UNIVERSITY OF CALIFORNIA, SAN DIEGO Regulatory, genetic, and genomic investigations of natural products biosynthesis in marine cyanobacteria A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Oceanography by Adam Christopher Jones Committee in charge: William Gerwick, Chair Michael Burkart Pieter Dorrestein Lena Gerwick Bradley Moore Brian Palenik 2011 UMI Number: 3456277 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent on the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI 3456277 Copyright 2011 by ProQuest LLC. All rights reserved. This edition of the work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, MI 48106 - 1346 Copyright Adam Christopher Jones, 2011 All rights reserved. ii The dissertation of Adam Christopher Jones is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2011 iii DEDICATION My doctoral dissertation is dedicated to my parents. Thank you so much for all you have done for me and the constant support, guidance, and love you provide. My doctoral dissertation is dedicated to my wife, Carla. Thank you for being with me on this journey and for making me a better person. I love you. iv EPIGRAPH Our deepest fear is not that we are inadequate. Our deepest fear is that we are powerful beyond measure. It is our light, not our darkness that most frightens us. We ask ourselves, who am I to be brilliant, gorgeous, talented and fabulous? Actually, who are you not to be? You are a child of God. Your playing small doesn't serve the world. There is nothing enlightened about shrinking so that other people won't feel insecure around you. We were born to make manifest the glory of God that is within us. It is not just in some of us: it's in everyone. And when we let our own light shine, we unconsciously give other people permission to do the same. As we are liberated from our own fear, our presence automatically liberates others. Nelson Mandela, 1918 - Walk away quietly in any direction and taste the freedom of the mountaineer. Camp out among the grasses and gentians of glacial meadows, in craggy garden nooks full of Nature's darlings. Climb the mountains and get their good tidings. Nature's peace will flow into you as sunshine flows into trees. The winds will blow their own freshness into you, and the storms their energy, while cares will drop off like autumn leaves. As age comes on, one source of enjoyment after another is closed, but Nature's sources never fail. The grand show is eternal. It is always sunrise somewhere; the dew is never dried all at once; a shower is forever falling; vapor is ever rising. Eternal sunrise, eternal dawn and gloaming, on sea and continents and islands, each in its turn, as the round Earth rolls. John Muir, 1838 - 1914 v TABLE OF CONTENTS Signature page .............................................................................................................iii Dedication.................................................................................................................... iv Epigraph .......................................................................................................................v Table of Contents .........................................................................................................vi List of Abbreviations.....................................................................................................x List of Figures..............................................................................................................xii List of Tables..............................................................................................................xvi Acknowledgements ...................................................................................................xvii Vita .............................................................................................................................xxi Abstract of the Dissertation.......................................................................................xxv Chapter 1: Introduction..................................................................................................1 1.1 Importance of natural products in drug discovery.................................................1 1.2 Cyanobacteria........................................................................................................7 1.3 Biosynthesis of natural products in marine cyanobacteria..................................14 1.4 Current limitations in accessing natural products from marine cyanobacteria for biotechnology and biomedicine.................................................................21 1.5 Contents of the dissertation .................................................................................29 1.6 References ...........................................................................................................32 Chapter 2: Transcriptional analysis of the jamaicamide gene cluster from the marine cyanobacterium Lyngbya majuscula JHB .......................................... 43 2.1 Abstract................................................................................................................43 2.2 Introduction .........................................................................................................44 2.3 Results .................................................................................................................47 2.3.1 RT-PCR using L. majuscula RNA to search for the transcriptional start site (TSS) and promoter regions in the jamaicamide pathway............... 47 2.3.2 Use of promoter prediction and β-galactosidase reporter gene assays to search for promoter activity .......................................................................51 2.4 Discussion............................................................................................................56 2.5 Materials and methods.........................................................................................61 2.5.1 Bacterial strains, culture conditions, PCR reactions, and DNA measurements..................................................................................................61 2.5.2 RT-PCR using L. majuscula RNA to search for the transcription start site (TSS) and promoter regions in the jamaicamide pathway................62 2.5.3 Use of promoter prediction and β-galactosidase reporter gene assays to search for promoter activity ........................................................................63 2.6 Acknowledgements .............................................................................................65 2.7 References ...........................................................................................................66 2.8 Supplemental information ...................................................................................70 vi Chapter 3: Investigations into jamaicamide regulation and the temporal dynamics of jamaicamide biosynthesis in Lyngbya majuscula JHB ...............................73 3.1 Abstract................................................................................................................73 3.2 Introduction .........................................................................................................74 3.3 Results .................................................................................................................76 3.3.1 Isolation and characterization of possible transcription factors from a pulldown assay ....................................................................................76 3.3.2 Recombinant expression of identified proteins and Electromobility Shift Assays (EMSAs)....................................................................................84 3.3.3 Temporal dynamics of jamaicamide biosynthesis in Lyngbya majuscula JHB ................................................................................................86 3.3.4 Growth rate, and turnover of pheophytin a and jamaicamide B in Lyngbya majuscula JHB .................................................................................87 3.3.5 The effect of environmental parameters on jamaicamide B and pheophytin a production..................................................................................88 3.4 Discussion............................................................................................................95 3.5 Materials and methods.......................................................................................104 3.5.1 Bacterial strains, culture conditions, PCR reactions, and DNA measurements.......................................................................................104 3.5.2 Isolation of possible transcription factors from a pulldown assay .......104 3.5.3 Identification of DNA binding proteins ...............................................106 3.5.4 Characterization of putative transcription factors from a pulldown assay.....................................................................................................106 3.5.5 Recombinant expression of identified proteins ....................................107