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Functional Analysis of the Anion Exchanger 1 by Knock in Mouse Models

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Functional Analysis of the Anion Exchanger 1 by Knock in Mouse Models Functional analysis of the anion exchanger 1 by knock in mouse models DISSERTATION zur Erlangung des akademischen Grades doctor rerum naturalium (Dr. rer. nat.) vorgelegt dem Rat der Medizinischen Fakultät der Friedrich-Schiller-Universität Jena von Rizwan Mumtaz (M.sc.) geboren am 01.12.1979 in Lahore (Pakistan) im Oktober 2011 Gutachter 1. Prof. Dr. Christian Hübner Institute of Human Genetics, University Hospital Jena, Germany 2. Prof. Dr. Carsten A. Wagner Institute of Physiology, University of Zurich, Switzerland 3. Prof. Dr. Dominique Eladari Faculty of Medicine, University of Paris Descartes, France Tag der öffentlichen Verteidigung: 5th June 2012 To my Abbu, Ammi and Phophoo List of abbreviations °C Degree celsius AD Autosomal dominant AE 1 Human Anion exchanger 1 Ae 1 Mouse Anion exchanger 1 AR Autosomal recessive ATP Adenosine triphosphate bp Base pair CA II Carbonic anhydrase 2 CCD Cortical collecting duct cDNA Complementary deoxyribonucleic acid Cl− Chloride CO2 Carbon dioxide C-terminal Carboxyl terminal DAPI 4',6-Diamidino-2-phenylindole dATP Deoxyadenosine-5’-triphosphate dCTP Deoxycytidine-5’-triphosphate dGTP Deoxyguanosine-5’-triphosphate DIDS 4,4’-Diisothiocyanatostilbene-2,2’-disulfonate DNA Deoxyribonucleic acid dRTA Distal renal tubular acidosis DTA Diphtheria toxin A dTTP Deoxythymidine-5’-triphosphate eAE1 Erythrocyte AE1 isoform EDTA Ethylene diamide tetra acetic acid ER Endoplasmic reticulum h Hour (s) H+ Proton H+-ATPase Hydrogen adenosine triphosphatase − HCO3 Bicarbonate HEK-293 cells Human embryonic kidney 293 cells HEPES 4-(2-hydroxyethyl)-1-Piperazineethanesulfonic acid HS Hereditary spherocytosis IMCD cells Inner medullary collecting duct cells K+ Potassium kAE1 Kidney AE1 isoform kDa kilo Dalton KI Knock In KO Knockout LB medium Luria Bertani medium MCD Medullary collecting ducts MDCK cells Madin Darby canine kidney cells mg Milligram (s) min Minute (s) ml Milliliter (s) mM Millimolar mmol Millimole MOPS 3-(N-morpholino) propanesulphonic acid mRNA Messenger ribonucleic acid Na+ Sodium NaCl Sodium chloride NBC Sodium/bicarbonate co-transporter neo Neomycine Casette ng Nanogram (s) NH4Cl Ammonium chloride NHE Sodium/proton exchanger nM Nanomolar nmol Nanomole nt Nucleotide (s) N-terminal Amino terminal PBS Phosphate-buffered solution pCO2 Partial pressure of carbon dioxide PCR Polymerase chain reaction pmol Picomole pO2 Partial pressure of oxygen RNA Ribonucleic acid RNase Ribonuclease rpm Revolutions per minute RT Room temperature SAO Southeast Asian ovalocytosis SDS Sodium dodecyl sulfate sec Second (s) SEM Standard error of the mean SLC Solute carrier SOC medium Super optimal broth TAE Tris-acetate-EDTA Taq Thermus aquaticus TBST Tris-buffered saline added with Tween 20 TM Transmembrane UV Ultraviolet v H+ATPase Vacuolar Hydrogen adenosine triphosphatase WT Wild-type α-IC cells α-Intercalated cells β-IC cells β-Intercalated cells μg Microgram (s) μl Microliter (s) μM Micromolar Contents Summary .................................................................................................................................... 1 Zusammenfassung ...................................................................................................................... 2 1. Introduction ............................................................................................................................ 3 1.1. Body homeostasis and acid-base balance ........................................................................ 3 1.2. Role of membrane proteins in acid-base balance ............................................................ 4 1.2.1. Passive and active transport across membranes ........................................................ 5 1.3. Solute carriers and anion exchanger proteins .................................................................. 5 1.3.1. Solute carrier family 4 (SLC4) and anion exchanger 1 (AE1) ................................. 6 1.4. Anion exchanger 1 (AE1, SLC4A1) ................................................................................ 7 1.4.1. Topological organization of AE1 .............................................................................. 9 1.5. The Kidney as an organ for acid-base balance .............................................................. 10 1.5.1. Basic anatomy ......................................................................................................... 10 1.5.2. Physiology of acid secretion by the kidney ............................................................ 10 1.6. Familial renal tubular acidosis ....................................................................................... 