PROTEIN PHOSPHATASE

By JOSHUA GARCIA

1 INTRODUCTION TO MITOCHONDRIAL OXIDATIVE PHOSPHORYLATION 1 2 MITOCHONDRIAL DYNAMICS THE INTERSECTION OF FORM AND FUNCTION 13 3 BIOGENESIS OF MITOCHONDRIAL PROTEINS 41 4 ASSEMBLY FACTORS OF HUMAN MITOCHONDRIAL RESPIRATORY CHAIN COMPLEXES PHYSIOLOGY AND PATHOPHYSIOLOGY 65 5 SUPRAMOLECULAR ORGANISATION OF THE MITOCHONDRIAL RESPIRATORY CHAIN A NEW CHALLENGE FOR THE MECHANISM AND CONTROL OF OXIDATIVE PHOSPHORYLATION 107 6 MOLECULAR MECHANISMS OF SUPEROXIDE PRODUCTION BY THE MITOCHONDRIAL RESPIRATORY CHAIN 145 7 STUDIES ON THE FUNCTION AND REGULATION OF MITOCHONDRIAL UNCOUPLING PROTEINS 171 8 EVOLUTION OF THE COUPLE CYTOCHROME C AND CYTOCHROME C OXIDASE IN PRIMATES 185 CONTENTS 9 REACTION MECHANISM OF MAMMALIAN MITOCHONDRIAL CYTOCHROME C OXIDASE 215 10 PHOSPHORYLATION OF MAMMALIAN CYTOCHROME C AND CYTOCHROME C OXIDASE IN THE REGULATION OF CELL DESTINY RESPIRATION APOPTOSIS AND HUMAN DISEASE 237 11 INDIVIDUAL BIOCHEMICAL BEHAVIOUR VERSUS BIOLOGICAL ROBUSTNESS SPOTLIGHT ON THE REGULATION OF CYTOCHROME C OXIDASE 265 12 BIGENOMIC REGULATION OF CYTOCHROME C OXIDASE IN NEURONS AND THE TIGHT COUPLING BETWEEN NEURONAL ACTIVITY AND ENERGY METABOLISM 283 13 CYTOCHROME C OXIDASE AND ITS ROLE IN NEURODEGENERATION AND NEUROPROTECTION 305 14 THE MANY CLINICAL FACES OF CYTOCHROME C OXIDASE DE CIENCY 341 ABSTRACT THE BASIC MECHANISM OF ATP SYNTHESIS IN THE MITOCHONDRIA BY OXIDATIVE PHOSPHORYLATION OXPHOS WAS REVEALED IN THE SECOND HALF OF THE TWENTIETH CENTURY THE OXPHOS COMPLEXES I V HAVE BEEN ANALYZED CONCERNING THEIR SUBUNIT COMPOSI TION GENES AND X RAY STRUCTURES THIS BOOK PRESENTS NEW DEVELOPMENTS REGARDING THE MORPHOLOGY BIOGENESIS GENE EVOLUTION HEAT AND REACTIVE OXYGEN SPECIES ROS GENERATION IN MITOCHONDRIA AS WELL AS THE STRUCTURE AND SUPERCOMPLEX FOR MATION OF OXPHOS COMPLEXES IN ADDITION MULTIPLE MITOCHONDRIAL DISEASES BASED ON MUTATIONS OF NUCLEAR ENCODED GENES HAVE BEEN IDENTI ED LITTLE IS KNOWN HOWEVER OF THE REGULATION OF OXPHOS ACCORDING TO THE VARIABLE CELLULAR DEMANDS OF ATP IN PARTICULAR THE FUNCTIONS OF THE SUPERNUMERARY NUCLEAR ENCODED SUBUNITS OF MITO CHONDRIAL OXPHOS COMPLEXES WHICH ARE MOSTLY ABSENT IN BACTERIA REMAIN LARGELY UNKNOWN ALTHOUGH THE CORRESPONDING AND CONSERVED CORE SUBUNITS EXHIBIT THE SAME CATALYTIC ACTIVITY IDENTI CATION OF REGULATORY PATHWAYS MODULATING OXPHOS ACTIVITY BY SUBUNIT ISOFORM EXPRESSION BY ALLOSTERIC INTERACTION WITH ATP ADP BY REVERS IBLE PHOSPHORYLATION OF PROTEIN SUBUNITS OR BY