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FROM Aristolochia Fimbriata, a BASAL ANGIOSPERM SEQUENCING AND ANALYSIS OF A cDNA ENCODING A PUTATIVE COCLAURINE N-METHYLTRANSFERASE (CNMT) FROM Aristolochia fimbriata, A BASAL ANGIOSPERM DISSERTATION Submitted To THE FACULTY OF LIFE & ENVIRONMENTAL SCIENCES UNIVERSITY OF PESHAWAR In fulfillment for the degree Of DOCTOR OF PHILOSOPHY by ROSHAN ALI THE CENTER OF BIOTECHNOLOGY AND MICROBIOLOGY UNIVERSITY OF PESHAWAR 2010 1 CENTER OF BIOTECHNOLOGY AND MICROBIOLOGY UNIVERSITY OF PESHAWAR SEMESTER 2010 This Dissertation is Submitted By ROSHAN ALI Titled SEQUENCING AND ANALYSIS OF A cDNA ENCODING A PUTATIVE COCLAURINE N-METHYLTRANSFERASE (CNMT) FROM Aristolochia fimbriata, A BASAL ANGIOSPERM In fulfillment of the requirements for the degree Of DOCTOR OF PHILOSOPHY In BIOTECHNOLOGY 2 APPROVAL The dissertation of Mr. Roshan Ali is approved SUPERVISOR: Dr. Ghosia Lutfullah Signature:______________ Professor, Date:__________________ Center of Biotechnology & Microbiology, University of Peshawar. EXAMINER: Signature:_______________ Date:___________________ 3 4 In the name of Allah, the Beneficent, the Merciful 5 Graphical Abstract of the dissertation: Image sources are: (http://1.bp.blogspot.com/_vKxDQBwCntA/S-DMy0e3g VI/AAAAAAAAAJo/e2ickYGXEas/s1600/2516243964_5e41ba8d14.jpg), (http://images19.fotki.com/v27/photos/6/642761/4094024/Aristolochiafimbriat a37-vi.jpg?1182176542), (http://www.scripps.edu/chem/wong/PIX/riboso me.jpg) and this dissertation. 6 TABLE OF CONTENTS Title Page ACKNOWLEDGEMENTS I ABSTRACT V LIST OF ABBREVIATIONS VII LIST OF FIGURES IX LIST OF TABLES XII LIST OF APPENDICES XIII 1. INTRODUCTION 1 1.1. S-adenosyl-L-Methionine-Dependent Methyltransferases 3 1.2. S-Adenosyl-L-Methionine (SAM or AdoMet) 4 1.3. Genes of Bezylisoquinoline Alkaloid Pathway 4 1.4. Alkaloids 6 1.4.1. Types of Alkaloids 8 1.4.2. Benzilisoquinoline Alkaloids (BIAs) 8 1.4.3. BIA Producing Pathway 10 1.4.4. Common Pathway 10 1.4.5. Sanguinarine Pathway 13 1.4.6. Morphine Pathway 14 1.4.7. Medicinal Value of Alkaloids 14 1.5. Aristolochia 20 1.5.1. Medicinal Value of Aristolochia 22 1.6. Aim of the Present Study 24 2. MATERIALS AND METHODS 27 I 2.1. Tissue Source 27 2.2. RNA Extraction 27 2.2.1. Ambion Method 27 2.2.2. Modified CTAB Method 28 2.3. Quality and Purity of the Total RNA 28 2.4. Messenger RNA (mRNA) Isolation 28 2.5. Unigene Selection from A. fimbriata EST Database 29 2.5.1. Papaver somniferum CNMT Gene Sequence Information 29 2.5.2. Tribe Identification of the P. somniferum CNMT Gene and Unigene 29 Selection 2.6. Analysis and Amplification of Gene Expression by Reverse Transcriptase RT-PCR 30 2.6.1. Polymerase Chain Reaction 30 2.6.2. Gene Cloning 31 2.7. Gene Identification and Prediction of the Function of its Putative Protein 32 2.7.1. Similarity Searches 32 2.7.2. Sequence Translation 33 2.7.3. Protein Parameters 33 2.7.4. ModBase Search 33 2.7.5. Function Predictions 34 2.7.6. Secondary Structure Prediction 36 2.8. Homology Model Building 37 2.8.1. Template Identification 37 2.8.2. Target-Template Alignment 38 2.8.3. Model Generation 38 II 2.8.4. Best Structure Selection and its Evaluation 39 2.9. Active Site Identification 40 2.10. Docking 40 2.11. Analysis of Ligand and Substrate Binding Interactions with the Active Site 42 Residues 2.12. Phylogenetic Analysis 