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Inferring Plastid Metabolic Pathways Within the Nonphotosynthetic Free-Living Green Algal Genus Polytomella

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Inferring Plastid Metabolic Pathways Within the Nonphotosynthetic Free-Living Green Algal Genus Polytomella Western University Scholarship@Western Electronic Thesis and Dissertation Repository 9-1-2015 12:00 AM Inferring plastid metabolic pathways within the nonphotosynthetic free-living green algal genus Polytomella Sara Asmail The University of Western Ontario Supervisor Dr. David Smith The University of Western Ontario Graduate Program in Biology A thesis submitted in partial fulfillment of the equirr ements for the degree in Master of Science © Sara Asmail 2015 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Bioinformatics Commons, Biology Commons, and the Plant Biology Commons Recommended Citation Asmail, Sara, "Inferring plastid metabolic pathways within the nonphotosynthetic free-living green algal genus Polytomella" (2015). Electronic Thesis and Dissertation Repository. 3225. https://ir.lib.uwo.ca/etd/3225 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. INFERRING PLASTID METABOLIC PATHWAYS WITHIN THE NONPHOTOSYNTHETIC FREE-LIVING GREEN ALGAL GENUS POLYTOMELLA (Thesis format: Integrated Article) by Sara R. Asmail Graduate Program in Biology A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science The School of Graduate and Postdoctoral Studies The University of Western Ontario London, Ontario, Canada © Sara Asmail 2015 Abstract The advent of photosynthesis facilitated the evolution of aerobic life on Earth. However, species such as Prototheca wickerhamii and Plasmodium falciparum, among many others, have lost photosynthesis and opted for a free-living/parasitic lifestyle. Despite this loss, these species have retained the plastid for its metabolic pathways, without which they would die. Polytomella is a nonphotosynthetic free-living alga, closely related to the photosynthetic model organism Chlamydomonas reinhardtii, and has been shown to lack a plastid genome. I set out to determine Polytomella plastid metabolic pathways using bioinformatics to look for mRNA and DNA homologous sequences matching pathway enzymes in model organisms. Interestingly, Polytomella possesses all enzymes required for amino acid, tetrapyrrole, starch, and carotenoid biosynthesis. However, it lacks enzymes that are plastid-encoded and/or are involved in chlorophyll biosynthesis. The progressive loss of carotenoid biosynthesis provides insight into photosynthetic loss, and Polytomella shows higher plastid functional complexity in comparison to parasitic species. Keywords Algae; Chlamydomonas; chloroplast; organelle; plastid; photosynthesis; metabolic pathways; starch; carotenoids; amino acids; biosynthesis; parasites ii Co-Authorship Statement Appendix A—Next generation sequencing data suggest that certain nonphotosynthetic green plants have lost their plastid genomes. This is a letter to New Phytologist that was coauthored by Dr. David Smith, my supervisor, and myself. I contributed intellectually to the writing of this letter while my supervisor wrote and polished the final manuscript, and submitted it to the journal. Appendix B—Retention, erosion, and loss of the carotenoid biosynthetic pathway in the nonphotosynthetic green algal genus Polytomella. This was again a letter to the journal New Phytologist that was coauthored by myself and Dr. David Smith. I contributed intellectually, as well as conducted the data analyses and wrote the draft manuscript. Dr. Smith verified my results and wrote, polished, and submitted the final manuscript to the journal. Both articles are free-access papers, and further publication permitted. iii Acknowledgments I would like to thank my supervisor, Dr. David Smith, for all his invaluable help and patient guidance throughout my graduate years. It was truly a blessing to have a supervisor like him. He was always very comfortable to talk to and was always eager to provide wonderful advice and suggestions, whenever and wherever I had trouble with the project. It is a great feeling to know that you could always rely on someone to debate your points of view as well as to offer help. In my graduate experience with David, I’ve learnt that the key to succeeding in science requires patience, persistence, and hardwork, and that no organism is too small or too insignificant to inquire about and investigate. Thank you, David, for always being there and for helping me to grow up as a scientist and succeed with this milestone. I would also like to thank my advisory committee, Dr. Norm Hüner and Dr. Kathleen Hill, for all their great assistance and support. Their questions and suggestions made for a valuable project, and helped me think of new directions. They have also facilitated my realization that scientific thinking requires investigating the whole organism, and all of its genetic and environmental aspects, and knowing that one could spend a lifetime trying to know one organism. I would like to thank my lab mates and office colleagues, in specific, Michael Del Vasto and Jennifer McDonald, for all their stress relieving techniques and for always being there to help me emotionally and academically. Finally, I would like to thank my family and especially my mother for always being a great role model and showing me that courage and kindness do not require strength, power, or money; that you only need to do the right thing. You’ve taught me that even ordinary people can be heroes. iv Table of Contents Abstract ............................................................................................................................... ii Co-Authorship Statement .................................................................................................. iii Acknowledgments .............................................................................................................. iv Table of Contents ................................................................................................................ v List of Tables ................................................................................................................... viii List of Figures ..................................................................................................................... ix List of Appendices ............................................................................................................... x List of Abbreviations .......................................................................................................... xi Chapter 1 ............................................................................................................................. 1 1 The evolutionary loss of photosynthesis: from parasites to Polytomella ....................... 1 1.1 Photosynthesis ......................................................................................................... 1 1.2 The origins and spread of photosynthesis ............................................................... 2 1.2.1 Cyanobacteria to Eukarya ............................................................................ 2 1.2.2 Integration and the rise of Archaeplastida ................................................... 3 1.2.3 Plastid Evolutionary Origins ....................................................................... 5 1.3 The Loss of Photosynthesis ..................................................................................... 5 1.3.1 The general loss of photosynthesis .............................................................. 5 1.3.2 Loss of photosynthesis yet plastid retention hypotheses ............................. 9 1.4 Metabolic Pathways in Nonphotosynthetic Species .............................................. 10 1.5 Polytomella ............................................................................................................ 12 1.6 Thesis Rationale and Hypothesis ........................................................................... 14 1.7 References ............................................................................................................. 16 Chapter 2 ........................................................................................................................... 22 2 The Starch Metabolic Pathway ..................................................................................... 22 v 2.1 Introduction: starch metabolism at a glance. ......................................................... 22 2.2 Starch biosynthesis pathway in detail. ................................................................... 22 2.3 Methods: the transcriptomic and genomic data analyses of Polytomella spp. ...... 24 2.3.1 Using C. reinhardtii as a reference organism ............................................ 24 2.3.2 Transcriptomic analyses ............................................................................ 25 2.3.3 Genomic Analyses ..................................................................................... 28 2.4 Results ................................................................................................................... 29 2.5 Discussion .............................................................................................................. 30 2.6 Abbreviations ........................................................................................................ 32 2.7 References ............................................................................................................
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