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Molecular Analysis of Coenzyme a Ligase from Benzoate-Metabolizing Sorbus Aucuparia Cell Cultures

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Molecular Analysis of Coenzyme a Ligase from Benzoate-Metabolizing Sorbus Aucuparia Cell Cultures Molecular analysis of coenzyme A ligase from benzoate-metabolizing Sorbus aucuparia cell cultures Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat) genehmigte D i s s e r t a t i o n von Hussein Ramadan aus Rabta, Libyen 1. Referee: Prof. Dr. Ludger Beerhues 2. Referee: apl. Prof. Dr. Dirk Selmar eingereicht am: 14.08.2006 mündliche Prüfung (Disputation) am: 19.10.2006 Druckjahr : 2006 Parts of this work have previously been published with permission of the Faculty of Life Science, represented by the mentor of this work: Presentations -Short lecture Ramadan, H , Beerhues, L (2005) Coenzyme A ligases involved in benzoic acid biosynthesis XVII International Botanical Congress Austria Center Vienna, 17 - 23 July 2005 -Poster Ramadan, H , Beerhues, L (2004) Coenzyme A ligases involved in benzoic acid biosynthesis Botanikertagung der Deutschen Botanischen Gesellschaft und der Vereinigung für Angewandte Botanik Braunschweig, 05-10 September 2004 ACKNOWLEDGEMENTS I would like to express my gratitude to many individuals who assisted me throughout the course of my doctoral research. First and foremost, I would like to express my gratitude to my advisor, Professor Dr. Ludger Beerhues, for the wonderful opportunity of participating in this exciting research endeavour and for constant guidance, unwavering moral support during my years as PhD student. More thanks for his patience to correct from the beginning to the end my thesis tirelessly, and for the extraordinary advice, caring, encouragement, and affection he bestowed on me. My sincere thanks go to Prof. Dr. Benye Liu and Dr. Heiko Schwarz for invaluable assistance, suggestions, and discussion. Especially, for the first success in molecular biology of my career. Sincere gratitude is also extended to Dr. Rainer Lindigkeit for special attention, personal help, using his time and effort to show me different computer programs. Many thanks go to all staff and faculty members of the Institute of Pharmaceutical Biology of TU Braunschweig, present or past, who in one way or another have contributed a lot for my life in the institute to be so enjoyable and unforgettable, and making this study a successful experience, specially I extend immense appreciation and thanks to Mrs. Ines Rahaus for providing a stimulating and fun environment and for all her help. I also owe heartfelt exceptional thanks to my wife, Dr. Zakia Boubakir, for her patient love. Without her support and love, I would have not been able to complete this work. I also thank my kids Retaj and Roba for their patience and emotional support. My sincere thanks are to my family: my parents for educating me with aspects from both arts and sciences and for unconditional support and encouragement to finish my PhD work; my brothers and my sisters for their ever-loving care towards me throughout. Lastly, I would like to thank the Libyan Government for providing financial support for my doctoral study and the Deutsche Forschungsgemeinschaft (DFG) for funding this research project. Contents I CONTENTS...............................................................................................................................I List of Tables………………………………………………………………………...…........VI List of Figures…………………………………………………………………………......VIII Abbreviations……………………………………………………………………………......IX 1. INTRODUCTION.................................................................................................................1 1.1 Secondary Metabolism…………………………………………………...……………....1 1.2 Phenylpropanoid Metabolism……...………………………………………………….....2 1.3 Benzoic Acids...……………………………………………………………………..…...6 1.3.1 Salicylic Acid and Systemic Acquired Resistance to Pathogens………...………......8 1.3.2 Benzoic Acids as precursors of Benzophenones Biosynthesis…...………..………...9 1.4 Hypericum androsaemum (Tutsan)……...………………………………………..…….14 1.5 Benzoic Acids as Precursors of Biphenyl Biosynthesis…...………………………........15 1.6 Sorbus aucuparia (mountain ash)……...………………………………………….........17 1.7 Biosynthesis of Benzoic Acids in Hypericum androsaemum Cell Cultures...……..…...19 1.8 Research Strategies and Objective………….....………………………………………..22 2. MATERIALS.....................................................................................................................23 2.1 Plant Material………...………………………..………………………………………..23 2.1.1 Hypericum androsaemum ……...……..………………………………………........23 2.1.2 Sorbus aucuparia …………...……………………………………………..…….....23 2.2 Chemicals…………...…………………………………………………………..……....23 2.2.1 Special Chemicals……...……………………………..............................................24 2.2.1.1 Chemicals for Enzyme Assays………...