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Quantitative Proteome Analysis of Alfalfa in Drought Stress Under the Influence of Mir156

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Quantitative Proteome Analysis of Alfalfa in Drought Stress Under the Influence of Mir156 Western University Scholarship@Western Electronic Thesis and Dissertation Repository 3-1-2019 10:00 AM Quantitative proteome analysis of alfalfa in drought stress under the influence of miR156 Alpa Puri The University of Western Ontario Supervisor Marsolais Frederic The University of Western Ontario Co-Supervisor Kohalmi Susanne 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 © Alpa Puri 2019 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Cellular and Molecular Physiology Commons, and the Plant Biology Commons Recommended Citation Puri, Alpa, "Quantitative proteome analysis of alfalfa in drought stress under the influence of miR156" (2019). Electronic Thesis and Dissertation Repository. 6032. https://ir.lib.uwo.ca/etd/6032 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]. Abstract Medicago sativa is one of the most produced perennial forage crops in Canada. Drought stress is a major form of abiotic stress affecting the productivity and annual yield of alfalfa. A small noncoding RNA, miR156 has a role in abiotic stress tolerance, while regulating downstream SPL genes. In this study, whole leaf proteome and amino acid concentrations of miR156OE (A8) genotype of alfalfa under drought stress were quantified. Using MaxQuant, 3,000 proteins groups were identified when searched against the Medicago truncatula protein sequence database. Gene ontology analysis showed that enriched proteins were involved in biological and molecular processes such as antioxidant response, response to stress, abscisic acid signaling, and biosynthesis of secondary metabolites. These proteins/pathways might be involved in enhancing drought stress tolerance mediated by miR156. This study provides a better understanding and an insight into the role of miR156 in drought stress tolerance in alfalfa. Keywords miR156, SPL genes, proteome, drought stress, abiotic stress, alfalfa i Acknowledgments I would like to thank my supervisor Dr. Frederic Marsolais, for the privilege to work on this project. I sincerely appreciate your support, mentorship and open-door policy. Working with you has been a great and wonderful experience. I greatly appreciate the advice and kind assistance of my co-supervisor, Dr. Susanne Kohalmi. Thank you for your valuable suggestions and taking the time to review the proposal and thesis drafts. A special thanks to members of my advisory committee: Dr. Abdelali Hannoufa and Dr. Robert Cumming, for their availability, kind suggestions, advice and guidance at all levels of the research project. I am grateful to Agnieszka Pajak for technical support. Many thanks to the present and past lab mates for their kind help, educative discussions, and advice along the way like Dr. Marwan Diapari, Dr. Jaya Joshi, and Dr. Shrikaar Kambhampati. Also, I would like to thank Dr. Justin Renaud for his immense support and guidance while analyzing my results. My gratitude also goes to the management, staff, and friends at the London Research and Development Center-Agriculture and Agri-Food Canada, for providing a supportive and stimulating work environment. I thank Western University and the Biology department for the opportunity and support throughout the completion of my degree. Finally, I wish to thank my family and friends for their support and prayers. ii Table of Contents Abstract ................................................................................................................................ i Acknowledgments .............................................................................................................. ii Table of Contents ............................................................................................................... iii List of Tables ..................................................................................................................... vi List of Figures ................................................................................................................... vii List of Abbreviations ....................................................................................................... viii 1: Introduction .................................................................................................................... 1 1.1 Importance of alfalfa ............................................................................................ 1 1.2 Alfalfa improvement ............................................................................................ 3 1.3 Plant drought stress .............................................................................................. 6 1.4 miRNAs and abiotic stress tolerance ................................................................. 13 1.5 miR156 and SPL genes ....................................................................................... 17 1.6 Proposed research ............................................................................................... 19 1.7 Hypotheses and objectives ................................................................................. 19 2: Material and Methods ................................................................................................... 21 2.1 Plant materials and drought treatment ................................................................ 21 2.2 Mid-day leaf water potential .............................................................................. 22 2.3 Protein extraction for proteomics ....................................................................... 22 2.4 Protein lysis and digestion.................................................................................. 23 2.5 Mass spectrometry.............................................................................................. 23 2.6 Data analysis ...................................................................................................... 24 iii 2.7 Bioinformatics .................................................................................................... 26 2.8 Immunoblotting .................................................................................................. 27 2.9 RNA extraction and gene expression analysis ................................................... 28 2.10 Quantification of amino acids after hydrolysis .................................................. 29 2.11 Statistical analysis .............................................................................................. 32 3: Results .......................................................................................................................... 33 3.1 miR156 overexpression enhances shoot biomass and reduces water loss under drought stress ................................................................................................................ 33 3.2 Leaf proteome of miR156OE genotype under drought stress. ........................... 36 3.3 Gene ontology enrichment analysis ................................................................... 38 3.4 Network analysis and visualization of functionally grouped terms ................... 40 3.5 Protein families involved in drought stress ........................................................ 47 3.6 Immunoblot analysis for validation of proteins identified in label- ................... 49 free quantification under drought stress condition ........................................................ 49 3.7 Transcriptional regulation under drought stress ................................................. 49 3.8 Effect of miR156OE and drought stress on amino acid composition in alfalfa . 54 4: Discussion ..................................................................................................................... 56 4.1 Research overview ............................................................................................. 56 4.2 Physiological response to drought stress in alfalfa ............................................ 57 4.3 Enriched functional categories/pathways in miR156OE genotype under drought stress 59 4.3.1 Effect of miR156OE on alfalfa water status ................................................... 60 4.3.2 Effect of miR156OE on photosynthesis in alfalfa .......................................... 62 4.3.3 miR156 enhances accumulation of secondary metabolites and antioxidants under drought stress ...................................................................................................... 64 iv 4.3.4 Effect of miR156OE on stress-related proteins .............................................. 66 4.3.5 Transcription factors: potential targets of miR156 ......................................... 67 4.4 Immunoblotting for validation of proteomic data and transcriptional regulation ...................................................................................................................... 68 4.5 Enhanced protein quality and quantity in alfalfa under the influence of miR156 .......................................................................................................................... 69 4.6 Conclusion .......................................................................................................... 71 5: Future
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