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The Relevance of Transhydrogenases and Heterologous Phosphagen Kinases for Microbial Cofactor Metabolism

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The Relevance of Transhydrogenases and Heterologous Phosphagen Kinases for Microbial Cofactor Metabolism Research Collection Doctoral Thesis The relevance of transhydrogenases and heterologous phosphagen kinases for microbial cofactor metabolism Author(s): Canonaco, Fabrizio Publication Date: 2003 Permanent Link: https://doi.org/10.3929/ethz-a-004525971 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH.Nr. 15040 The relevance of transhydrogenases and heterologous phosphagen kinases for microbial cofactor metabolism A dissertation submitted to the SWISS FEDERAL INSTITUTE OF TECHNOLOGY ZURICH for the degree of Doctor of Natural Science Presented by Fabrizio Canonaco Dipl. Natw. ETH born April 22nd, 1975 in Locarno, Switzerland Accepted on the recommendation of PD Dr. U. Sauer Prof. T. Wallimann PD Dr. U. Schlattner Prof. H. Hennecke 2003 Seite Leer Blank 2 ACKNOWLEDGEMENTS and further back to the When I think back to the time point where I began my PhD, in a how one recalls as have being important years of the study, it is surprising many people I owe a it is not to name them all, but to some people way or another. In this section, possible PhD. tribute, because without them I would not have succeeded in finishing my and it could not have been else. They The first big 'thank you' goes to my family, to without me in I did not want do, always played a central role in my life, pushing anything their sacrifices and their encouragements I but supporting me in everything I chose. Without would not have been writing these pages. for the sincere they offered mc To other people I owe my deepest gratitude, friendship for the stories behind the in the difficult moments I encountered. There is no place here to me alive' in the last years, and essential contribution every one of them gave 'keeping these nicknames, in neither I would be able to put them in words, so I simply list people by as casual order. Jonne, Maud, Droopy, Pimpa, Zambo, Sonda, Claudia, Mitch, your loyalty friends will never be forgotten. in Uwe Sauer. In his My scientific and professional career had a very competent mentor later as a PhD a student five and I continued group I began my scientific career as years ago, and to blame when are going bad student. As group leader, it would be easy people things Uwe had words of encouragement when congratulate them as they succeed, but always critics as small successes made motivation was low. He also had precise and appropriated my For his of 'the boss' and the me blind towards new upcoming problems. original way being I owe him contribution to my scientific maturation my deepest gratitude. kinases was conducted in collaboration The part of the project involving phosphagen the Cell Institute of the ETH Zürich. I'm with the group of Theo Wallimann, at Biology also co-referees for this deeply thankful to Uwe Schlattner and Theo Wallimann, which are had. I also thank work, for their intriguing suggestions and the stimulating discussions we in the examination of this Prof. Hauke Hennecke for having accepted the role of co-referee doctoral thesis. 3 the contribution of students I had Parts of the results presented here were achieved with Pascal Baillod and Lorena the opportunity to train. I hope I could have helped Sylvia Heri, Jaramillo, the way they helped me. is not I therefore will miss and No job results in success if the work atmosphere optimal. collaborative attitude of the Sauer Group people, where I always never forget the friendly and and Last to Marco, Eliane, Ursi, Lars, Jörg. felt part of a team. Special thanks Peter, Nicola, I the at the Institute of which had but not least, thanks to all the other people Biotechnology opportunity to know and work with. 4 TABLE OF CONTENTS 7 SUMMARY/ SOMMARIO 11 CHAPTER 1 General introduction isomerase 55 CHAPTER 2 Metabolic flux response to phosphoglucose knock-out in Escherichia coli and impact of overexpression of the soluble transhydrogenase UdhA 69 CHAPTER 3 Dissecting the role of soluble and membrane-bound transhydrogenases UdhA and PntAB in Escherichia coli 95 CHAPTER 4 Functional expression of phosphagen kinase systems confers resistance to transient stresses in Saccharomyces cerevisiae by buffering the ATP pool 119 CHAPTER 5 Functional expression of arginine kinase improves recovery from pH stress of Escherichia coli 133 CONCLUSIONS AND OUTLOOK 135 ABBREVIATIONS LIST 139 CURRICULUM VITAE 5 Seite Leer / Blank leaf 6 "Obstacles are thosefrightful things you see when you take your eyes offyour goal" Henry Ford SUMMARY NADPH and how The scientific topic of this thesis is how micro-organisms generate that transient protection during they can be equipped