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DISSECTING the ROLE of PEROXISOMES in MODULATING ENVIRONMENTAL STRESS RESPONSE and PHOTOSYNTHESIS by Jiying Li

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DISSECTING the ROLE of PEROXISOMES in MODULATING ENVIRONMENTAL STRESS RESPONSE and PHOTOSYNTHESIS by Jiying Li DISSECTING THE ROLE OF PEROXISOMES IN MODULATING ENVIRONMENTAL STRESS RESPONSE AND PHOTOSYNTHESIS By Jiying Li A DISSERTATION Submitted to Michigan State University in partial fulfillment of the requirements for the degree of Genetics - Doctor of Philosophy 2015 ABSTRACT DISSECTING THE ROLE OF PEROXISOMES IN MODULATING ENVIRONMENTAL STRESS RESPONSE AND PHOTOSYNTHESIS By Jiying Li Peroxisomes are essential organelles that house a wide array of metabolic reactions important for plant growth and development. These organelles also interact with other organelles to support cellular functions. However, our knowledge regarding the role of peroxisomal proteins in various biological processes, including plant stress response and photosynthesis, is still incomplete. To address this question at the systems level, I exploited in silico analysis, mutant screens and in-depth physiological and biochemical characterizations. First, I used microarray data to generate a comprehensive view of transcript level changes for Arabidopsis peroxisomal genes during development and under abiotic and biotic stress conditions. Second, mutants of LON2 protease and the photorespiratory enzyme hydroxypyruvate reductase 1 (HPR1) were identified to have enhanced susceptibility to drought, suggesting the involvement of peroxisomal quality control and photorespiration in drought resistance. Third, I conducted a comprehensive peroxisomal mutant screen, in which 147 mutants of 104 Arabidopsis genes encoding peroxisomal proteins were subjected to an automated screening system, the Dynamic Environment Phenotype Imager (DEPI). This screen identified multiple peroxisomal proteins required for robust photosynthesis efficiency under dynamically changing light, including peroxisomal biogenesis and division proteins, photorespiratory proteins, and a NAD+ transporter protein PXN, which was found to be an additional player in photorespiration. Fourth, further characterization of the photorespiratory mutants provided insights into the molecular mechanisms regarding how the blocking of photorespiration alters photosynthetic efficiency. My data supported an integrated model for the events that occur in the photorespiration mutants, where metabolites and molecules resulting from the block of photorespiration inhibit triose phosphate isomerase (TPI) activity, compromise photosystem integrity, reduce photosystem subunit abundance, decrease proton efflux and diminish ATP synthase conductivity, induce cyclic electron flow (CEF) and activate energy dissipation. In summary, my work has provided significant insights into the connection between peroxisomal function and drought stress response and the links between photorespiration and photosynthesis. Knowledge gained from my dissertation research opens up new avenues to further investigate environmental stress response, photosynthesis, photorespiration and interorganellar communication. ACKNOWLEDGEMENTS First of all, I want to thank my beloved grandmother, mother and father for their endless love, encouragement and support. I would not be the person I am today and I would not have achieved so much if it was not for their constant confidence in me. I want to express my special appreciation to Dr. Jianbing Yan, who influenced me a lot in my undergraduate study in China Agricultural University. His passion for science and his care for nurturing students enlightened my avid interest in science. I gratefully thank my advisor Dr. Jianping Hu for giving me the opportunity to study and do research in her lab. Jianping is a great mentor, not only because of her knowledge and guidance, but also because she allowed me the freedom to explore different directions in research. What I have learned from her will be a significant impact in my future career. I also want to acknowledge present and previous Hu lab members for their great help to improve my critical thinking and experimental skills. I appreciate the precious time and suggestions from my committee members: Drs. Kathy Osteryoung, Sheng Yang He, Christoph Benning and Thomas Sharkey, as well as the Genetic Program representative Dr. Barb Sears. I want to gratefully thank our collaborators Drs. David Kramer, Thomas Sharkey and Jin Chen, as well as members in their labs, for sharing knowledge, ideas and experimental devices. Other colleagues at MSU also offered a great deal of help to me. I feel very fortunate to study at MSU. Besides its academic excellence, the fame of MSU’s football and basketball made me very proud of being a Spartan. I have made many good friends at MSU. The time we spent in sharing stories, travelling and playing iv together will be forever memorable. Our friendship will be a lifelong treasure to me. Thank you all for being a part of my life. v TABLE OF CONTENTS LIST OF TABLES ........................................................................................................... ix LIST OF FIGURES .......................................................................................................... x KEY TO ABBREVIATIONS ....................................................................................... xiii CHAPTER 1 ...................................................................................................................... 1 Literature review: Peroxisomal functions and photosynthesis ........................................ 1 1.1. Peroxisomal functions .............................................................................................. 2 1.1.1. Introduction ....................................................................................................... 2 1.1.2. Major peroxisomal metabolism ......................................................................... 3 1.1.3. The role of peroxisomes in stress response ....................................................... 9 1.2. Photosynthesis ........................................................................................................ 12 1.2.1. Introduction ..................................................................................................... 12 1.2.2. PSII .................................................................................................................. 13 1.2.3. PSI ................................................................................................................... 16 1.2.4. Cytochrome b6f ................................................................................................ 20 1.2.5. ATP synthase ................................................................................................... 21 1.2.6. Adaptive mechanisms to changing light conditions ........................................ 24 1.2.7. NPQ ................................................................................................................. 25 1.2.8. State transition ................................................................................................. 27 1.2.9. Cyclic electron flow ......................................................................................... 28 1.3. Aims of dissertation research ................................................................................. 31 APPENDIX ................................................................................................................... 33 REFERENCES .............................................................................................................. 40 CHAPTER 2 .................................................................................................................... 58 Using co-expression analysis and stress-based screens to uncover Arabidopsis peroxisomal proteins involved in drought response ...................................................... 58 2.1. Abstract .................................................................................................................. 59 2.2. Introduction ............................................................................................................ 61 2.3. Result ...................................................................................................................... 64 2.3.1. Co-expression analysis of genes that encode peroxisomal proteins during development and in response to stresses ................................................................... 64 2.3.2. A drought tolerance mutant screen revealed the role of the LON2 protease and the photorespiratory enzyme hydroxypyruvate reductase 1 (HPR1) in drought response ..................................................................................................................... 67 2.4. Discussion .............................................................................................................. 69 2.5. Materials and methods ........................................................................................... 73 2.5.1. Plant materials and growth conditions............................................................. 73 2.5.2. Microarray data analysis and heatmap visualization ....................................... 73 2.5.3. Chlorophyll fluorescence measurements ......................................................... 74 2.5.4. Drought stress assays ....................................................................................... 74 2.6. Acknowledgement .................................................................................................. 76 vi APPENDIX ..................................................................................................................
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