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Arabidopsis Thaliana Proteins Involved in Signalling Pathways: Structural and Functional Studies

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Arabidopsis Thaliana Proteins Involved in Signalling Pathways: Structural and Functional Studies Marta Grzechowiak Arabidopsis thaliana proteins involved in signalling pathways: structural and functional studies Thesis presented to the Scientific Council of the Institute of Bioorganic Chemistry Polish Academy of Sciences in Poznan as a Ph.D. dissertation Poznań 2015 1 The research described in this thesis has been carried out at the Institute of Bioorganic Chemistry, Polish Academy of Sciences in Poznan in Protein Engineering Laboratory Department of Crystallography – Center for Biocrystallographic Research under the supervision of Associate Professor Michal M. Sikorski, Ph.D., Dr.Sc. Financial support for this work was provided by the European Union within the European Regional Developmental Fund. International PhD Programme was supervised by the Foundation for Polish Science. In year 2015, the dissertation was partially supported by grant for Young Scientists provided by the Polish Ministry of Science and Higher Education. 2 I would like to thank: my advisor, Prof. Michal Sikorski for support, care and understanding Prof. Mariusz Jaskolski for valuable comments dr Miłosz Ruszkowski for introducing me to the secrets of crystallography, many scientific discussions and friendship my Family my Lab Mates my Friends for endless support, help and understanding 3 Table of content Abbreviations........................................................................................... 8 Preface ..................................................................................................... 10 List of publications ................................................................................. 12 Part I-Structural studies of WRKY transcription factors 1. Introduction…………………………………………………………. 14 1.1. WRKY transcription factors ………………………………………………………… 14 1.1.1. Distribution among species…………………………………………………….. 14 1.1.2. Structural features and classification…………………………………………… 15 1.2. Biological function…………………………………………………………………... 19 1.2.1. The plant immune system ................................................................................... 20 1.2.2 The role of WRKY transcription factors in plant defense ……………………... 24 1.2.3. The role of WRKY transcription factors in abiotic stress……………………… 25 1.2.4. The role of WRKY transcription factors in other processes……………….…… 27 1.3. The WRKY interactions……………………………………………………………… 32 1.3.1. WRKY-WRKY interactions……………………………………………………. 32 1.3.2. WRKY-VQ interactions………………………………………………………… 33 1.3.3. WRKY-MAP kinase interactions......................................................................... 34 1.3.4. WRKY-interactions with other proteins………………....................................... 34 1.4. Structural studies of WRKY proteins........................................................................... 35 2. Goal of the thesis…………………………………………………..... 38 3. Results……………………………………………………………….. 39 3. 1. WRKY selection…………………………………………………………………….. 39 3.2. Screening for soluble recombinant AtWRKY proteins…………..………………….. 40 3.2.1. Cloning of WRKY genes ………………………………………………………. 40 3.3.2. Expression and purification…………………………………………………….. 41 3.2.2.1. TOPO-cloning………………………………………………………… 43 3.2.2.2. Ligase Independent Cloning – LIC…………………………………… 44 3.2.2.3. Cloning into pET-32a vector…………………………………………. 47 3.3. Arabidopsis thaliana WRKY50 protein…………………………………………….. 47 3.3.1. Cloning and overexpression……………………………………………………. 47 3.3.2. Purification……………………………………………………………………… 47 3.3.3. Crystallization of AtWRKY50…………………………………………………. 48 3.3.3.1. Crystallization of AtWRKY50……………………………………….. 48 3.3.3.2. Crystallization of modified AtWRKY50.............................................. 50 3.3.4 Functional and structural studies of AtWRKY50………………………………. 52 4 3.3.4.1. DNA-binding analyses (EMSA, ITC)................................................... 52 3.3.4.2. Secondary structure prediction………………………………………... 55 3.3.4.2.1.Circular dichroism…………………………………………. 55 3.3.4.2.2. Bioinformatics analyses…………………………………... 56 3.4. Arabidopsis thaliana WRKY18 DNA-binding domain............................................... 58 3.4.1. Cloning and overexpression................................................................................. 58 3.4.2. Recombinant protein purification......................................................................... 58 3.4.3. Crystallization of AtWRKY18DBD........................................................................ 59 3.4.4. DNA-binding (EMSA)......................................................................................... 60 4. Discussion ........................................................................................... 62 4.1. WRKY cloning, overexpression and purification……………………………………. 