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And Carbohydrate-Converting Enzymes from Thermophilic Bacteria

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And Carbohydrate-Converting Enzymes from Thermophilic Bacteria Molecular studies on protein- and carbohydrate-converting enzymes from thermophilic bacteria Leon D. Kluskens Promotor prof. dr. W.M. de Vos Hoogleraar in de Microbiologie Wageningen Universiteit Co-promotor dr. J. van der Oost Universitair docent bij de Leerstoelgroep Microbiologie Wageningen Universiteit Leden van de prof. dr. dr. h.c. G. Antranikian promotie Technical University Hamburg-Harburg, Germany commissie prof. dr. J.A.M. Leunissen Wageningen Universiteit prof. dr. R.J. Siezen Katholieke Universiteit Nijmegen prof. dr. A.G.J. Voragen Wageningen Universiteit dr. ir. G. Beldman Wageningen Universiteit Molecular studies on protein- and carbohydrate-converting enzymes from thermophilic bacteria Leon D. Kluskens Proefschrift ter verkrijging van de graad van doctor op gezag van de rector magnificus van Wageningen Universiteit, prof. dr. ir. L. Speelman, in het openbaar te verdedigen op vrijdag 9 januari 2004 des namiddags te vier uur in de Aula Molecular studies on protein- and carbohydrate-converting enzymes from thermophilic bacteria Leon D. Kluskens In Dutch: Moleculaire studie naar eiwit- en suikerafbrekende enzymen uit thermofiele bacteriën Ph.D. thesis Wageningen, Wageningen, The Netherlands 2004 138 p., with summary in Dutch ISBN: 90-5808-971-1 Voor mijn ouders BEDANKT! Met het schrijven van dit dankwoord kan ik eindelijk beginnen aan het laatste, maar ook belangrijkste gedeelte van mijn proefschrift. Want zonder de hulp van een groot aantal mensen zou de verwezenlijking van dit boekje een stuk moeizamer, zoniet onmogelijk zijn geweest, en die personen wil hieronder graag bedanken. John en Willem, het tweejarig project kwam voor mij als een geschenk uit de hemel, aangezien ik nog niet wist wat ik wilde gaan doen, en omdat de stap naar een volledig AIO-project op dat moment nog zo groot leek. John, als copromotor, bedankt voor het vertrouwen dat je in me uitsprak door het contract een jaar later ‘gewoon’ te verlengen tot 4 jaar. Grotendeels dankzij de motiverende discussies en je relativeringsvermogen werden tegenslagen tijdens het onderzoek steeds weer overwonnen. Willem, als promotor, ondanks je drukke agenda was er altijd wel een afspraak te maken. Gesprekken met jou waren enorm prikkelend en dankzij jou werden de onderzoeksdoelen nooit uit het oog verloren. Paranimfen en vrienden Frank en Helmut, bedankt voor jullie steun. Frank, omdat je tijdens je onderzoek, het verhuizen, en het grootbrengen van je pasgeboren dochter nog tijd vond om mij te helpen met de vormgeving van dit boekje en al het andere wat er bij promoveren komt kijken. Helmut, bedankt voor het dienen als elektronische Amsterdamse praatpaal wanneer de onderzoeksfrustraties om een relativerende of ironische oneliner vroegen. Thijs Kaper, al vanaf 1995 kruisen onze wegen regelmatig, via afstudeervak en promotieonderzoek bij Bacteriële Genetica, tot nu in Groningen. Ontzettend bedankt voor het tijdelijk onderdak, maar ook voor de Murmeltiere- en elandenjacht, het ontbrekende bergverzet, de vele whisky’s en die ene Jägermeister. Alle ‘BacGenootjes’ bedankt: Alexandra, Ana, als Sister-in-arms tijdens de schrijfuurtjes in de avond; Ans, voor de vele etentjes, lab-aria’s en al die kleine dingen die het labwerk aangenamer maakten; Arjen, voor de kritische discussies over Bassie en Adriaan, het verschil tussen enkel- en dubbelgebeid en de gedeelde passie voor luchtgitaarmuziek; non-canonical Corné, dank voor de ontelbare practical jokes; Don, thanks for the enjoyable bike tours and your unlimited desire to get at least one drink; Gaël, Hauke, dank voor het zeer toffe weekendje Seattle; Ineke, voor de aanstekelijke golvende lachsalvo’s; Johan, ofwel de Beul van Bakel, voor de geselingen tijdens de Brug-tot-Brug tochtjes; Joyce, voor de vezelrijke discussies aan de lunchtafel; Judith, Ken, Krisztina, Nina, Odette, Pino, thanks for the hospitality during the Extremophiles meeting in Naples; Ronnie, Servé, kamergenoten Stan en Thijs Ettema (in één adem), dank voor het beheren van de Sudden-death schatkist, het triestighedenbord, de vlijmscherpe, rake en oergeestige toewensingen en het bijhouden van de thermofielengenoomsequentieteller; Valerie en Wilfried. Allen bedankt voor de talrijke ‘buitenschoolse activiteiten’, (post-)congres uitstapjes, kartwedstrijden, waaierkoersen, broodnodige lunchgesprekken, cafésessies en uiteraard ook de wetenschappelijke discussies. Wim, ontzettend bedankt voor het bij-de-tijd houden van mijn computer en voor het opleuken van mijn laptop. Ria (door geen koffieautomaat te vervangen), Nees, Francis, en Renée, bedankt voor het orde scheppen in alle administratieve bijkomstigheden. Iedereen die werkzaam is op het Laboratorium voor