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Molecular Reprogramming in Tomato Pollen During Development And Molecular reprogramming in tomato pollen during development and heat stress Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften vorgelegt beim Fachbereich Biowissenschaften (FB15) der Goethe-Universität Frankfurt am Main von Mario Keller geboren in Frankfurt am Main (Hessen) Frankfurt am Main 2018 (D30) Vom Fachbereich Biowissenschaften (FB15) der Goethe-Universität als Dissertation angenommen. Dekan: Prof. Dr. Sven Klimpel Gutachter: Prof. Dr. Enrico Schleiff, Jun. Prof. Dr. Michaela Müller-McNicoll Datum der Disputation: 25.03.2019 Index of contents Index of contents Index of contents ....................................................................................................................................... i Index of figures ........................................................................................................................................ iii Index of tables ......................................................................................................................................... iv Index of supplemental material ................................................................................................................ v Index of supplemental figures ............................................................................................................... v Index of supplemental tables ................................................................................................................ v Abbreviations ........................................................................................................................................... vi Zusammenfassung ................................................................................................................................. vii Das Transkriptom von sich entwickelnden und wärmebelasteten Pollen ......................................... viii Die regulatorische Rolle von miRNAs in der Entwicklung und Hitzestressantwort von Pollen ........... ix Regulation von Proteinen während der Entwicklung und Hitzestressantwort von Pollen ................... xi Abstract ................................................................................................................................................. xiii 1 Introduction....................................................................................................................................... 1 1.1 Cellular transcriptome and proteome dynamic ........................................................................ 1 1.2 Development of pollen in flowering plants ............................................................................. 10 1.3 Response of pollen to elevated temperature ........................................................................ 13 1.4 Objectives of this study ......................................................................................................... 16 2 Methods.......................................................................................................................................... 17 2.1 Biological methods ................................................................................................................ 17 2.2 Databases ............................................................................................................................. 19 2.3 Programs ............................................................................................................................... 20 2.4 Determination of publication rates of transcriptomics technologies ...................................... 23 2.5 Transcriptome analysis ......................................................................................................... 23 2.6 Analysis of miRNAs in pollen ................................................................................................ 26 2.7 Analysis of the relationship between the transcriptome and proteome of pollen .................. 29 i Index of contents 3 Results ........................................................................................................................................... 32 3.1 The transcriptome of developing and heat-stressed pollen .................................................. 32 3.2 The regulatory role of miRNAs in the development and heat stress response of pollen ...... 45 3.3 Regulation of proteins during the development and heat stress response of pollen ............ 54 4 Discussion ...................................................................................................................................... 67 4.1 New insights in the development of pollen by transcriptome and proteome analyses ......... 67 4.2 Response of the pollen transcriptome and proteome to heat stress ..................................... 76 5 Conclusion and outlook .................................................................................................................. 83 6 References ..................................................................................................................................... 86 7 Supplemental Material ................................................................................................................. 102 Danksagung ............................................................................................................................................ A Erklärung ................................................................................................................................................. B Versicherung ........................................................................................................................................... B Lebenslauf ............................................................................................................................................... C ii Index of figures Index of figures Figure 1: Publication rates of transcriptomics technologies .................................................................... 3 Figure 2: Development of pollen in tomato ........................................................................................... 11 Figure 3: Determination of an mRNA detection threshold .................................................................... 33 Figure 4: PCA on the MACE libraries of non- and heat-stressed pollen ............................................... 34 Figure 5: Detected and stage-accumulated mRNAs in developing pollen ............................................ 35 Figure 6: Enriched MapMan terms within the groups of stage-accumulated mRNAs .......................... 37 Figure 7: Detected mRNAs between non- and heat-stressed pollen stages ........................................ 40 Figure 8: Response of pollen transcriptomes to HS.............................................................................. 41 Figure 9: HS regulation of Hsf and Hsp families in pollen developmental stages ................................ 42 Figure 10: Hsf and Hsp family members pointing towards a developmental priming of tetrads ........... 43 Figure 11: Stage-accumulated mRNAs differentially regulated in response to HS .............................. 44 Figure 12: Detected miRNAs in developing pollen................................................................................ 47 Figure 13: Clusters of stage-accumulated miRNAs .............................................................................. 48 Figure 14: Developmentally relevant MTIs ............................................................................................ 49 Figure 15: TFs regulated by miRNAs in a developmental context ........................................................ 50 Figure 16: Detected miRNAs between non- and heat-stressed pollen stages ..................................... 51 Figure 17: Protein group sizes and mRNA levels of majority and minority proteins ............................. 55 Figure 18: Correlation of non-stressed pollen transcriptomes and proteomes ..................................... 56 Figure 19: Detected and stage-accumulated protein groups in developing pollen ............................... 57 Figure 20: Two possible translation modes in developing pollen .......................................................... 58 Figure 21: mRNAs with direct and delayed translation during pollen development .............................. 59 Figure 22: Proteins accumulated in mature pollen as a result of direct and delayed translation .......... 62 Figure 23: Detected protein groups between non- and heat-stressed pollen stages ........................... 64 Figure 24: HS regulation of mRNAs encoding down- and upregulated proteins .................................. 65 Figure 25: Alteration of RP levels in response to HS ............................................................................ 66 Figure 26: New molecular insights in the development and HSR of pollen .......................................... 85 iii Index of tables Index of tables Table 1: Alignment statistics of the MACE libraries .............................................................................. 32 Table 2: Known and novel miRNAs among the predicted miRNAs ...................................................... 46 Table 3: HS-relevant MTIs with opposite regulation between miRNA and target mRNA ..................... 53 iv Index of supplemental material Index of supplemental material Index of supplemental figures Supplemental Figure 1: Overlap of down- and upregulated
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