43 3. RESULTS AND DISCUSSION 45 3.1. Qualitative Assessment of Extracted Total RNA 45 3.2. PCR and Gel Extraction 51 3.3. Nucleotide Sequence Chromatogram Analysis 54 3.4. Tribe Identification 58 3.5. Identification of the Gene and Prediction of the Putative Function of its 68 Protein 3.5.1. Pairwise Sequence Alignment 68 3.5.2. BLASTn, BLASTx and tBLASTx NCBI Similarity Searches 70 3.5.3. Sequence Translation and BLASTp Search 77 3.5.4. Protein Parameters 83 3.5.5. Protein Properties and Functional Analysis 86 3.5.6. ModBase Search 91 3.5.7. Conserved Domain Database Predictions 93 3.6. Homology Model Building 93 3.6.1. Template Identification 93 3.6.2. Secondary Structure Analysis 100 3.6.3. Model Generation 104 III 3.6.4. Models Evaluation and Selection of the Best Model 106 3.6.5. PROCHECK and ProSA Results 106 3.6.6. Z-Score Values and Their Comparison 113 3.6.7. Ramachandran Plot 119 3.6.8. Superimposition 124 3.7. 3D Structure of the Model 132 3.8. Comparison with Theoretical Models of Other CNMTs 136 3.9. Binding Site 146 3.9.1. Active Site Identification 146 3.9.2. A. fimbriata Putative CNMT Model Active Site Residues as Calculated by Ligplot 151 3.9.3. SAM Binding Site 155 3.9.4. Substrate Binding Pocket 160 3.10. Putative Reaction Mechanism 162 3.11. Phylogenetic Analysis 169 4. CONCLUSIONS 179 5. APPENDIX 182 6. REFERENCES 184 IV ACKNOWLEDGEMENTS To begin with, all praise and thanks to Allah, God Almighty, most Beneficent and Merciful for giving me tremendous courage and power to complete this research and dissertation work. May Allah shower his blessings on Muhammad (SAWWS) and his Ahlulbait (AS), who always have been the sources of knowledge and guidance for humanity. I am greatly thankful to my supervisor Prof. Dr. Ghosia Lutfullah, Professor at the Center of Biotechnology and Microbiology, University of Peshawar, Pakistan for her great help, nice advices, guidance, and encouragement. I am happy to acknowledge my deep sense of gratitude to the Director, Center of Biotechnology and Microbiology Prof. Dr. Bashir Ahmad for his great help, inspiring encouragement and overwhelming support. I wish to express my deep gratitude to my ever smiling Professor Dr. Claude dePamphilis for his excellent guidance, constant encouragement and affectionate patronage throughout the experimental work conducted at dePamphilis laboratory, Department of Biology, The Huck Institute of Life Sciences, University Park, The Pennsylvania State University, USA under his kind supervision. The experimental work embodied in this dissertation was carried out at his laboratory. I am also thankful to him for providing me with all the facilities in the laboratory and financial support. This work would not have been possible without the fellowship award from the Higher Education Commission, Pakistan for which I am thankful to the Government of I Pakistan and particularly grateful to Dr. Atta-u-Rehman who devised this fellowship program. I wish to express my special thanks to Dr. Sayed Awlad Hussain and Dr. Sayed Mussarat Hussain for their sincere guidance, valuable suggestions, inspiring encouragement, fruitful discussion, nice advices and kind prayers. I would like to pay my special regards to their family, Baba buzargawar and their forefathers. I wish my gratitude to the research fellows Kerr Wall, Paula Ralph, Lena Landherr and