62 4.2. WRKY crystallization………………………………………………………………... 71 4.3.Structural studies of WRKY proteins…………………………………………………. 75 4.4. DNA-binding…………………………………………………………………………. 78 4.5. Conclusions…………………………………………………………………………... 80 5. Materials and Methods ...................................................................... 81 5.1. Materials………........................................................................................................... 81 5.1.1. Materials used in the experiments........................................................................ 81 5.1.2. Oligonucleotides ................................................................................................. 84 5.1.3. Media and antibiotics........................................................................................... 86 5.1.4. Buffers.................................................................................................................. 87 5.2. Methods ....................................................................................................................... 90 5.2.1. Recombinant protein production.......................................................................... 90 5.2.1.1. Plant growing ....................................................................................... 90 5.2.1.2. Isolation of total RNA………………………………………………… 90 5.2.1.3. Reverse transcription…………………………………………………. 91 5.2.1.4. Cloning of the WRKY protein coding sequences……………………. 91 5.2.1.4.1. TOPO Cloning……………………………………………. 91 5.2.1.4.2. Ligase Independent Cloning-LIC………………………… 93 5.2.1.4.3. Cloning into pET-32a(+) vector………………………….. 97 5.2.1.5. Overexpression of recombinant WRKY……...................................... 99 5.2.1.6. Purification of soluble and insoluble fraction of WRKY proteins…… 99 5.2.1.7. Cloning, expression and purification of AtWRKY50 and AtWRKY18DBD……………………………………………………… 101 5.2.2.Crystallization of AtWRKY50............................................................................. 103 5.2.2.1. Crystallization of ligand free AtWRKY50…………………………… 103 5.2.2.2. AtWRKY50 crystalization with DNA…………………………….…. 104 5.2.2.3. Protein modifications……………………………………………….… 104 5.2.2.3.1. Reductive lysine methylation…………………………….. 104 5.2.2.3.2. Limited proteolysis……………………………………….. 105 5.2.2.4. Crystallization of AtWRKY18DBD……………………………………. 106 5.2.3. Recombinant protein analyses............................................................................. 106 5.2.3.1. Protein concentration measurements.................................................... 106 5.2.3.2. DNA preparation.…………………………………………………….. 107 5.2.3.3. Electromobility shift assay (EMSA)…………………………………. 107 5 5.2.3.4. Isothermal Titration Calorimetry (ITC)………………………………. 108 5.2.3.5. Secondary structure prediction……………………………………….. 109 5.2.3.5.1.Circular Dichroism (CD)………………………………..… 109 5.2.3.5.2. Intrinsically disordered region prediction………………… 111 6. Summary……………………………………………………………. 113 7. Streszczenie…………………………………………………………. 114 8. References…………………………………………………………… 115 Part II-Structural studies of enzymes involved in phosphate metabolism 1. Introduction ........................................................................................ 127 1.1. Role of phosphorus in plants ………………………………………………………... 127 1.2. Phosphate homeostasis………………………………………………………………. 128 1.3. Inorganic pyrophosphatases…………………………………………………………. 129 1.4. Plant PPases................................................................................................................. 131 1.5. Mechanisms of the PPases activity…………………………………………………... 134 2. Goal of the thesis................................................................................. 138 3. Results and Discussion ....................................................................... 139 3.1. Cloning, overexpression and purification of AtPPA1.................................................. 139 3.2. Crystallization conditions of AtPPA1………………………………………………... 140 3.3. Structure solution, refinement and deposition……………………………………….. 142 3.4. Overall structure of AtPPA1....................................................................................... 144 3.5. Metal ions associated with the AtPPA1 protein……………………………………… 146 3.6. N-terminus analysis……………………………………..…………………………… 148 3.7. Oligomeric structure……………………………………..…………………………... 151 3.8. Enzymatic assays and activity……………………………………..………………… 157 3.9. Comparison of AtPPA1with other pyrophosphatases……………………………….. 161 4. Materials and Methods ...................................................................... 165 4.1. Materials ..................................................................................................................... 165 4.1.1. Materials used in the experiments …………………………………………….. 165 4.1.2. Oligonucleotides ................................................................................................
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