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Dissertation DISSERTATION Titel der Dissertation „Biochemistry meets sequence analytics - investigation of predicted posttranslational lipid modifications and characterization of a predicted acetyltransferase “ Verfasser Mag. Wolfgang Benetka angestrebter akademischer Grad Doktor der Naturwissenschaften (Dr. rer. nat.) Wien, 2009 Studienkennzahl lt. Studienblatt: A 091 419 Dissertationsgebiet lt. Studienblatt: Dr.-Studium der Naturwissenschaften Chemie Betreuerin / Betreuer: Dr. Frank Eisenhaber ii Acknowledgments First and most important, my thanks go to my family, especially my wife Patricia who always raised my spirits when a day at the lab had left nothing but dark clouds over my head, my parents who gave me the opportunity to go to university and always supported me, and my son Felix whose smile made me forget any problems occupying my thoughts. Second, I want to express my gratitude to all the colleagues who accompanied me during my PhD. Manfred Koranda and Michaela Sammer were my lab colleagues during the first half of my PhD. Manfred was my direct contact person for a long time and Michaela provided the results my work concerning mec-17 was based upon and also participated in the experiments on the localization of NFAT5 and now continues this project. I want to thank Birgit Eisenhaber, Sebastian Maurer-Stroh, Maria Novatchkova, Alex Schleiffer and all other members of the Eisenhaber group from the Institute of molecular pathology (IMP), who provided the basis for my work and always found a reason to get together and enjoy some Belgian cherry beer and chocolate or other delicious food. In addition, I want to thank the group of Cecile Brocard, especially Sophie Merich and Johannes Koch, who shared the lab and their experiences and ideas with me during the second half of my PhD, as well as the members of the lab of Andreas Hartig. Special thanks go to my supervisor Frank Eisenhaber who always valued my work and provided me with the opportunity to finish my PhD in Vienna. I also want to thank all the people who contributed to my work by providing material or a helping hand. Egon Ogris from the Department of Medical Biochemistry provided a mouse brain cDNA library, the yeast strain EGY48 as well as the bacterial strain KC8 and a LexA antibody. Andreas Hartig kindly provided all plasmids needed in the yeast two-hybrid screen. James E. Samuel from the Texas A&M Health Science Center provided all cDNA clones from Coxiella burnetii (C. b. ). The cDNA encoding Epb4.1l3 was provided by John Conboy from the Ernest Orlando Lawrence Berkeley Laboratory in California, and the cDNAs encoding numb-A and neur-B from Drosophila melanogaster (D. m. ) were provided by Jürgen A. Knoblich from the Institute of Molecular Biotechnology. His group also helped with the localization experiments in transgenic flies, especially Jörg Betschinger and Ralph Neumüller. iii iv Abstract Sequence analytical tools can provide predictions of aspects of protein function such as enzymatic activities or sites of posttranslational modifications in protein sequences. Generally, an experimental verification is needed for these predictions. In the case of lipid posttranslational modifications, the standard experimental techniques are time-consuming and laborious. In this work, a new in vitro assay based upon the detection of incorporation of radioactively labeled lipid anchor precursors into in vitro translated proteins with a thin layer chromatography scanner was developed. This method drastically reduces time effort, it combines protein yield and anchor incorporation testing in a single experiment, and it is both applicable for prenylation and myristoylation. This assay has been used for investigation of prenylation and myristoylation of selected candidate proteins. Localization studies with GFP fusion proteins were used to verify the in vivo relevance of the results. The general potential of prenylation motifs in bacterial proteins to be modified by eukaryotic prenyltransferases was demonstrated in vitro for a so far uncharacterized, ankyrin repeat containing protein from Coxiella burnetii . The localization studies also suggest prenylation of an F-Box containing protein from Legionella pneumophila . The influence of SNPs on the functionality of prenylation motifs was investigated and found significant in the case of W353G in human ALDH3B2. Myristoylation of fly proteins important in asymmetric cell division and neuronal development (numb-A, neuralized B and C and Par-1 isoform Q) as well as homologous proteins from mouse (neuralized-like 1 and 2) was demonstrated. The importance of distinguishing between isoforms with differing capabilities for posttranslational modifications is discussed. Myristoylation of the human transcription factor NFAT5-A was shown to influence localization to the