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Evolution and Expression of Polyketide Synthase Gene in the Lichen-Forming Fungal Families Cladoniaceae and Ramalinaceae

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Evolution and Expression of Polyketide Synthase Gene in the Lichen-Forming Fungal Families Cladoniaceae and Ramalinaceae ! ! ! ! EVOLUTION AND EXPRESSION OF POLYKETIDE SYNTHASE GENE IN THE LICHEN-FORMING FUNGAL FAMILIES CLADONIACEAE AND RAMALINACEAE By Brinda Adhikari Timsina A Thesis submitted to the Faculty of Graduate Studies of The University of Manitoba In partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Biological Sciences University of Manitoba Winnipeg Manitoba Canada Copyright © 2013 by Brinda Adhikari Timsina ! i! ! ! ! ! ABSTRACT Fungal polyketides are synthesized by polyketide synthases (PKS) encoded by PKS genes. The function of many PKS genes is unknown and the number of PKS genes exceeds the number of polyketides in many genomes. The lichen-forming fungi, Cladonia and Ramalina have chemical variants separated by habitat suggesting that environmental conditions may influence polyketide production. The goal of this thesis was to examine evolutionary relationships as a framework to investigate PKS gene function in the lichen-forming fungal families Cladoniaceae and Ramalinaceae. A phylogenetic analysis of the genus Ramalina (Chapter 2) using nuclear and mitochondrial ribosomal DNA sequences showed monophyly for seven species and included three species, which were not examined in phylogenies prior to this study. One monophyletic species, R. dilacerata was chosen for further tests of the effect of growing conditions on PKS gene expression (Chapter 3). Growth media containing yeast extracts produced the largest colony diameters and the fewest number of polyketides. A significant negative relationship occurred between colony diameter and number of secondary metabolites. Expression of two types of PKS genes was correlated with pH-level and media conditions that produced larger numbers of secondary products in R. dilacerata. A PKS gene phylogeny was constructed for 12 paralogs detected in members of the C. chlorophaea complex (Chapter 4) and gene selection was inferred using dN/dS estimations. The gene phylogeny provided evidence for independent origins and purifying and positive selection of PKS paralogs. This research provided insight into the evolution of PKS genes in the C. ! ii! ! ! ! ! chlorophaea complex and identified potential genes that produce non-reduced polyketides present in C. chlorophaea. This thesis provided evidence for diversification of both morphological and chemical species and monophyly of previously unstudied Ramalina species. This research also supported theories of secondary metabolite synthesis based on growing conditions of R. dilacerata, and it revealed that PKS genes under selection in the Cladonia chlorophaea group provide the lichen with the adaptive capacity to survive under variable conditions. Knowledge of the ecological function of fungal polyketides can be valuable for conservation management and policy makers; and for understanding the potential pharmaceutical roles of these natural products. ! iii! ! ! ! ! ACKNOWLEDGEMENTS I am indebted and express my profound respect and thanks to my advisor, Dr. Michele D. Piercey-Normore for her continuous support, guidance, patience, motivation, having her door always open and a willingness to assist at any time. I could not have asked for a better supervisor. I would like to take this opportunity to express my gratitude to my thesis Supervisory Committee Members: Dr. Georg Hausner, Dr. John L. Sorensen, Dr. Dirk Weihrauch and the late Dr. Gunner Valdimarsson. I am immensely grateful for their good advice, valuable suggestions, ideas and enthusiasm. To the Head of the Department of Biological Sciences, Dr. Judy Anderson, and others, Dr. Tom Booth, Dr. Robinson, Dr. Bruce Ford, professors, instructors, and colleagues who have inspired me throughout this journey, I thank them for sharing their joy of learning. I would also like to thank Maureen Foster, Doreen Davis, Urmilla Deonaught and Jamie for their help and assistance. Special thanks to my lab mates for all their help, troubleshooting ideas, lab assistance, enthusiasm and company. I would also like to thank my colleagues from Dr. Weihrauch’s lab, Dr. Sorensen’s lab and Dr. Hausner’s lab for providing me with space and technical assistance. To my husband, Narayan, thank you for believing in me, giving me shoulder to lean on, love, strength and support at all times. I thank my son, Ahaan, for his patience, love and understanding. To my parents, in-laws, other family members, friends and loved ones, I thank them for their love, inspiration and encouragement. ! iv! ! ! ! ! I gratefully acknowledge financial support from Faculty of Science; Department of Biological Sciences; Graduate student’s Association, Faculty of Graduate Studies, Manitoba Student Aid, and the National Sciences and Engineering Research Council of Canada (NSERC). ! v! ! ! ! ! Thesis, the publication status of chapters, and the role of each coauthor in each chapter! Chapter Author Contribution of each author Article status 1 Brinda A. Timsina B. T. wrote the Introduction and Parts of this chapter are included in a published C. Deduke, and M. Literature Review for the thesis. I book chapter. Open Access and online. ISBN: Piercey-Normore wrote the portions included in the book 978-953-307-815-1, InTech. chapter and did all the literature searching for those parts of the chapter. 