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Final 130607 Jury: Prof. dr. ir. Walter Steurbaut (chairman) Prof. dr. ir. Erick Vandamme (promotor) Prof. dr. ir. Wim Soetaert (promotor) Prof. dr. ir. Nico Boon Prof. dr. ir. Monica Höfte Prof. dr. Els Van Damme Dr. Roel Bovenberg Dr. Thierry Dauvrin Promotors: Prof. dr. ir. Erick VANDAMME Prof. dr. ir. Wim SOETAERT Laboratory of Industrial Microbiology and Biocatalysis Department of Biochemical and Microbial Technology Ghent University Dean: Prof. dr. ir. Herman VAN LANGENHOVE Rector: Prof. dr. Paul VAN CAUWENBERGE S. De Maeseneire was supported by a fellowship of the Flemish Institute for the Promotion of Scientific and Technological Research in the Industry (IWT-Vlaanderen). The research was conducted at the Laboratory of Industrial Microbiology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University. ir. Sofie De Maeseneire MYROTHECIUM GRAMINEUM AS A NOVEL FUNGAL EXPRESSION HOST Thesis submitted in fulfilment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences Cell and Gene Biotechnology Titel van het doctoraatsproefschrift in het Nederlands: Myrothecium gramineum als een nieuwe fungale expressie-gastheer Cover illustration: ‘ Myrothecium gramineum’ by Sofie De Maeseneire (June 2007) To refer to this thesis: De Maeseneire, S. L. (2007) Myrothecium gramineum as a novel fungal expression host. PhD-thesis, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium, 308 p. ISBN-number: 978-90-5989-176-0 The author and the promotors give the authorisation to consult and to copy parts of this work for personal use only. Every other use is subject to copy right laws. Permission to reproduce any material contained in this work should be obtained from the author. Woord vooraf Vier jaren, een eeuwigheid, doch véél te snel voorbij gegleden… Hoog tijd voor een woordje van dank! Graag wil ik mijn promotoren, prof. dr. ir. Erick Vandamme en prof. dr. ir. Wim Soetaert bedanken om mij toe te laten mijn doctoraatsonderzoek uit te voeren in hun labo, en voor de vrijheid en het vertrouwen waarvan ik steeds heb mogen genieten. Ik wil ook de leden van de leescommissie bedanken, prof. dr. ir. Nico Boon, prof. dr. ir. Monica Höfte, prof. dr. ir. Els Vandamme en dr. Roel Bovenberg voor de kritische beoordeling van dit proefschrift. Een speciaal woord van dank ook voor dr. Thierry Dauvrin, voor de hulp tijdens het schrijven van dit proefschrift en voor de vele nuttige suggesties. Ik mag ook zeker de ‘leescommissie van het thuisfront’ niet vergeten! Liefste tante, dank je wel voor de vele uren die je doorgebracht hebt met het lezen en verbeteren van deze voor jou ongetwijfeld moeilijke en vermoedelijk ook saaie tekst ☺!! En Wouter, bedankt voor de last- minute correcties! Dit proefschrift zou ook nooit af geraakt zijn moest de sfeer op het labo niet zo goed zijn als ze is! Ik wil graag iedereen bedanken die bijdraagt tot het ‘Limab-gevoel’. Ik weet het, het is een beetje sentimenteel, maar ik geloof dat iedereen die op ons labo werkt of gewerkt heeft, weet wat wij hiermee bedoelen. De vriendschap en de steun die wij van elkaar krijgen helpen ons door te gaan, zelfs tot in de late uurtjes en tijdens de weekends. Het risico lopend hier iemand te vergeten, wil ik toch een paar mensen speciaal bedanken. Marjan in het bijzonder, voor alles; Cassandra, voor het delen van de whisky in de Jan Van Gent; An, Bart en Katja, voor de gezellige en lekkere etentjes; Joeri, voor je steun tijdens de overuren en Inge, voor het luisteren naar mijn schimmelgeklaag. Bedankt voor jullie vriendschap en steun, voor de vele onvergetelijke momenten, voor het aanhoren van mijn gezaag en om er mij steeds weer in te laten geloven. Een oprecht woord van dank ook voor mijn thesisstudenten, voor hun onvermoeibare inzet tijdens de vele uren die ze op het labo doorbrachtten en om er ondanks hun vele tegenslagen toch in te blijven geloven. In het bijzonder dank ik Manu, Veerle en Eline voor hun bijdrage aan dit doctoraat. En, last but not least, wil ik ook mijn familie bedanken. Liefste mama en papa, bedankt voor jullie liefde en onvoorwaardelijke steun, bedankt om steeds het beste voor ons te willen en uit ons te halen, bedankt om er steeds voor ons te zijn! Ook Zussie en Wesley, dank jullie wel en veel succes als jullie binnenkort in jullie eigen stekje gaan wonen. Liefste nichteke, bedankt voor de peptalks tijdens onze ‘vrouwenonderonsjes’! Ook voor Do en Jan: merci voor alles en dat we nog lang samen van alles mogen genieten!!! Lieve schat, woorden schieten te kort om jou te bedanken… Dank je wel voor je liefde, voor je eeuwige optimisme, voor je ongelooflijk geduld, voor het aanhoren van mijn razernijen en teleurstellingen, om er mij steeds weer bovenop te brengen en zo veel meer! Nu dit hoofdstuk is afgerond zal ik mijn best doen wat minder te werken, zodat er wat meer tijd is voor ons tweetjes. The best has yet to come! Sofie, Zaterdag 9 juni 2007 ‘Success is the ability to go from one failure to another with no loss of enthousiasm’ Sir Winston Churchill, British politician of, vrij vertaald: ‘Een echte winnaar is een verliezer die nooit opgeeft!’ Prof. Erick Vandamme, Professor at the University of Ghent Table of contents Table of contents Abbreviations i Literature review 1. Introduction 1 2. Introduction to the fungi 7 2.1. Organisation of the thallus 7 2.2. Reproduction and life cycle 8 2.3. Regulatory circuits in filamentous fungi 11 2.3.1. Glucose repression in fungi 12 2.3.2. Nitrogen catabolite repression 12 2.3.3. pH regulation 13 2.3.4. Phosphorous regulation 13 2.3.5. Sulphur regulation 14 3. The fungus Myrothecium gramineum 14 4. Transformation methods of filamentous fungi 18 4.1. Electroporation 19 4.2. Lithium acetate treatment 19 4.3. Biolistical transformation 19 4.4. Agrobacterium tumefaciens -mediated transformation 20 4.5. Protoplast transformation 21 4.5.1. Preparation of the protoplasts 21 4.5.2. DNA-uptake 23 4.5.3. Protoplast regeneration 24 5. Selection markers 25 6. Fate of the transforming DNA 29 7. Applications of transformation technology 32 7.1. Using transformation for cloning genes (heterologous and homologous) 32 7.2. Gene inactivation and gene targeting 34 7.3. Manipulation of gene expression using transformation 39 8. (Heterologous) protein production by fungi 40 8.1. Structure of fungal expression systems 40 8.1.1. Promoters of filamentous fungi 41 8.1.2. Introns 48 8.1.3. Transcription termination 49 8.1.4. Initiation of translation 49 8.1.5. Secretion of heterologous proteins 50 Table of contents 8.2. The fungal secretion pathway 51 8.3. Post-translational modifications 54 8.4. Reporter genes and expression studies 56 8.5. Strategies for the improvement of (heterologous) protein production 58 9. Research objectives 64 Part I Chapter I 69 Transformation of M. gramineum with the hygromycin B resistance marker gene 69 1. Introduction 69 2. Materials and methods 70 2.1. Strains and plasmids 70 2.2. Culture conditions 71 2.2.1. Standard culture conditions 71 2.2.2. Test of the hygromycin selection medium 71 2.2.3. Test of the acetamidase selection medium 71 2.2.4. Amylase production conditions 71 2.3. Plasmid preparation 71 2.4. Protoplast preparation and transformation of M. gramineum 72 2.5. Amylase enzyme test 73 2.5.1. Cell dry weight measurement 73 2.6. PCR control of the transformants 73 2.7. Southern analysis of the transformants 74 2.7.1. Construction and labelling of the probe 74 2.7.2. Genomic DNA preparation and Southern analysis 74 3. Results and discussion 74 3.1. Development of the selective media 74 3.1.1. Hygomycin selective medium 74 3.1.2. Acetamide selective medium 75 3.2. Transformation of M. gramineum 75 3.3. Development of an amylase enzyme test 76 3.4. Amylase enzyme tests on the transformant cultures 78 3.5. Control of the stability of the amylase production 79 3.6. PCR control of the transformants 80 3.7. Southern analysis 81 4. Conclusion 83 Table of contents Chapter II 84 Rapid sample preparation for long distance PCR on genomic DNA of M. gramineum 84 1. Introduction 84 2. Materials and methods 86 2.1. Strains and culture conditions 86 2.2. Collection of material 86 2.3. Extraction methods 86 2.4. PCR amplifications 86 2.4.1. Amplification of ‘small’ fragments 86 2.4.2. Amplification of ‘longer’ fragments 87 3. Results and discussion 90 3.1. DNA extractions 90 3.2. PCR 1 and 2 91 3.3. PCR 3 93 4. Conclusion 95 Part II Chapter III 99 Cloning and sequence analysis of the gpd -gene of M. gramineum 99 1. Introduction 99 2. Materials and methods 102 2.1. Strains and growth conditions 102 2.2. Standard DNA manipulation 102 2.3. Cloning of the Myrothecium gramineum gpd -gene 103 2.3.1. Genomic DNA isolation 103 2.3.2. Genome walking 103 2.3.3. Cloning and sequence analysis 103 3. Results and discussion 105 3.1. Isolation of the full length gpd -gene 105 3.1.1. Construction of the BD GenomeWalker banks 106 3.1.2. Genomic walking 106 3.1.3. Cloning and sequencing of the complete gpd -gene of M. gramineum 109 3.2. Nucleotide sequence analysis 109 3.2.1. Analysis of the coding sequence 109 3.2.2. Analysis of the 5’ and 3’ flanking sequences 111 3.3. Determination of the gpd copy number 116 3.4. Protein sequence analysis 117 3.5. Phylogenetic analysis 119 Table of contents 3.6.
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