Laura Warg of USA, Nadira Naznin and Bindhu Abinah of India, Yan Zhang, Yuannian Jiao of China, Norman Wickett of Canada in the dePamphilis laboratory for their great help, cooperation, sincere wishes, invaluable assistance and for their nice company during my stay in USA. I am also thankful to Dr. Ahmad, Zaid, Najeem, Khalid, Wael, Jouke Postma, Maria Postma and their daughter Leizbeth for their beautiful company during my stay in USA. My expressions of gratitude and sincere thanks are due to Mr. Zahid Khan, Mr. Abid Ali Khan, Aziz-ur-Rehman, Ashfaq Ahmad, Sadiq Azam, Ibrar Khan, Sajid Ali, Johar Jameel, Riaz Khan and other research fellows who helped me immensely with their fruitful discussions, valuable suggestions and continuous cooperation. I am thankful to Faculty members Dr. Nafees Bacha, Mr. Akhtar Hussain, Mr. Noor Muhammad, Mr. Jamshid Ahmad, Mr. Abu Nasar Sidiqui, Mr. Momin Khan and Mr. Khalid Javed lecturers at the Center of Biotechnology and Microbiology, University of Peshawar, for their sincere wishes and help during my course work. II Great contribution has been made in polishing my dissertation by Dr. Claude, Paula Ralph, Lena Landherr, Yuannian Jiao. I would convey my thanks to Prof. Dr. S. Mustafa and Dr. Rasool Khan for their guidance, encouragement and cooperation. I am also thankful to all my friends Shuja-u-Din, Aftab Khan, Ashiq Hussain, Nabi Hassan, Muzamil Hussain, Mudasir Hussain, Wahab Ali, S. Mahboob Ali Shah, Izhar Ali, Anwar Ali, Iqbal Hussain and Javed Hussain for their nice company, prayers and encouragement. I wish to express my special thanks to Mr. Javid Hussain and Mr. Shafaat Hussain for their help, cooperation, encouragement, nice company and financial support. I am thankful to all my relatives Noor Alam Jan, Jabir Hussain, Muhammad Ayub, Aftab Hussain, Kamal Hussain, Javid Hussain, Amjad Hussain, Muhammad Ibrahim, Khalid Hussain, Wajid Hussain, Kiramat Hussain, Amir Hussain, Abdullah Jan, Faras Ali, Asad Ali, Tanvir Hussain, Mehdi Hussain, Muhammad Zulqarnain, Hadi Hussain, Muhammad Saki, Qamar Abbas, Ansar Hussain, Ihtisham, Basit Ali, Hassanain, Awais, Nishat Hassan, Waqar Hussain, Anis, Mahmood Ali, Maroof Ali, Ashfaq Hussain, Banaras Hussain, Qaim Hussain, Khatib Hussain and Komail Hussain for their kind prayers. Finally I would like to forward a special word of gratitude to my very supportive mother, my father, Muslim Jan, and my sisters for their enormous cooperation throughout my life, especially my mother whose love, prayers and moral support enabled me to continue with perseverance. Roshan Ali III ABSTRACT IV ABSTRACT Alkaloids are produced in plants through various pathways involving several enzymes that lead to diverse alkaloids. One of the most important alkaloid biosynthetic enzymes is coclaurine N-methyltransferase (CNMT) which is an S-adenosyl-L- methionine-dependent methyltransferase (SAM-MTase). SAM-MTases utilize S- adenosyl-L-methionine (SAM) as a cofactor to methylate other molecules. CNMT catalyzes the methylation of coclaurine. Crystal structures of more than hundred SAM-MTases have been investigated. Several O-methyltransferases have been characterized at the molecular as well as structural levels, but there have been very few molecular studies of N-methyltransferases especially about CNMTs.
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