2 Brinda A. Timsina B. T. performed all the lab work, data Manuscript is published in the journal, Botany. analysis, wrote the manuscript and Botany, 2013, 90(12): 1295-1307. served as a corresponding author. Elfriede Stocker- E. S-W. performed HPLC on 14 out of Wörgötter 50 samples to confirm my results and she edited the paper before submission to the journal. Michele D. Piercey- M. P-N. served as my supervisor and Normore provided funding. 3 Brinda A. Timsina B. T. performed all the lab work, Manuscript available online, analysis and wrote the manuscript and (http://dx.doi.org/10.1016/j.funbio.2013.09.003) served as the corresponding author for Fungal Biology.. the manuscript. John Sorensen J. S. provided guidance on how to do HPLC and its interpretation; and he edited the paper before submission to the journal. Dirk Weihrauch D. W. provided guidance on how to do Real Time PCR and the interpretation; and he edited the paper before submission to the journal. Michele D. Piercey- M. P-N. served as my supervisor and Normore provided funding. 4 Brinda A. Timsina B. T. performed all the lab work, the Manuscript is in review in the American data analysis, and wrote the Journal of Botany. Date of submission: July 4, manuscript; and B. T. 2013. is a corresponding author for the manuscript. Georg Hausner G. H. provided guidance on how to analyse data using dN/dS estimations and interpretation; and he edited the paper before submission to the journal. Michele D. Piercey- M. P-N. served as my supervisor and Normore provided funding. 5 Brinda A. Timsina I wrote the Final Discussion and Conclusions for the thesis. This chapter has not been submitted for publication. ! vi! ! ! ! ! TABLE OF CONTENTS ABSTRACT ii! ! ACKNOWLEDGEMENTS iv! ! THESIS, THE PUBLICATION STATUS OF CHAPTERS AND THE ROLE vi! OF EACH COAUTHOR IN EACH CHAPTER ! ! TABLE OF CONTENTS vii! ! LIST OF TABLES xi! ! LIST OF FIGURES xiv! CHAPTER 1: GENERAL INTRODUCTION AND LITERATURE REVIEW 1.1 Introduction 1 1.2 Thesis goals and objectives 5 1.3 Literature review 7 1.3.1. The lichen association 7 1.3.2. Classification and taxonomy 9 1.3.3. Lichen morphology 11 1.3.4. Scientific progress on studying lichens 15 1.3.5. Evolutionary studies of lichen fungi 17 1.3.6. Ramalinaceae 17 1.3.7. Cladoniaceae 19 1.3.8. Fungal secondary metabolites 22 1.3.9. Polyketide synthases 24 1.3.10. Functional significance of polyketides 31 ! vii! ! ! ! ! 1.3.11. Regulation of polyketide production 33 ! CHAPTER 2: MONOPHYLY OF SOME NORTH AMERICAN SPECIES OF RAMALINA AND INFERRED POLYKETIDE SYNTHASE GENE FUNCTION ! 2.1. Abstract 38 ! 2.2. Introduction 39 ! 2.3. Materials and Methods 42 2.3.1. Lichen material and chromatography 42 2.3.2. DNA extraction and amplification 50 2.3.3 DNA sequencing and alignment 53 2.3.4. Data analysis 54 2.4. Results 56 2.5. Discussion 63 ! 2.5.1. Monophyly in North American species of Ramalina 63 ! 2.5.2. PKS gene function in Ramalina 65 ! ! CHAPTER 3: EFFECT OF APOSYMBIOTIC CONDITIONS ON COLONY GROWTH AND SECONDARY METABOLITE PRODUCTION IN THE LICHEN-FORMING FUNGUS, RAMALINA DILACERATA 3.1. Abstract 69 3.2. Introduction 70 3.3. Materials and Methods 75 3.3.1. Lichen material and mycobiont isolation 75 3.3.2. Generation of single spore mycobiont cultures 76 3.3.3. DNA extraction and sequencing 79 ! viii! ! ! ! ! 3.3.4. RNA isolation and cDNA synthesis 81 3.3.5. Quantitative PCR (qPCR) 82 3.3.6. Thin Layer Chromatography (TLC) and High Performance 83 Liquid Chromatography (HPLC) 3.3.7. Data analyses 84 3.4 Results 85 3.4.1. Changes in colony diameter over time 86 3.4.2. Effect of media composition and pH level on colony diameter 89 3.4.3. Effect of media and pH on number of secondary metabolites 91 3.4.4. Effect of colony growth on secondary metabolite production 93 3.4.5. Relative mRNA expression of wA1 and MSAS type PKS genes 93 3.5 Discussion 98 3.5.1. Growth of R. dilacerata 98 3.5.2. Stress induces the production of secondary metabolites 100 3.5.3. PKS gene expression 101 3.5.4. Relationship of optimal culture conditions to habitat 104 ! ! CHAPTER 4: EXPLORING THE FUNCTION OF PKS PARALOGS IN THE CLADONIA CHLOROPHAEA SPECIES COMPLEX 4.1. Abstract 106 4.2. Introduction 107 4.3. Materials and Methods 110 4.3.1. Lichen material and chromatography 110 4.3.2. DNA extraction and amplification 119 ! ix! ! ! ! ! 4.3.3. Extracting DNA sequences from NCBI and JGI databases 121 4.3.4. DNA sequencing and alignment 121 4.3.5. Data analysis 122 4.3.6. Scoring PKS paralogs 124 4.4.
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