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Induktion, Regulation Und Latenz Von Organisation and transcriptional regulation of the polyphenol oxidase (PPO) multigene family of the moss Physcomitrella patens (Hedw.) B.S.G. and functional gene knockout of PpPPO1 Dissertation zur Erlangung des Doktorgrades - Dr. rer. nat. - im Department Biologie der Fakultät Mathematik, Informatik und Naturwissenschaften an der Universität Hamburg von Hanna Richter Hamburg, Januar 2009 TABLE OF CONTENTS TABLE OF CONTENTS SUMMARY...................................................................................................................5 ZUSAMMENFASSUNG...............................................................................................6 1. INTRODUCTION ................................................................................................. 8 1.1. Polyphenol oxidases ................................................................................................................ 8 1.2. Phenolic compounds ............................................................................................................. 14 1.3. The model plant Physcomitrella patens ............................................................................... 15 1.4. Aim of this research ............................................................................................................... 19 2. MATERIALS AND METHODS .......................................................................... 20 2.1. Chemicals ................................................................................................................................ 20 2.2. Plant material and cell culture .............................................................................................. 20 2.2.1. Plant material and standard growth conditions ................................................................... 20 2.2.2. Application of phenolic compounds to Physcomitrella liquid cultures ................................. 21 2.2.3. Irradiation with strong light intensities (sun simulator) ........................................................ 22 2.2.4. Application of tritiated isopentenyladenine (3H-iP) to Physcomitrella liquid cultures .......... 22 2.2.5. Harvest of Physcomitrella tissue from liquid culture and weight measurements ................ 22 2.2.6. Protoplast isolation from Physcomitrella liquid cultures ...................................................... 23 2.2.7. Transformation of Physcomitrella ........................................................................................ 23 2.3. Molecular biology ................................................................................................................... 24 2.3.1. E. coli strains ....................................................................................................................... 24 2.3.2. DNA vectors......................................................................................................................... 24 2.3.3. Oligonucleotides .................................................................................................................. 25 2.3.4. Polymerase chain reaction (PCR) ....................................................................................... 26 2.3.5. Electrophoretic separation of DNA and RNA ...................................................................... 29 2.3.6. Purification of PCR products and DNA elution from agarose gels ...................................... 29 2.3.7. Small- and large-scale preparation of plasmid DNA ........................................................... 29 2.3.8. Restriction analysis of DNA ................................................................................................. 30 2.3.9. Klenow reaction, dephosphorylation and ligation of DNA fragments .................................. 30 2.3.10. Preparation and transformation of electrocompetent E. coli cells ....................................... 30 2.3.11. TOPO®-TA cloning and transformation .............................................................................. 31 2.3.12. Isolation of genomic DNA from Physcomitrella ................................................................... 31 2.3.13. Isolation of RNA from Physcomitrella .................................................................................. 32 2.3.14. DNase treatment of RNA and reverse transcription (RT) for cDNA synthesis .................... 32 2.3.15. Sequencing of DNA ............................................................................................................. 33 2.4. Protein biochemistry .............................................................................................................. 33 2.4.1. Preparation of protein extracts from Physcomitrella tissue ................................................. 33 2.4.2. Preparation of protein extracts from Physcomitrella medium .............................................. 33 2.4.3. Preparation of protein extracts from E. coli and purification of recombinant PPO .............. 34 2.4.4. Determination of protein concentrations .............................................................................. 34 2.4.5. Polarographical determination of in vitro PPO activity ........................................................ 35 2.4.6. SDS polyacrylamide gel electrophoresis (PAGE) ............................................................... 35 2.4.7. Coomassie brilliant blue staining ......................................................................................... 36 2.4.8. Western blot ........................................................................................................................ 36 2.5. Determination of cell vitality ................................................................................................. 37 TABLE OF CONTENTS 2.5.1. Fluorescein diacetate (FDA) staining .................................................................................. 37 2.5.2. PAM fluorometry .................................................................................................................. 37 2.6. Quantification of tritiated isopentenyladenine (3H-iP) from culture medium to determine extracellular CKX activity ...................................................................................................... 38 2.7. Qualitative determination of tritiated isopentenyladenine (3H-iP) by RP-HPLC-online- LSC ........................................................................................................................................... 38 2.8. Extraction of phenolic compounds from Physcomitrella tissue and culture medium ... 39 2.9. Reverse phase HPLC and LC-MS HPLC for separation of acetone extracts ................... 40 2.10. Flow cytometric measurement .............................................................................................. 41 2.11. Brightfield and fluorescence microscopy............................................................................ 41 2.12. Sequence analysis ................................................................................................................. 41 2.12.1. Sequence search and comparison using basic local alignment tool (BLAST) .................... 41 2.12.2. Gene model prediction ........................................................................................................ 42 2.12.3. Prediction of protein properties ........................................................................................... 42 2.12.4. Sequence alignments and phylogenetic tree construction .................................................. 42 3. RESULTS .......................................................................................................... 43 3.1. Cloning and characterisation of the PpPPO1 gene ............................................................ 43 3.2. In vitro PPO activity in culture medium of Physcomitrella ................................................ 44 3.3. Identification and characterisation of the PPO multigene family from Physcomitrella .. 45 3.3.1. Identification, manual adaptation and sequence comparison of PPO genes on DNA level 45 3.3.2. Sequence comparison of PpPPO1 to PpPPO13 on amino acid level ................................ 50 3.3.3. Phylogeny and classification of PpPPO1 to PpPPO13 ....................................................... 53 3.4. Heterologous expression of PpPPO11 in E. coli and in vitro PPO activity of recombinant PPO .......................................................................................................................................... 57 3.5. Expression profiles of PPO gene family members in Physcomitrella .............................. 59 3.5.1. PPO expression under standard growth conditions ............................................................ 60 3.5.2. PPO expression under strong light irradiation with a sunlight like spectrum ...................... 62 3.5.3. PPO expression after caffeic acid (CA) application to the culture medium ......................... 65 3.6. Analysis of putative PPO substrates from Physcomitrella tissue and culture medium . 67 3.6.1. Analysis of Physcomitrella tissue for phenolic substances ................................................. 67 3.6.2. Analysis of Physcomitrella culture medium for phenolic substances .................................. 69 3.7. Targeted knockout of PpPPO1 in Physcomitrella ............................................................... 73 3.7.1. Generation and molecular analysis
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