…………………….………………..24 2.2.1.2 Chemicals for Gel Electrophoresis and Molecular Biology…...……………..25 2.3 Equipments…………………………………………..……………………………….....25 2.4 Nutrient Media for Plant Tissue Cultures……..……………...………………………...27 2.5 Solutions and Buffers for Biochemical Analysis…….…………………………………28 2.5.1 Buffers for Extraction and Enzyme Incubation…………...………………..……...28 2.5.2 Solution for Regeneration of PD 10 -Columns (Amersham Biosciences)……….......28 2.5.3 Buffer for Protein Determination ………...……………..…………………………28 2.5.4 Buffers and Solutions for Gel Electrophoresis (SDS-PAGE) …………………......29 2.5.5 Buffers and Solutions for Protein Purification………………………………..…....30 Contents II 2.5.5.1 Buffers for Affinity Chromatography………………………...………...…….30 2.5.5.2 Buffer for Gel Filtration (HiPrep16/60 SephacryS-200)……………......……30 2.6 Buffers and Media for Molecular Biology………..…………………………………....31 2.6.1 Media for the Cultivation of E. coli ………………...…...…..…………………......31 2.6.2 Solutions for the Transformation and Selection of E. coli …...……...…………….31 2.6.3 Buffer for Cell Lysis…………………...…..…………...………………………….32 2.6.4 Buffers and Solutions for DNA Electrophoresis…………...……………………...33 2.7 Enzymes for Molecular Biology……………………………...………………………...33 2.8 Primers…………………...……………………………………..………………………34 2.8.1 SMART-RACE and Vector Primers……………...………..……...…………….....34 2.8.2 RLM-RACE Primers ……..……...……………………………………………...…34 2.8.3 Degenerate Primers for Use in H. androsemum and S. acuoparia ….…...…….......35 2.8.4 Gene Specific Primers (GSP) for Use in H. androsaemum ……...…..………….....35 2.8.5 Gene Specific Primers for CoA-ligases from S. aucuparia ……..…...…………….35 2.9 Molecular Biology Materials………………………………………..………...………..36 2.9.1 Kits………………………...…………………………………..…………...…...….36 2.9.1.1 Nucleic Acids Isolation and Purification Kits……...…………………..……..36 2.9.1.2 Amplification of 3`and 5`Ends of cDNA…………...…………………..…….37 2.9.1.3 Cloning of DNA………...………………………………………………….....37 2.9.2 Buffers and Solutions for Plasmid DNA Isolation (mini-prep.)………...................37 2.9.3 Host Cells…………………...……………………………………………...............38 3. METHODES......................................................................................................................39 3.1 Nucleic Acids……………………………………………………………………...……39 3.1.1 Isolation of mRNA…………...…………………………………………………….39 3.1.2 Isolation of Total RNA……………………...…………………………………......40 3.1.3 Isolation of DNA from Phages…………………...………………………………...40 3.2 cDNA Synthesis………………………...……………………………………………...41 3.2.1 5` and 3`- RACE using the RACE-SMART method………...…………………….41 3.2.2 cDNA Synthesis using Terminal Transferase……………………...……………...42 3.2.3 cDNA Synthesis using RLM-RACE………...……………………………………..43 3.3 Phenol/Chloroform Extraction in Nucleic Acids Preparation………...………………..44 3.4 Precipitation of DNA……...…………………………………………………………...45 Contents III 3.5 Purification of DNA………………...………………………………………………….45 3.6 Determination of Nucleic Acids concentration………...………………………………45 3.6.1 Spectrophotometric Determination……………………...…………………………45 3.6.2 Estimation by Agarose Gel Analysis……………………………………………...45 3.7 Polymerase Chain Reaction (PCR)…………………………………………………….46 3.7.1 Hot start PCR………..…………………………………………………………….46 3.7.2 Reverse Transcriptase-PCR (RT-PCR)………………………………………........47 3.7.3 Touch-down PCR ……………………………………...………………………….47 3.7.4 Nested PCR……………………………………………………………………......48 3.7.5 Rapid Amplification of cDNA Ends (RACE) PCR…………………………….....48 3.8 Primer design……………………………………………………………………….…49 3.8.1 Degenerate Primers………………………………..………………………………50 3.8.2 Design of Gene Specific Primers (GSP)………………………………………..…50 3.9 Cloning of PCR Products……………………………………………………….……..51 3.9.1 Cloning in pGEM-T Easy Vector…………………………………………............51 3.9.2 Cloning in pRSET B (Invitrogen) Expression Vector………………………….....52 3.9.3 Ligation of Plasmid Vector and DNA Insert…………………………………..….52 3.10 Host Cells and Transformation………….…………………………………………...53 3.10.1 Host Cells………………………………………………………..……………….53 3.10.1.1 DH5 αT…………..………………………………………………………......53 3.10.1.2 BL21 (DE3)………………………………………….……………………...53 3.10.1.3 BL21 (DE3) PLys S…………………………………………………...........54 3.10.2 Transformation…………………………………………………………………...54 3.10.2.1 Preparation of competent cells……………………………………………...54 3.10.2.2 Transformation of Competent Cells…………………………………….......55 3.10.3 Selection of Target Recombinants…………………………………………….....55 3.10.3.1 Blue / White Colony Selection………………………………………...........55 3.10.3.2 PCR Colony Screening …………………………………….………………55 3.10.3.3 Restriction Analysis………………………………………….......................56 3.11 Isolation of Plasmid DNA…………………………………………………………....57 3.11.1 Isolation of Plasmid DNA (Mini-prep) by Alkaline lysis……………………..…57 3.11.2 Plasmid Spin Mini-preparation………………………………………………..…58 3.12 Gel Electrophoresis…………………………………………………………………..58
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