nucleus suggesting a new mechanism for regulation of nuclear shuttling of transcription factors. Sequence similarities with the HATs from the GNAT superfamily suggested a function as histone acetyltransferase for mec-17 from C. elegans as well as homologous proteins from other organisms. Preliminary results of enzymatic activity tests and localization studies indicated that the protein has N-acetyltransferase activity; yet, histones might not be the primary substrate for acetylation by mec-17. A yeast two-hybrid screen revealed several proteins interacting with mouse mec-17 that could be either substrates or members of a multiprotein complex. Interaction with one of the found proteins, Kctd13, was verified biochemically by co-immunoprecipitation. v vi Zusammenfassung Sequenzanalytische Methoden ermöglichen die Vorhersage verschiedener Aspekte der Funktion von Proteinen, wie enzymatische Aktivität oder die Position von posttranslationalen Modifikationen in Proteinsequenzen. In den meisten Fällen bedürfen diese Vorhersagen experimenteller Überprüfung. Im Fall von posttranslationalen Lipidmodifikationen ist die gängige Methodik zeit- und arbeitsaufwendig. In dieser Arbeit wurde deshalb ein neuer in vitro Assay entwickelt, der auf der Detektion des Einbaus radioaktiv markierter Vorläufermoleküle der Lipidanker in in vitro translatierte Proteine mittels eines Dünnschichtchromatographie-Scanners basiert. Diese Methode reduziert den Zeitaufwand merklich, sie kombiniert die Bestimmung der Proteinausbeute und des eingebauten Lipidankers in einem einzelnen Experiment und ist für die Untersuchung von sowohl Prenylierung als auch Myristoylierung anwendbar. Diese Technik wurde zur Untersuchung von Prenylierung und Myristoylierung ausgewählter Proteine verwendet. Lokalisationsstudien mit GFP-Fusionsproteinen wurden zur Bestätigung der in vivo Relevanz der Ergebnisse herangezogen. Die prinzipielle Möglichkeit der Modifikation von Prenylierungsmotiven bakterieller Proteine durch eukaryotische Prenyltransferasen wurde in vitro am Beispiel eines bisher nicht charakterisierten Proteins aus Coxiella burnetii gezeigt, welches so genannte Ankyrin repeats enthält. Die Lokalisationsstudien legen auch die Prenylierung eines Proteins mit einer F-Box-Domäne aus L egionella pneumophila nahe. Weiters wurde der Einfluss von SNPs auf die Funktionalität von Prenylierungsmotiven untersucht und im Fall von W353G im humanen Protein ALDH3B2 als signifikant bewertet. Die Myristoylierung von Fliegenproteinen mit biologischer Bedeutung in asymmetrischer Zellteilung und Entwicklung des Nervensystems (numb-A, neuralized B und C und Par-1 Isoform Q) sowie deren homologen Mausproteinen (neuralized-like 1 und 2) wurde gezeigt. Die Wichtigkeit der Unterscheidung zwischen Isoformen mit unterschiedlichem Potential für posttranslationale Modifikationen wird diskutiert. Die Myristoylierung des humanen Transkriptionsfaktors NFAT5-A sowie deren Bedeutung für dessen nukleare Lokalisation wurden gezeigt und legen einen neuen Mechanismus für die Regulierung des Kerntransports von Transkriptionsfaktoren nahe. Ähnlichkeiten der Sequenz von mec-17 aus C. elegans und homologen Proteinen aus anderen Organismen mit HATs aus der GNAT-Familie deuteten auf eine Funktion als Histon-Acetyltransferase hin. Die Ergebnisse von Experimenten zur Enzymaktivität und vii Lokalisation des Proteins zeigen N-Acetyltransferase-Aktivität. Allerdings scheinen Histone nicht das bevorzugte Substrat zu sein. Mit einem Yeast 2-Hybrid Screen wurden daher einige Interaktionspartner des Maushomologs identifiziert. Diese kommen als Substrat oder Bestandteile eines Multiproteinkomplexes in Frage. Die Interaktion mit einem der Kandidaten, Kctd13, wurde durch Co-Immunopräzipitation biochemisch bestätigt. viii Table of contents 1 AIM OF THE THESIS ..........................................................................................................................1 1.1 DEVELOPMENT AND APPLICATION OF AN IN VITRO ASSAY FOR THE INVESTIGATION OF LIPID POSTTRANSLATIONAL MODIFICATIONS ..........................................................................................................1 1.2 CHARACTERIZATION OF A PREDICTED PROTEIN N-ACETYLTRANSFERASE .......................................2 1.3 SUMMARY OF AIMS ..........................................................................................................................3 2 INTRODUCTION..................................................................................................................................5 2.1 MYRISTOYLATION ...........................................................................................................................5 2.1.1 Function in membrane attachment.............................................................................................5
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