanted a roommate, but looking back, I am very happy that I agreed. As I told you recently, one of the things I liked best about our friendship was coming home from the lab, and telling each other about all the good/bad/annoying/funny/stressful things that happened to us at work that day. There aren’t many people who I would let draw a fake moustache on me every day for a week (during undergrad interviews none the less!!), and even though I entirely disagree that drawing a fake smile on my upper lip counts as a moustache, these are the types of things I iv will miss. I hope your prediction that we probably won’t stay in touch proves incorrect, because you have become a great friend to me. Fei – Although this is a recent memory, I already know that making that “fancy four-layer cake” with you will be a culinary feat that I will think about and try to live up to every time I bake in the future. It was great to have a friend with me while taking that grad school course – going to the library every second week after lab meeting so we could work on the questions together and submit before 12 (11:58:00-11:59:45 is the perfect range right??). Even though I won’t be there, I expect you to keep that “look at David every day” tape on your lab bench as a way to remember me by. Matt (Moody) – Your friendliness and inclusivity played a major role in my initial love of the Elliot lab. Even though I was the new undergrad student, I was always grateful that you seemed to go out of your way to invite me to everything and ensure I had a smooth transition into the lab. It was very fun having another competitive person like myself in the lab.... although some of our bets definitely got out of hand (the Phoenix Christmas party and me singing Taylor Swift karaoke are two nightmarish memories that come to mind). Past and present lab members – I consider myself lucky to have worked along side such a wonderful group of smart and friendly people. Thank you for the scientific advice and amusement you have given me during the past three years. Family - I hope you all know that I will never let you forget I have two degrees now, and I promise to bring it up during every argument. Seriously though, I love you all very much and thank you for the support you’ve given me – the knowledge that all I had to do was call, and you’d be in Hamilton for me within 24 hours is a level of unspoken support that I am so grateful to have from you. v Table of contents Descriptive note……………..………………………..………………………..………………………..……..…ii Abstract……………………………………………………………………………………………………………...iii Acknowledgements…………………………………………………………………………………………..…iv Table of contents…………………………………………………………………………………………………vi List of figures………………………………………………………………………...……………….……………ix List of tables……………………………………………………………………………..…………………….……x List of abbreviations………………………………………………………………………………… ………...xi Chapter One: Introduction…………………………………………………………………………………1 1.1 Amyloid proteins……………………………………………………………………………………………1 1.1.1 Characteristics of amyloid proteins………………………………………………….1 1.1.2 Amyloid fibers and factors that affect fiber formation….….….….…………1 1.1.3 Harmful amyloids…………………………………………………………………………...2 1.1.4 Functional amyloids………………………………………………………………………..3 1.1.4.1 The curli proteins – functional amyloids used in biofilms…………………………………………………………………...4 1.1.4.2 Hydrophobins – functional amyloids used for development and virulence………………………………………5 1.1.4.3 Chaplins – developmental amyloids from Streptomyces……………………………………………………………5 1.2 The Streptomycetes………………………………………………………………………………………..5 1.2.1 Streptomyces venezuelae as a model organism………………………………….6 1.2.2 The two life cycles of S. venezuelae…………………………………………………..6