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NUCLEOSIDE CATABOLIZING ACTIVITIES in SELECTED SEEDS by Nogood Almarwani a Thesis Submitted to the Faculty of the College Of

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NUCLEOSIDE CATABOLIZING ACTIVITIES in SELECTED SEEDS by Nogood Almarwani a Thesis Submitted to the Faculty of the College Of NUCLEOSIDE CATABOLIZING ACTIVITIES IN SELECTED SEEDS By Nogood Almarwani A Thesis Submitted to the Faculty of the College of Graduate Studies at Middle Tennessee State University in Partial Fulfillment of the Requirements for the Degree of Master of Science in Chemistry Middle Tennessee State University December 2016 Thesis Committee: Dr. Paul C. Kline, Chair Dr. Andrew Burden Dr. Anthony Farone I dedicate this research work to my husband, parents, my sisters, and my brothers. ii ACKNOWLEDGMENTS This research work would not be possible without the support of a great people around me. In the beginning, I would like to thank my loving husband, Fahad Almarwani, for his endless encouragement and support me. I would also like to thank Dr. Paul C. Kline, my major professor. I cannot convey how much I appreciate him for his help and support me. Also, I would like to thank Dr. Anthony Farone and Dr. Andrew Burden as my committee members. I am grateful for their invaluable suggestions and for taking time to read my thesis. In addition, I would like to thank all the staff and faculty of the Department of Chemistry for their help and support throughout my stay at MTSU. Finally, special thanks to my parents, my sisters, my brothers, my little son, Sultan, and my friends. I would not have an opportunity to achieve this dream without their support and love. iii ABSTRACT The efficacy of pyrimidine and purine nucleotide metabolism plays a critical role in the progression of biological systems. The process of nucleotide degradation exists in all organisms. The nucleoside degradation and salvage of nucleotides, nucleosides, and nucleobases require several enzymes including deaminases and nucleosidases. Deaminases play a substantial role in the course of removing amino groups from selected nucleobases to convert one nucleoside to another. The cleavage of the N-glycosidic bond in nucleosides is catalyzed by the nucleoside hydrolases or nucleosidases. This process facilitates the recycling of nucleobases. Nucleoside degradation protein extracts were assessed in some seed sources including Alaska pea, okra, organic okra, peas (Cascadia Sugar Snap), yellow lupin, soybean, spinach, and cantaloupe. Extracts of un-germinated seeds were incubated with reaction mixtures containing 1 mM uridine, inosine, purine riboside, cytidine, adenosine, or 2'-deoxyadenosine in 10 Mm Tris pH 7.2 buffer. Using an HPLC with a Kinetex 5 μ, EVO C18 reverse phase column eluted with ammonium phosphate/ methanol, nucleosidase and deaminase activities were quantified. The results show the existence of active nucleosidases and deaminases in seeds tested. However, there were differences in the levels of activities based on the plant and substrate observed. Uridine, cytidine, and thymine exhibited the highest levels of activity among the nucleosides, while lower activities were observed with guanosine, purine riboside, inosine, and 2'-deoxyadenosine. Among the seeds, soybeans had the lowest activity levels, while okra had the highest activity levels. iv TABLE OF CONTENTS PAGE LIST OF TABLES ......................................................................................................... vii LIST OF FIGURES ........................................................................................................ viii CHAPTER I: INTRODUCTION......................................................................................1 Purines and Pyrimidines......................................................................................................2 Purine Metabolism .............................................................................................................5 Pyrimidine Metabolism ....................................................................................................10 Nucleoside Hydrolases......................................................................................................13 Uridine Nucleosidase.........................................................................................................15 Adenosine Nucleosidase…................................................................................................16 Guanosine Nucleosidase................................................................................................... 19 Inosine Nucleosidase….................................................................................................... 