Molecular characteristics of cold adaptation and subzero growth in polar microorganisms By Isabelle Raymond-Bouchard Natural Resource Sciences McGill University, Montreal July, 2017 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of PhD © Copyright by Isabelle Raymond-Bouchard 2017 "The road to wisdom? - Well, it's plain and simple to express: Err and err and err again, but less and less and less." — Piet Hein "I almost wish I hadn’t gone down that rabbit-hole — and yet — and yet — it’s rather curious, you know, this sort of life!" — Alice in Wonderland (Lewis Carroll) “The most exciting phrase to hear in science, the one that heralds new discoveries, is not ‘Eureka!’ but ‘That’s funny…’” — Isaac Asimov ii Acknowledgments I would like to thank, first and foremost, my supervisor Lyle Whyte. Thank you for taking me on as a doctoral student, for introducing me to the wondrous and exciting worlds of polar microbiology and astrobiology, and for your support and guidance throughout the years. Your strength of character is inspiring. I will always be eternally grateful for the opportunities and experiences that this lab brought me, both as a scientist and an individual. Thank you to the members of my supervisory committee, Charles Greer and Sebastien Faucher, for your guidance, ideas, and critical feedback. A special acknowledgment to all my collaborators and co-authors. Your contributions to my PhD research were greatly appreciated and my work benefited from your expertise. I am grateful to the National Sciences and Engineering Research Council of Canada and the Canadian Astrobiology Training Program which provided the funding that supported my doctoral studies. A special thank you to all the members of the Whyte lab, past and present, with whom I shared so much throughout my PhD. You made my time in the lab an experience I will never forget and I will be eternally grateful for your help, insight, laughter, and inspiration. A very special mention and thank you to Jesse Colangelo-Lillis, Ianina Altshuler, Rachel Backer, Jackie Goordial, Hana Trigui, Jen Ronholm, Haley Sapers, Shaun Turney and Krittika Mittal for your friendship, support, and all that you brought me during my PhD. Cassandra, even though we were worlds apart during my doctoral studies, I feel like we walked this path side by side! I value your friendship and support more than you know. Thank you for always being there, for listening, and for all the great skype calls. Un gros merci à tous mes amis et ma famille pour votre amour et soutien pendant toutes ces années. A big thank you to all my friends and family for your love and support during all these years. Thank you Karène and Christiane for your help in translating the abstract to French. David, quiet but always present. Thank you for your love and support. Caro, ma chère sœur, tu es une inspiration et je suis éternellement heureuse de t’avoir dans ma vie, de savoir que tu es toujours là pour m’écouter, m’aimer et m’encourager. À Karène, merci grandement pour ton soutien, ton encouragement et ton affection ces derniers mois, durant la période la plus importante. Ta présence dans ma vie a rendu mon travail de rédaction de thèse plus plaisant et m'a énormément aidée. Le plus gros des merci, profondément, à ma mère, Christiane, et mon père, Raymond, pour toutes ces années d’amour, d’écoute, d’encouragement, et de soutien. Il n’y a pas de mot pour d’écrire l’admiration, l’amour, et la gratitude que j’éprouve pour vous et pour tout ce que vous m’avez apporté et appris. Je dédie cette thèse à la jeune fille, curieuse et passionnée, qui, après avoir vu une cellule pour la première fois, a voulu tout savoir. I dedicate this thesis to the young woman, curious and passionate, who, upon seeing a cell for the first time, wanted to know it all. iii Table of Contents Acknowledgments........................................................................................................................... iii Table of Contents ............................................................................................................................ iv Abstract ........................................................................................................................................... ix Résumé........................................................................................................................................... xii Contributions to knowledge .......................................................................................................... xv List of Figures ................................................................................................................................ xvi List of Tables ................................................................................................................................ xvii List of Abbreviations ..................................................................................................................... xix Chapter 1. Introduction and Literature Review .............................................................................. 1 1.1 Introduction: Polar microbiology ........................................................................................ 2 1.2 Polar cryoenvironments ...................................................................................................... 2 1.3 Permafrost .......................................................................................................................... 3 1.4 Survival in cryoenvironments ............................................................................................. 5 1.5 Psychrophiles and cold adaptation ..................................................................................... 6 1.6 Omic insights of cold adaptation in psychrophiles ............................................................. 7 1.6.1 Cold shock proteins and chaperones ...................................................................... 8 1.6.2 Translation and ribosomal processes ..................................................................... 9 1.6.3 Cell wall and cell membrane ................................................................................. 10 1.6.4 Universal and oxidative stress responses ............................................................. 10 1.6.5 Compatible solutes and antifreeze proteins ........................................................ 11 1.6.6 Metabolisms and energy/nutrient acquisition ..................................................... 11 1.7 Omics of psychrophiles in cryoenvironments................................................................... 12 iv 1.7.1 Permafrost and associated soils ........................................................................... 13 1.7.2 Sea water, sea ice, and lakes ................................................................................ 15 1.8 Cold adapted proteins ...................................................................................................... 17 1.9 Conclusion ......................................................................................................................... 19 1.10 Objectives of this thesis .................................................................................................... 20 Connecting Text: ........................................................................................................................... 31 Chapter 2. Mechanisms of subzero growth in the cryophile Planococcus halocryophilus determined through proteomic analysis ................................................................................. 32 2.1 Abstract ............................................................................................................................. 32 2.2 Introduction ...................................................................................................................... 33 2.3 Results and Discussion ...................................................................................................... 35 2.3.1 Pathways and mechanisms ................................................................................... 36 2.3.2 Cold shock proteins, chaperones, and helicases .................................................. 37 2.3.3 Cell wall biosynthesis and remodeling.................................................................. 38 2.3.4 Fatty acid and lipid synthesis and modifications .................................................. 40 2.3.5 Transporters .......................................................................................................... 41 2.3.6 Translation and ribosomal processes ................................................................... 42 2.3.7 Nucleotide and amino acid synthesis and turnover ............................................. 43 2.3.8 Replication, repair and transcription .................................................................... 44 2.3.9 Oxidative and carbonyl stress ............................................................................... 46 2.3.10 Osmotolerance and compatible solutes ............................................................... 47 2.3.11 Energy metabolism ............................................................................................... 48 2.3.12 Cell growth and cell cycle control ......................................................................... 49 2.3.13 Genomic redundancy ...........................................................................................