Microbiologie en die enigerwijze heeft bijgedragen tot dit proefschrift, van harte bedankt. Een aantal studenten hebben in de afgelopen jaren een wezenlijke bijdrage geleverd aan mijn onderzoek. Teun, Fokko, Jasper en Jurrit, zeer bedankt voor jullie inzet. De contacten zijn niet beperkt gebleven tot het Laboratorium voor Microbiologie alleen. Gert- Jan, de beslissing om met jou samen te gaan werken is van wezenlijk belang geweest voor mijn onderzoek. Ik heb veel opgestoken van je doelgerichte aanpak en kennis van zaken op het gebied van pectinolytische enzymen, en dit is maximaal ten goede gekomen van twee hoofdstukken. Professor Antranikian and Ruth Schwerdtfeger, thank you both for the nice collaboration and your contribution to the characterization of the keratinase; Jeong-Sun Kim, thank you for its successful crystallization. I am very grateful to Professor Kelly and the people from the Hyperthermophile Group. Thanks to you my stay in Raleigh has been both fruitful and enjoyable. Don, many thanks for letting me stay at your place, not to mention for getting me hooked on ice hockey and Krispy Kremes. I’m sure we’ll meet again somewhere. Mijn (voormalig) huisgenoten van Asterstraat 205, Always-vrienden Ingrid, Henriette en Marc als bewoners van het eerste uur, en verder Lea, Sander, Thijs E., en Krisztina, hartelijk dank voor de nodige uurtjes ontspanning naast mijn werk. Erbijblijfbijen, ontstaan in Wageningen en inmiddels bijna allemaal uitgevlogen, bedankt voor de afleiding en de blijvende contacten. Mijn huidige werkgever BioMaDe en in het bijzonder Gert Moll wil ik bedanken voor het in de gelegenheid stellen mijn proefschrift af te kunnen ronden. Alcina docinha, agradeço-te imenso pelo teu apoio moral, pelos teus conselhos e pelo teu carinho embora por vezes tivesse que ser à distância. Dentro em breve vamos estar finalmente juntos. Tot slot wil ik mijn ouders en zus Marion bedanken voor de morele steun en interesse die jullie altijd getoond hebben, ook al was het soms moeilijk om precies uit te leggen wat ik allemaal aan het doen was. Pap en mam, bedankt voor alle mogelijkheden die ik dankzij jullie heb kunnen benutten: Dit boekje is voor jullie. TABLE OF CONTENTS CHAPTER 1 General introduction 1 CHAPTER 2 Molecular characterization of fervidolysin, a subtilisin-like serine protease 25 from the thermophilic bacterium Fervidobacterium pennivorans CHAPTER 3 Crystal structure of fervidolysin from Fervidobacterium pennivorans, a 45 keratinolytic enzyme related to subtilisin CHAPTER 4 Isolation, expression and characterization of a glucose isomerase produced 63 by the thermophilic bacterium Fervidobacterium gondwanense CHAPTER 5 Molecular and biochemical characterisation of the thermo-active family 1 73 pectate lyase from the hyperthermophilic bacterium Thermotoga maritima CHAPTER 6 PelB from the hyperthermophilic bacterium Thermotoga maritima 91 encodes a fungal-like intracellular exopolygalacturonase CHAPTER 7 Transcriptional analysis of pectin catabolic pathways in the 107 hyperthermophile Thermotoga maritima CHAPTER 8 Summary and concluding remarks 125 CHAPTER 9 Samenvatting en conclusies 129 Curriculum vitae 135 List of publications 137 General Introduction 1 General Introduction 1 Chapter 1 Life at high temperatures Life as we know it has been observed in all existing ecological niches, including extreme conditions, such as high and low temperatures (thermophiles vs. psychrophiles), acidic and alkaline pH conditions (acidophiles vs. alkaliphiles), high pressure (barophiles), and high salt concentrations (halophiles)(Table 1.1). Of all these so-called extremophiles, the organisms isolated most frequently and studied most extensively over the last two decades, are the thermophilic microorganisms. Whereas certain animals and plants can cope with temperatures up to 50°C, some prokaryotes can exhibit optimal growth near the boiling point of water, or even beyond. In particular, the group of thermophilic and hyperthermophilic microorganisms has caught the attention of many scientists. In general, thermophiles have their temperature optimum between 50 and 80°C, whereas the hyperthermophiles exhibit growth beyond 80°C (121)(Table 1.1). Currently topping the list is the crenarchaeon “Strain 121”, most closely related to Pyrodictium occultum and Pyrobaculum aerophilum, which is able to grow at 121°C with doubling time of 24 hours (52). For a long time the subdivision of organisms was based on their cellular architecture, which resulted in two domains: prokarya and eukarya (20). This traditional concept came to an end with the discovery of a third domain by Woese and coworkers (126). Based on comparison of 16S/18S rRNA sequences, present in all living organisms, the prokaryotes were subdivided in bacteria and archaea. It is mainly this last domain that concludes the extremophiles; with the exception
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