13 1.7. Mutations associated with the human AE1 gene ........................................................... 15 1.7.1. Mutations in AE1 causing erythrocyte phenotypes ................................................ 15 1.7.2. Distal renal tubular acidosis (dRTA) due to AE1 mutations .................................. 15 1.8. Aim of this study ........................................................................................................... 18 2. Materials and methods ......................................................................................................... 19 2.1. Materials ........................................................................................................................ 19 2.1.1. Chemicals ................................................................................................................ 19 2.1.2. Microbial strains and laboratory animals ................................................................ 19 2.1.3. Bacterial vectors ...................................................................................................... 19 2.1.4. Antibodies ............................................................................................................... 20 2.2. Methods ......................................................................................................................... 21 2.2.1. Microbiology methods ............................................................................................ 21 2.2.1.1. Preparation of chemocompetent bacteria ............................................................. 21 2.2.1.2. Transformation of competent bacteria ................................................................. 21 2.2.1.3. Screening of lambda phage library ...................................................................... 22 2.2.2. Molecular biology methods .................................................................................... 24 2.2.2.1. Cloning of targeting vector .................................................................................. 24 2.2.2.1.1. Restriction digest .............................................................................................. 24 2.2.2.1.2. Blunting of sticky ends and dephosphorylation ................................................ 24 2.2.2.1.3. Agarose gel electrophoresis .............................................................................. 24 2.2.2.1.4. DNA ligation ..................................................................................................... 25 2.2.2.1.5. DNA sequencing ............................................................................................... 25 2.2.3. Isolation and purification of nucleic acids .............................................................. 26 2.2.3.1. Isolation of DNA from -phage ........................................................................... 26 2.2.3.2. Mini preparation of plasmid DNA bacterial clones ............................................. 27 2.2.3.3. Midi preparation of plasmid DNA ....................................................................... 27 2.2.3.4. Slot lysis ............................................................................................................... 27 2.2.3.5. Purification of DNA from an agarose gel ............................................................ 28 2.2.3.6. Purification of DNA for ES cell culture .............................................................. 28 2.2.3.7. Phenol-chloroform extraction of mouse genomic DNA from tail biopsy ........... 29 2.2.3.8. DNA extraction from mouse tail biopsies by hot-shot method ........................... 29 2.2.3.9. Purification of RNA from mouse tissues ............................................................. 29 2.2.4. Polymerase chain reaction (PCR) ........................................................................... 30 2.2.4.1. Genotyping PCR .................................................................................................. 31 2.2.4.2. Reverse transcription ........................................................................................... 32 2.2.4.3. Real time Q-PCR ................................................................................................. 33 2.2.5. Cell biology methods .............................................................................................. 33 2.2.5.1. Mouse embryonic stem cell culture and blastocyst injection .............................. 33 2.2.6. Southern blot ........................................................................................................... 33 2.2.7. Radio-labelling of probes with 32P .......................................................................... 33 2.2.8. Biochemical techniques .........................................................................................
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