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Inhibition and Nucleic Acid Binding Studies of the Carboxyltransferase

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Inhibition and Nucleic Acid Binding Studies of the Carboxyltransferase Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2011 Inhibition and nucleic acid binding studies of the carboxyltransferase component of bacterial acetyl- CoA carboxylase Brian Benson Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Benson, Brian, "Inhibition and nucleic acid binding studies of the carboxyltransferase component of bacterial acetyl-CoA carboxylase" (2011). LSU Doctoral Dissertations. 3117. https://digitalcommons.lsu.edu/gradschool_dissertations/3117 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. INHIBITION AND NUCLEIC ACID BINDING STUDIES OF THE CARBOXYLTRANSFERASE COMPONENT OF BACTERIAL ACETYL-COA CARBOXYLASE A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biological Sciences by Brian K. Benson B.S., Louisiana State University, May 2002 December 2011 ACKNOWLEDGEMENTS I would like to thank Dr. Grover Waldrop, my major professor, for accepting me into his laboratory and providing technical expertise throughout this work and for fostering my belief that our efforts someday will help sick people get out of hospital beds. I am also appreciative of my graduate committee members, Professor Paul Russo, Professor Roger Laine, Professor Jeffrey Gimble, and Associate Professor Anne Grove, for their valuable advice. Thanks to Patrick Bilder and Michael Oldham for their suggestions and to Carol Dieckmann, Cindy Fleming-Wood and Angela Hopp for their careful consideration of this dissertation. I wish also to acknowledge my wife; without her communicable faith and indispensable support, I certainly would not have achieved this task. Finally, to my children: Thanks for helping me realize how precious life is and for inspiring me to always work smarter and harder. ii TABLE OF CONTENTS ACKNOWLEDGEMENTS ............................................................................................................ ii ABSTRACT .................................................................................................................................... v CHAPTER 1 INTRODUCTION .................................................................................................... 1 SECTION 1 ..................................................................................................................................... 1 Overview of Fatty-Acid Biosynthesis ......................................................................................... 1 The Biotin Molecule ................................................................................................................... 2 The History of Biotin .............................................................................................................. 2 Biotin in Nutrition ................................................................................................................... 3 Structure and Chemistry of Biotin .......................................................................................... 3 Biotin-Dependent Enzymes ........................................................................................................ 5 Acetyl-CoA Carboxylase, a Biotin-Dependent Carboxylase ..................................................... 6 Enzyme Biotinylation ............................................................................................................. 8 Structure of Biotin Carboxyl Carrier Protein .......................................................................... 9 Catalytic Mechanism of Biotin Carboxylase ........................................................................ 10 Structure of Biotin Carboxylase ............................................................................................ 14 Catalytic Mechanism of Carboxyltransferase ....................................................................... 19 Structure of Carboxyltransferase .......................................................................................... 20 Regulation of Acetyl-CoA Carboxylase ............................................................................... 23 Acetyl-CoA Carboxylase in Agriculture and Medicine ........................................................... 26 Acetyl-CoA Carboxylase as a Herbicide Target ................................................................... 26 The United States’ Obesity Epidemic ................................................................................... 28 Acetyl-CoA Carboxylase in Chronic Diseases ..................................................................... 28 Need For New Antibiotics — Acetyl-CoA Carboxylase a Valid Target .............................. 30 SECTION 2 ................................................................................................................................... 35 Some Metabolic Enzymes Bind Nucleic Acids ........................................................................ 35 The Types and Functions of the Zinc Fingers .......................................................................... 40 The Tetracyclines, Additional Inhibitors of Carboxyltransferase ............................................ 45 Objectives and Rationale for Study .......................................................................................... 47 References ................................................................................................................................. 48 CHAPTER 2 LINKAGE BETWEEN NUCLEIC ACID BINDING AND CATALYSIS IN THE CARBOXYLTRANSFERASE SUBUNIT OF ACETYL-COA CARBOXYLASE ................... 65 Introduction ............................................................................................................................... 65 Materials and Methods .............................................................................................................. 68 Purification and Enzymatic Assay of Carboxyltransferase .................................................. 68 Substrate Nucleic Acids ........................................................................................................ 69 Eletrophoretic Mobility Shift Assay (EMSA) ...................................................................... 70 Data Analysis ........................................................................................................................ 71 Results ....................................................................................................................................... 73 DNA Binding by Carboxyltransferase .................................................................................. 73 RNA Binding by Carboxyltransferase .................................................................................. 81 iii Inhibition of Enzyme Activity .............................................................................................. 82 Discussion ................................................................................................................................. 88 DNA Binding Enzymes ........................................................................................................ 88 Zinc Domains Associated with Proteins Involved in DNA Metabolism .............................. 91 Does Carboxyltransferase Bind DNA in Vivo? .................................................................... 92 The Mode of DNA Binding Suggests Communication Between the Dual Active Sites ...... 94 Pharmaceutical Relevance .................................................................................................... 95 References ................................................................................................................................. 96 CHAPTER 3 INHIBITION OF THE CARBOXYLTRANSFERASE SUBUNIT OF ACETYL- COA CARBOXYLASE FROM ESCHERICHIA COLI AND STAPHYLOCOCCUS AUREUS BY TETRACYCLINES.............................................................................................................. 100 Introduction ............................................................................................................................. 100 Materials and Methods ............................................................................................................ 102 Purification and Enzymatic Assay of Carboxyltransferase ................................................ 102 Electrophoretic Mobility Shift Assays ................................................................................ 104 Data Analysis ...................................................................................................................... 104 Results and Discussion ........................................................................................................... 105 Tetracyclines Inhibit Carboxyltransferase Activity ............................................................ 105 Effect of Tetracycline on DNA Binding ............................................................................. 111 Does Tetracycline Bind Carboxyltransferase in Vivo?
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