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Nirmala Padmanabhan-Phd Thesis The Saccharomyces cerevisiae HtrA orthologue, Ynm3, is a chaperone-protease that aids survival under heat stress PhD Thesis in partial fulfilment of the requirements for the degree “Doctor of Philosophy” in the Molecular Biology Program at the Georg August University Göttingen, Faculty of Biology submitted by Nirmala Padmanabhan born in Trivandrum, India 2008 I hereby declare that the PhD thesis entitled “The Saccharomyces cerevisiae HtrA orthologue, Ynm3, is a chaperone-protease that aids survival under heat stress” has been written independently and with no other sources and aids than quoted. Nirmala Padmanabhan i To my grandfather, Late Mr. P. Rama Iyer ii Acknowledgements Acknowledgements This work was performed in the Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg August University, Goettingen. I am grateful to my mentor and supervisor Prof. Gerhard H. Braus for giving me the opportunity to pursue my PhD work in his laboratory and for his constant encouragement and support. I am thankful to Dr. Lars Fichtner for his involvement in my work and for his friendly support throughout my PhD. My doctoral committee members, Prof. Christiane Gatz and Prof. Jörg B. Schulz have given me their time and support, for which I am thankful. Prof. Schulz was involved in my work from the very beginning and has invited me to regularly present my work in his departmental seminars. I am beholden to the following people for their help and collaborations, without which this work would not be in its present form. Ms. Maria Meyer for the vast amount of technical assistance and for organizing the activities of Lab 107, which made working easier. Dr. Achim Dickmanns for his interest in my work, which resulted in a fruitful collaboration. Ms. Annette Berndt for performing the protein purifications. Dr. Susanne Behrens-Kneip for teaching me how to perform the chaperone activity assay. Dr. Özgur Bayram for his willingness to help with difficult molecular biology techniques. Dr. Oliver Valerius for performing mass spectrometry during my search for protein interaction partners of Ynm3. Dr. Micheal Hoppert for performing electron microscopy during the initial phase of this work. Ms. Heidi Northemann and Ms. Nicole Scheiter for helping me with official tasks and ordering of chemicals. I thank all the lab rotation students who have worked with me and all the other members of the department who have helped me during the course of my work. For an enjoyable working atmosphere, I wish to thank both past and present members of lab 107, Dr. Lars Fichtner, Ms. Maria Meyer, Ms. Seema Singh, Dr. Susanna Braus-Stromeyer, Mr. Tran Van Tuan, Mr. Christian Timpner, Ms. Peggy Findeisen, Mr. Christoph Braun, Mr. Marc Dumkow, Ms. Melanie Nolte and Ms. Katrin Hartwich. I am thankful to Dr. Steffen Burkhardt, the co-ordinator of the International Molecular Biology Program for making life easier in Göttingen. I would like to thank my husband Dr. Tabrez J. Siddiqui for his immense patience, love, encouragement and for being my pillar of support. My deep fondness and gratitude for my mother Ms. Parvathy Padmanabhan and my father Mr. R. Padmanabhan for all that they have given me and my sister Ms. Sumathy Mohan for her love and support. I remember with deep respect all my grandparents, all of whom are no more. I dedicate this work to my late grandfather, Mr. P. Rama Iyer who dreamed to see me fly in colours. Lastly, I wish to thank all my relatives and friends for their faith in what I do. iii Table of contents Table of contents Abbreviations ................................................................................................... 1 Abstract ............................................................................................................ 3 1. Introduction................................................................................................. 5 1.1 Protein quality control....................................................................................... 5 1.2 Classic chaperones and proteases...................................................................... 6 1.2.1 Molecular chaperones ...........................................................................................7 1.2.2 ATP-dependent proteases......................................................................................7 1.2.3 The 26S proteasome..............................................................................................8 1.3 Substrate recognition by chaperones and proteases ........................................... 9 1.4 Role of chaperones in protein degradation ...................................................... 11 1.5 Protein folding catalysts.................................................................................. 12 1.6 Autophagy ...................................................................................................... 13 1.7 Quality control of secretory proteins ............................................................... 14 1.8 Failure of protein quality control: implications for the development of neurodegenerative diseases .................................................................................... 15 1.9 The HtrA family of serine proteases................................................................ 18 1.9.1 Bacterial HtrAs ....................................................................................................18 1.9.2 Mammalian HtrA2/Omi ......................................................................................19 1.9.3 The Saccharomyces cerevisiae HtrA orthologue Ynm3.......................................21 1.10 Aims of this study......................................................................................... 22 2. Materials and Methods ............................................................................. 24 2.1 Materials......................................................................................................... 24 2.1.1 Yeast strains........................................................................................................24 2.1.2 Growth conditions...............................................................................................26 2.1.3 Plasmids..............................................................................................................26 2.1.4 Oligonucleotides .................................................................................................26 2.2 Methods.......................................................................................................... 36 2.2.1 DNA sequence analysis.......................................................................................36 2.2.2 Polymerase Chain Reaction.................................................................................36 2.2.3 Restriction digestion of DNA..............................................................................37 2.2.4 Preparation of DNA for ligation..........................................................................37 2.2.5 Preparation of chemically competent E.coli cells.................................................37 2.2.6 Transformation of chemically competent E.coli cells...........................................38 2.2.7 Plasmid DNA purification...................................................................................38 2.2.8 DNA sequencing.................................................................................................39 2.2.9 Site directed mutagenesis ....................................................................................39 2.2.10 Overlap extension PCR .....................................................................................40 2.2.11 Amplification of DNA libraries following electroporation.................................40 2.2.12 Transformation of yeast cells.............................................................................41 2.2.12.1 Preparation of competent yeast cells..............................................................41 2.2.12.2 Transformation of competent yeast cells.........................................................41 2.2.13 Isolation of DNA from yeast cells .....................................................................42 2.2.14 Genetic suppressor screen .................................................................................43 2.2.15 Growth tests......................................................................................................43 2.2.16 Survival after heat shock treatment....................................................................44 2.2.17 Preparation of yeast cell crude extracts for Western blotting..............................44 2.2.18 Protein immunoblotting.....................................................................................45 iv Table of contents 2.2.19 Dihydrorhodamine staining ...............................................................................46 2.2.20 Fluorescence microscopy of yeast cells .............................................................46 2.2.21 Protein purification from E. coli........................................................................46 2.2.22 Proteolysis assay ...............................................................................................47 2.2.23 Chaperone activity assay ...................................................................................47 2.2.23.1 Preparation of substrate (citrate synthase).......................................................47
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