19 Cytidine Nucleosidase.......................................................................................................20 Nucleoside Deaminases ....................................................................................................21 Adenosine Deaminases (EC 3.5.4.4) .....................................................................21 Cytidine Deaminases (EC 3.5.4.1).........................................................................22 Guanosine Deaminases (EC 3.5.4.3).....................................................................22 Current Research ..............................................................................................................23 CHAPTER II: MATERIALS AND METHODS ...........................................................24 Equipment and Instrumentation .......................................................................................24 Materials and Reagents......................................................................................................24 Methods..............................................................................................................................25 v Preparation of Crude Extract...............................................................................25 Enzymatic Activity Measurement..........................................................................25 Measurement of Protein Concentration ...............................................................26 CHAPTER III: RESULTS AND DISCUSSION............................................................28 Enzyme Activities in Okra, Organic Okra and Yellow Lupin..........................................32 Enzyme Activities in Spinach and Cantaloupe.................................................................45 Enzyme Activities in Alaska Peas and Sugar Snap Peas..................................................54 Enzyme Activities in Soybean...........................................................................................62 CHAPTER IV: CONCLUSIONS…...............................................................................67 REFERENCES ................................................................................................................70 vi LIST OF TABLES TABLE PAGE 1. Summary of retention times of nucleosides and nucleobase…………………….31 2. Rate of disappearance of nucleoside with okra seed extract……...……..…….....42 3. Rate of disappearance of nucleoside with organic okra seed extract …………....43 4. Rate of disappearance of nucleoside with yellow lupin seed extract ..…..……....44 5. Rate of disappearance of nucleoside with spinach seed extract……..…………...52 6. Rate of disappearance of nucleoside with cantaloupe seed extract.……………....53 7. Rate of disappearance of nucleoside with Alaska pea seed extract...……….........60 8. Rate of disappearance of nucleoside with sugar snap pea seed extract………......61 9. Rate of disappearance of nucleoside with soybean seed extract…………............66 vii LIST OF FIGURES FIGURE PAGE 1. Representative structure of a nucleoside and a nucleotide……………………………2 2. General structure of a purine …………………….………….......................................3 3. General structure of purine bases adenine, hypoxanthine and guanine………………3 4. General structure of a pyrimidine …………….…………............................................4 5. Common pyrimidine bases……………………………………………………………4 6. Schematic representation of the purine nucleotides de novo pathway….…….............6 7. Purine salvage reactions ………………………...........................................................9 8. Schematic representation of the pyrimidine de novo pathway in plants………..…….11 9. Pyrimidine salvage reactions in plants…………………….………………….............12 10. Reaction mechanism of hydrolases .…………………….…………..........................14 11. Hydrolysis of uridine by uridine nucleosidase to uracil and ribose catalyzed by uridine nucleosidase...………………………………..................15 12. Reaction catalyzed by adenosine nucleosidase between adenosine and water to yield adenine and ribose..………….………….....................16 13. Hydrolysis of guanosine by guanosine or inosine/guanosine nucleosidase to guanine and ribose………..............…………...…………..................19 14. Reaction between inosine and water catalyzed by inosine nucleosidase to yield hypoxanthine and ribose….….………….……………............20 15. Cytidine hydrolysis by cytidine nucleosidase to cytosine and ribose………………..20 16. Adenosine nucleosidase mediates conversion of adenosine to inosine and releases NH3………………………….………………………….……………….21 17. Cytidine deaminase converts cytidine to uridine…………………………………….22 viii 18. Bovine serum albumin (BSA) standard curve generated after plotting known amount of BSA against A595nm………………….…….……….27 19. 2'-Deoxyadenosine nucleosidase catalyzed hydrolysis of 2'-deoxyadenosine into adenine and 2’-deoxyribose….……………….…….……..……….....................29 20. Structure of xanthine and xanthosine…………………….…......................................29 21. Uridine to uracil conversion catalyzed by uridine nucleosidase in okra seed extract……………………………………………………………………………...…33
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