with ATP buffering systems provide nucleotides are essential cofactors for cellular metabolism, energy stress. ATP and pyridine utilized for linking catabolism to anabolism. While NADH is almost exclusively energy reactions. generation, NADPH provides reducing power for biosynthetic construction and metabolic flux In Chapter 2 and Chapter 3, we show through mutant have distinct roles in NADPH analysis that the two transhydrogenases of Escherichia coli is an source of metabolism. The membrane-bound transhydrogenase PntAB important the of NAPDH during exponential growth on glucose by catalyzing transhydrogenation in the reverse NADH to NADPH. The soluble transhydrogenase UdhA, contrast, catalyzes on but reaction from NAPDH to NADH. This function is not necessary during growth glucose of which a of critical on substrates such as acetate, the catabolism generates higher proportion NADPH. constitute and Vertebrates contain so-called phosphagen kinase systems, which spatial demand. In to overcome of fluctuating energy temporal energy buffering systems periods kinase in Saccharomcyes cerevisiae that Chapter 4 we install such phosphagen systems show the functional of arginine normally does not contain such systems. We then expression kinase Environmental conditions of fluctuating kinase, one particular phosphagen system. S. cerevisiae in chemostat culture energy demand are installed by growing glucose-limited intracellular ATP level was with interrupted feeding. In the absence of glucose feeding, the in but it was stabilized at a much higher level shown to drop significantly in the control strain, that buffering the arginine kinase-expressing strain. Our results demonstrate temporal energy kinases that can be transferred to phylogenetically very is an intrinsic property of phosphagen distant organism. 7 of kinase in the The 5th chapter affords then a short study on the expression arginine that kinase significantly bacterium E. coli. Specifically, we could show arginine expression other that was to exert among improves the recovery after a transient pH stress, anticipated effects and ATP stress. 8 che si "GH ostacoli sono quelle cose spaventose scorgono quando si perde di vista il proprio obiettivo" Henry Ford SOMMARIO l'NADPH nei L'argomento scientifico di questa tesi è come venga generato in con sistemi per FATP microorganismi e come questi possano venire equipaggiati tampone lo stress L'ATP e i nucleotidi a grado di fornire una protezione transitoria durante energetico. metabolismo cellulare e l'anabolismo al piridina sono cofattori essenziali del collegano di catabolismo. Mentre l'NADH è utilizzato quasi esclusivamente per la produzione energia, biosintetiche. l'NADPH fornisce potere riduttivo per le reazioni tramite la costruzione di mutanti e l'analisi Nel Capitolo 2 e nel Capitolo 3 mostriamo coli hanno ruoli dei flussi metabolici che le due transidrogenasi del batterio Escherichia membranare PntAB è un distinti nel metabolismo dell'NADPH. La transidrogenasi catalizzando la importante sorgente di NADPH durante la crescita esponenziale su glucosio, necessaria durante la transidrogenazione dell'NADH in NADPH. Questa funzione non è una in corne il cui catabolismo genera crescita su glucosio, ma è critica su substrati l'acetato, proporzione più NADPH. che costituisce un I vertebrati contengono il cosddetto sistema di fosfagene chinasi, momenti di fluttuazione energetica. Nel sistema tampone spaziale e temporale per affrontare chinasi nel lievito Saccharomyces Capitolo 4, installiamo un taie sistema di fosfagene mostriamo funzionale délia cerevisiae che ne è normalmente privo. In seguito l'espressione délia délie chinasi. Condizioni arginina chinasi, un particolare membro famiglia fosfagene crescendo S. ambientali che causano fluttuazioni nella domanda di energia vengono generate con alimentazione discontinua. In cerevisiae in un medium di coltura limitato in glucosio il livello intracellulare di ATP diminuisce in assenza di una alimentazione di glucosio, ma risulta stabilizzato e mantiene un livello più maniera significativa nel ceppo di controllo, chinasi. I nostri risultati dimostrano quindi corne alto nel ceppo in grado di esprimere arginina intrinseca délie chinasi la funzione di tampone temporale sia una proprietà fosfagene trasferibile ad organismi fîlogeneticamente molto distanti. 9 chinasi nel batterio Il 5° capitolo affronta un brève studio suU'espressione dell'arginina chinasi migliori in E. coli. Nello specifico, mostriamo come l'espressione dell'arginina transiente da conosciuto per generare tra maniera significativa il recupero da uno stress pH, gli altri effetti uno stress da ATP. 10 CHAPTER 1 General introduction 11 NADH TWO FACTORS LINK CATABOLISM TO ANABOLISM: ATP AND need to survive In principle, all living organisms have two goals. Firstly,
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