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Characterization of DCAF17 with Specific, Polyclonal Antibodies

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Characterization of DCAF17 with Specific, Polyclonal Antibodies Aus der Medizinischen Klinik und Poliklinik I der Universität Würzburg Direktor: Prof. Dr. med. Stefan Frantz Molecular mechanisms underlying Woodhouse-Sakati syndrome: characterization of DCAF17 with specific, polyclonal antibodies. Inaugural - Dissertation zur Erlangung der Doktorwürde der Medizinischen Fakultät der Julius-Maximilians-Universität Würzburg vorgelegt von Joanna Blocka aus Heidelberg Würzburg, März 2018 Referent: Priv.-Doz. Dr. med. Dr. rer. nat. Matthias Kroiß Korreferent: Prof. Dr. med. Thomas Haaf Dekan: Prof. Dr. med. Matthias Frosch Tag der mündlichen Prüfung: 10.12.2018 Die Promovendin ist Ärztin. TABLE OF CONTENTS 1 INTRODUCTION .................................................................................................................... 1 1.1 A PREVIOUSLY UNDESCRIBED MULTISYSTEMIC DISEASE .................................................... 1 1.1.1 First report and clinical characteristics of Woodhouse-Sakati syndrome .................................... 1 1.1.2 Molecular background of the disease .......................................................................................... 2 Mutations in C2orf37/DCAF17 gene cause WSS. ............................................................................ 2 WSS protein is the product of c2orf37/DCAF17 gene. ..................................................................... 3 DCAF17 is connected to the ubiquitin pathway through DDB1/Cul4 E3 ligase. ............................. 4 1.2 THE AIM OF THIS PROJECT .................................................................................................... 5 2 MATERIALS AND METHODS ............................................................................................. 6 2.1 BIOINFORMATICS ................................................................................................................. 6 2.2 DEVICES ............................................................................................................................... 6 2.3 DISPOSABLE UTENSILS ......................................................................................................... 7 2.4 CHEMICALS AND REAGENTS ................................................................................................ 7 Enzymes ............................................................................................................................................ 7 Commercial antibodies ..................................................................................................................... 8 Other reagents .................................................................................................................................. 8 DNA purification kits ........................................................................................................................ 9 Bacterial strains ............................................................................................................................... 9 2.5 MOLECULAR BIOLOGY METHODS ........................................................................................ 9 Rationale: establishment of specific, polyclonal antibodies: anti-WSS(493-520), -WSS(80-88), - WSS(412-423), and -WSS(493-511) ................................................................................................. 9 Preparative polymerase chain reaction .......................................................................................... 12 DNA gel electrophoresis ................................................................................................................. 13 DNA hydrolysis with restriction endonucleases ............................................................................. 13 Ligation of DNA fragments............................................................................................................. 14 Transformation of bacterial cells with plasmid constructs ............................................................. 15 Colony PCR of transformed DH5α E. coli clones .......................................................................... 16 2.6 PROTEIN ANALYSIS ............................................................................................................ 17 2.6.1 General methods of protein examination ................................................................................... 17 Expression of recombinant WSS(493-520)/His-tag in Rosetta 2 cells ............................................ 17 SDS-PAGE protein separation ....................................................................................................... 18 Gel staining with standard Coomassie method .............................................................................. 20 Affinity purification of WSS(493-520)/His-tag fusion protein on Ni-IDA Agarose ........................ 20 Protein dialysis ............................................................................................................................... 21 Coupling of WSS(493-520) peptide to CNBr-Activated Sepharose ................................................ 22 Affinity purification of anti-WSS(493-520) antibodies ................................................................... 22 Coupling of WSS(80-88) and WSS(412-423) peptides to SulfoLink Coupling Resin ...................... 23 Affinity purification of anti-WSS(80-88) and -WSS(412-423) antibodies ....................................... 24 Coupling of WSS(493-511) peptide to NHS-Activated Sepharose .................................................. 25 Affinity purification of anti-WSS(493-511) antibody ...................................................................... 25 BCA-Assay-based measurement of protein concentration ............................................................. 26 Western blot .................................................................................................................................... 27 Staining of PVDF membranes with Amido Black method .............................................................. 27 Application of primary and secondary antibodies to PDVF membranes ....................................... 27 Development of X-ray films ............................................................................................................ 28 Subcellular protein fractionation ................................................................................................... 28 Isolation of nuclear extract............................................................................................................. 30 Isolation of nuclear envelopes ........................................................................................................ 30 Isolation of nucleoli ........................................................................................................................ 31 2.6.2 Specific biochemical methods of protein characterization ........................................................ 32 Detachment of α- and β-WSS from nuclear envelopes with NaCl and urea ................................... 32 DNase and RNase digestion of nuclear and nucleolar extract ....................................................... 33 Analysis of a posttranslational modification of the WSS protein: deglycosylation and dephosphorylation .......................................................................................................................... 34 2.6.3 Immunofluorescence microscopy .............................................................................................. 39 3 RESULTS................................................................................................................................ 40 3.1.1 Cloning and expression of WSS(493-520) in pET28a(+) with subsequent affinity purification i of anti-WSS(493-520) antibodies ....................................................................................................... 40 Cloning of WSS(493-520) into pET28a(+) ..................................................................................... 40 Expression of WSS(493-520)/His-tag in E. coli .............................................................................. 41 Coupling and affinity purification of WSS(493-520)/His-tag on Ni-IDA agarose.......................... 41 Affinity purification of anti-WSS(493-520) antibodies ................................................................... 42 3.1.2 Affinity purification of anti-WSS(80-88), -(412-423), and -(493-511) antibodies .................... 44 Affinity purification of anti-WSS(80-88) and -WSS(412-423) antibodies on SulfoLink Couplin Resin ............................................................................................................................................... 44 Affinity purification of anti-WSS(493-511) antibodies on NHS-Activated Agarose ....................... 46 3.2 DETERMINATION OF THE SUBCELLULAR WSS PROTEIN LOCALIZATION AND REDISTRIBUTION OF ITS ISOFORMS .......................................................................................... 48 3.2.1 Immunofluorescence ................................................................................................................. 48 Anti-WSS(493-520) antibody shows a strong nucleolar and a dispersed nuclear signal. .............. 48 3.2.2 Biochemical methods of cell fractionation and characterization of DCAF17 ........................... 49 WSS protein is localized predominantly in the soluble nuclear fraction. ......................................
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