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Investigations on ABC and MFS Transporters of Streptomyces Spp Investigations on ABC and MFS transporters of Streptomyces spp. A dissertation presented to the Faculty of Chemistry and Pharmacy of Albert -Ludwigs University of Freiburg im Breisgau for the degree of Doctor rerum naturalium Submitted by Irene Santillana Larraona from Barcelona, Spain - June 2015 - Dean: Prof. Dr. Bernhard Breit Chair of the doctoral committee: Prof. Dr. Stefan Weber Referent: Prof. Dr. Andreas Bechthold Co-referent: Jun. Prof. Dr. Stefan Günther Third examiner: Prof. Dr. Oliver Einsle Date of the examination: June 29, 2015 Date of promotion: July 2, 2015 I hereby declare that the presented work was completed independently by me and using only the sources cited in the list of references. Freiburg, June 2015. | iii ____________________ Irene Santillana Larraona Parts of this work have been published: Presentation “Inactivation of transporters by Redirect Technology” PhD seminar. May 7, 2013. Poster Santillana, I.; Derochefort, J.; Zuo, C.; Bechthold, A.: “New insights into the rishirilide gene cluster: Minimal PKS, oxygenases, hydrolases and transporters”. DPhG, Annual meeting 2013. Drug discovery inspired by nature. Freiburg, October 09 – 11, 2013. Santillana, I.; Yan, X.; Wunsch-Palasis, J.; Bechthold, A.: “Characterization of the rishirilide transporters and their influence on its production”. Actinobacteria within soils. Symposium. Münster, October 25 - 28, 2012. Gessner, A.; Kroeger, J; Santillana, I.; Bechthold, A.: “Function, specificity and use of transporters involved in biosynthesis of saccharide antibiotics or involved in the efflux of antibiotics in Bacillus cereus”. Membrane proteins and biological membranes. GRK 1478. Freiburg, January 10, 2012. iv| | v This work was performed in the Institute of Pharmaceutical Biology and Biotechnology of the University of Freiburg in the research group of Prof. Dr. Andreas Bechthold, who I want to sincerely thank for giving me this opportunity. Thank you for opening me the doors of your working group and for supporting me during this time. Thank you for enabling me to develop my own research and to work independently on a topic that I enjoyed. vi| I also want to thank: . Jun. Prof. Dr. Stefan Günther for being my co-referent and for supporting me especially during the first months of this work. I want to express my gratitude for the welcome into the pharmaceutical bioinformatics working group. | vii . Prof. Dr. Oliver Einsle for so kindly accepting to be my third examiner. Dr. Gabriele Weitnauer for her help, organization and for the support with the MolBio Bachelor Praktikum. The whole working group of pharmaceutical bioinformatics, and particularly Dr. Anika Erxleben, Dr. Xavier Lucas, Stephan Flemming and Kersten Döring for introducing me into the bioinformatics world and for the great start of my stay in Freiburg. Thank you for enabling my participation in the StreptomeDB project. The former PhD students of the working group of Prof. Bechthold for all the initial support. I want to give a big thank-you to Dr. Julia Wunsch-Palasis for showing me everything necessary when I arrived to the lab and Dr. Theresa Siegl for her help, advices and also fun in our office. The current working group for the good atmosphere and all cakes and Fanta we enjoyed together. I want to especially thank Denise Deubel for her help and for bringing her energy and good mood into the lab; Stefanie Hackl for all great conversations about travelling and interesting life stories; Astrid Erber for taking me into “uni-sports” and other cool activities; Yvonne Schmidt-Bohli for helping me with protein related troubles and for being always available for a good advice; and Suzan Samra for her huge humanity and for doing this working group a better place. My “final phase” office colleagues Jasmin Kroeger and Tanja Heitzler for their daily motivation words and because despite the hard days, we also had fun! . Our TAs, Marcus Essing and Sandra Groß, for the computer and laboratory support. Elisabeth Welle for her big and immediate help, for teaching me about HPLC and for taking care of us and our lab. My “super” bachelor and diploma students Veronika Brinschwitz and Jannis Brehm for their dedication, their help and their sense of humor. It was a pleasure to share my project with you both. Dr. Tina Strobel and Stephan Flemming for all the time we enjoyed together, for the relax evenings on the sofa, for the trips and the parties, because you made possible that I never felt alone. Ihr seid so cool! . Anja Greule for reading and correcting all this work. For being my “half of the orange” in the lab, having fun and great scientific discussions. For sharing your knowledge and for finding always time to help me and all the others. For being an amazing colleague and even a better friend. viii| . Familie Löppenberg, für euer Interesse, eure Hilfe beim Schreiben während den Wochenenden und für eure immer netten Worte. A Pablo y Ana por disfrutar juntos de mis visitas a Barcelona y por venir a conocer Freiburg. A Mario, por ser la cosa más bonita, por sus enormes abrazos cuando llego de visita y porque, aunque él no lo sepa, siempre me saca una sonrisa. A mis padres, por su amor y apoyo incondicional. Porque a pesar de la distancia, siempre os siento conmigo y sois mi punto de referencia. Por recordarme cada día que esta vida está para disfrutarla. Marius for all the effort and time dedicated to enhance this work. For being always by my side and for taking me into your arms when everything felt “too much”. Thank you for being a huge motivation to improve myself every day. | ix “Happiness only real when shared” - Alexander Supertramp - x| | xi Contents I. SUMMARY / ZUSAMMENFASSUNG ...................................................................... 1 II. INTRODUCTION .................................................................................................... 4 1. Natural products .................................................................................................. 4 1.1. Polyketides .................................................................................................................... 4 Rishirilide B, a type II PKS secondary metabolite from Streptomyces bottropensis Goe C4/4 ......... 7 1.2. Terpenoides ................................................................................................................... 8 Phenalinolactone, a terpenoide metabolite from Streptomyces sp. Tü6071 ...................................... 10 2. Ins and outs across the membranes .................................................................... 11 2.1. Bacterial membranes .....................................................................................................11 2.2. ATP-binding cassette transporters ............................................................................... 13 2.3. Major facilitator superfamily transporters .................................................................. 15 3. Aim of this work ................................................................................................. 17 III. MATERIAL AND METHODS ................................................................................. 18 1. Material ............................................................................................................. 18 1.1. General manufacturer information ............................................................................. 18 Contents 1.2. Laboratory material, equipment and analytical instruments ..................................... 19 1.3. Chemicals and reagents ................................................................................................ 21 1.4. Enzymes, antibodies and kits ...................................................................................... 24 xii| 1.5. Solutions and buffers ....................................................................................................25 1.6. Antibiotic solutions ...................................................................................................... 31 1.7. Components of media ................................................................................................... 32 1.8. Bacterial stem lines ....................................................................................................... 32 1.9. Vectors .......................................................................................................................... 34 1.10. Software and database ................................................................................................. 38 2. Methods ............................................................................................................. 40 2.1. Methods in microbiology ............................................................................................. 40 2.1.1. Cultivation of bacterial strains ............................................................................................. 40 2.1.2. Transfer of DNA ..................................................................................................................... 42 2.1.3. Bacterial screening ................................................................................................................. 47 2.1.4. Minimal inhibitory concentration in E. coli ........................................................................ 48 2.1.5. Disc diffusion antibiotic sensitivity testing ......................................................................... 48 2.2. Methods in molecular biology ....................................................................................
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