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The Role of Siderophores in Algal-Bacterial Interactions in The UNIVERSITY OF CALIFORNIA, SAN DIEGO SAN DIEGO STATE UNIVERSITY The Role of Siderophores in Algal-Bacterial Interactions in the Marine Environment A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Chemistry by Shady Ahmed Amin Committee in charge: Professor Carl J. Carrano, Chair Professor Laurance G. Beauvais Professor Brian Palenik Professor Forest L. Rohwer Professor F. Akif Tezcan Professor Yitzhak Tor 2010 Copyright Shady Ahmed Amin, 2010 All rights reserved. To my father iv TABLE OF CONTENTS Signature Page ........................................................................................................................... iii Dedication ................................................................................................................................. iv Table of Contents ....................................................................................................................... v List of Symbols and Abbreviations .......................................................................................... vii List of Figures ........................................................................................................................... ix List of Tables ............................................................................................................................. xi Acknowledgements ................................................................................................................ xvii Vita and Publications ............................................................................................................... xx Abstract .................................................................................................................................. xxii 1. Introduction .......................................................................................................................... 1 1.1. Iron as a limiting micronutrient ................................................................................... 2 1.2. Bacterial iron acquisition: siderophores ....................................................................... 2 1.3. The multiple functions of siderophores ....................................................................... 6 1.3.1. Affinity towards other transition metals.............................................................. 6 1.3.2. Siderophores as signaling molecules .................................................................. 7 1.3.3. Affinity towards boron ...................................................................................... 10 1.3.3.1. The chemistry of boron ............................................................................ 11 1.3.3.2. Boron as a nutrient for marine algae ........................................................ 13 1.3.3.3. Boron transport and regulation ................................................................ 15 1.3.3.4. Boron-containing natural products from marine prokaryotes .................. 16 v 1.4. Algal iron acquisition ................................................................................................. 18 1.5. Phytoplankton blooms and associated bacterial siderophore production................... 20 1.6. Conclusion ................................................................................................................. 22 1.7. Acknowledgement ..................................................................................................... 22 1.8. References .................................................................................................................. 23 2. Boron binding by the marine siderophore vibrioferrin isolated from marine bacteria associated with the toxic dinoflagellate Gymnodinium catenatum .................................... 33 2.1. Introduction ................................................................................................................ 34 2.2. Results and discussion ............................................................................................... 35 2.3. Methods ..................................................................................................................... 40 2.3.1. Bacterial culture ................................................................................................ 40 2.3.2. Siderophore growth bioassay ............................................................................ 40 2.3.3. Vibrioferrin and boron-vibrioferrin purification ............................................... 41 2.3.4. B-VF and VF characterization .......................................................................... 42 2.3.5. EDTA binding competition ............................................................................... 42 2.4. Appendix .................................................................................................................... 44 2.5. Acknowledgements .................................................................................................... 47 2.6. References .................................................................................................................. 48 3. Borate binding to siderophores: structure and stability ..................................................... 51 3.1. Introduction ................................................................................................................ 52 3.2. Results ........................................................................................................................ 53 3.2.1. Boron binding to vibrioferrin ............................................................................ 53 3.2.2. Boron binding to rhizoferrin ............................................................................. 59 3.2.3. Boron binding to petrobactin ............................................................................ 61 3.2.4. Boron binding to aerobactin .............................................................................. 65 vi 3.3. Discussion .................................................................................................................. 66 3.3.1. α-hydroxy acid binding ..................................................................................... 66 3.3.2. Catechol binding ............................................................................................... 67 3.3.3. Hydroxamate “binding” .................................................................................... 69 3.3.4. Biological implications ..................................................................................... 69 3.4. Methods ..................................................................................................................... 72 3.4.1. Siderophore isolation ........................................................................................ 72 3.4.2. Potentiometric titrations .................................................................................... 72 3.4.3. NMR titrations .................................................................................................. 72 3.4.4. Electrospray-ionization mass spectrometry ...................................................... 73 3.5. Appendix .................................................................................................................... 75 3.6. Acknowledgements .................................................................................................... 82 3.7. References .................................................................................................................. 83 4. Photolysis of iron-siderophore chelates promotes bacterial-algal mutualism ................... 88 4.1. Introduction ................................................................................................................ 89 4.2. Results ........................................................................................................................ 90 4.3. Discussion .................................................................................................................. 98 4.4. Methods ................................................................................................................... 102 4.4.1. Bacterial isolation, culture and growth ........................................................... 102 4.4.2. Marinobacter phylogeny ................................................................................. 102 4.4.3. VF production and uptake ............................................................................... 103 4.4.4. Determination of the inability of the photoproduct to bind Fe........................ 103 4.4.5. PCR amplification of vibrioferrin biosynthetic genes, pvsAB........................ 103 4.4.6. Axenic algal culture generation and growth ................................................... 104 4.4.7. Algal-bacterial binary culture growth ............................................................. 105 vii 4.4.8. 55Fe uptake by S. trochoidea and Marinobacter sp. DG879 ........................... 105 4.4.9. Determination of the conditional stability constant of VF in seawater ........... 107 4.4.10. Photolysis of Fe(III)-chelates ....................................................................... 107 4.4.11. Ferrireductase assay ..................................................................................... 108 4.5. Appendix .................................................................................................................
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