SUPERCOMPLEX FORMATION WILL HELP TO UNDERSTAND THE ROLE OF MITOCHONDRIA IN THE MANY DEGENERATIVE DISEASES MOSTLY BASED ON ROS FORMATION IN MITOCHONDRIA AND OR INSUF CIENT ENERGY PRODUCTION 1 1 MITOCHONDRIAL OXIDATIVE PHOSPHORYLATION LIFE REPRESENTS AN EXERGONIC PROCESS REQUIRING ENERGY FOR ALL OF ITS MANIFESTATIONS AEROBIC ORGANISMS INCLUDING PLANTS FUNGI AND ANIMALS USE THE HIGH ENERGY YIELD OF THE OXYHYDROGEN GAS REACTION 2 H 2 O 2 2 H 2 O D G 193 KJ MOL UNDER PHYSIOLOGICAL CONDITIONS TO DRIVE THE ENDERGONIC SYNTHESIS OF ATP FROM ADP AND CHAPTER 1 INTRODUCTION TO MITOCHONDRIAL OXIDATIVE PHOSPHORYLATION 1 PHOSPHATE FOR MANY YEARS THE ENERGY RICH INTERMEDIATE OF ENERGY TRANSDUCTION BETWEEN THE ELECTRON TRANSPORT IN THE RESPIRATORY CHAIN OF MITOCHONDRIA AND BACTE RIA AND THE CHEMICAL SYNTHESIS OF ATP FROM ADP AND PHOSPHATE WAS A MATTER OF CONTROVERSIAL DISCUSSIONS UNTIL PETER MITCHELL S CHEMIOSMOTIC HYPOTHESIS MITCHELL 1961 1966 WAS NALLY ACCEPTED BY THE LEADING RESEARCHERS IN THE ELD OF OXIDATIVE PHOSPHORYLATION OXPHOS BOYER ET AL 1977 COUPLED TO OXYGEN CONSUMPTION IN THE MITOCHONDRIA ENERGY IS RELEASED IN THE RESPIRATORY CHAIN IN THREE STEPS AND TRANSIENTLY STORED AS AN ELECTROCHEMICAL PROTON GRADIENT ACROSS THE INNER MEMBRANE THE GRADIENT IS DISSIPATED BY THE ATP SYN THASE COMPLEX V TO GENERATE ATP REES ET AL 2009 OR CONVERTED INTO HEAT BY PASSIVE PROTON LEAKAGE JASTROCH ET AL 2010 OR THROUGH UNCOUPLING PROTEINS SEE CHAP 7 THE CHANGES OF FREE ENERGY D G O AT THE THREE STEPS ARE 52 KJ MOLE AT COMPLEX I NADH DEHYDROGENASE 42 KJ MOLE AT COMPLEX III CYTOCHROME BC 1 AND 100 KJ MOLE AT COMPLEX IV CYTOCHROME OXIDASE COX LEHNINGER 1970 IN THE LAST STEP THE YIELD OF FREE ENERGY IS TWICE AS HIGH COMPARED TO THE OTHER TWO STEPS SUGGESTING A REGULATORY ROLE FOR COX IN THE ELECTRON TRANSPORT CHAIN OF MITOCHONDRIA AND THUS IN OXPHOS IN GENERAL ENZYME REACTIONS INVOLVING LARGE CHANGES OF FREE ENERGY REPRESENT REGULATORY STEPS OF ENERGY METABOLISM IN FACT COX WAS FOUND TO REPRESENT THE RATE LIMITING STEP OF RESPIRATION IN INTACT CELLS VILLANI AND ATTARDI 1997 2001 PICCOLI ET AL 2006 DALMONTE ET AL 2009 PACELLI ET AL 2011 BUT NOT IN ISOLATED MITOCHONDRIA GROEN ET AL 1982 ALTHOUGH MANY OXIDASES REACT WITH MOLECULAR OXYGEN ONLY COX CONVERTS O 2 INTO WATER WITHOUT FORMING REACTIVE OXYGEN SPECIES ROS LIKE THE SUPEROXIDE RADICAL ANION O 2 OR HYDROGEN PEROXIDE H 2 O 2 LUDWIG ET AL 2001 YU ET AL 2011 SEE CHAP 9 HOWEVER SIGNI CANT AMOUNTS OF ROS CAN BE PRODUCED IN THE MITOCHONDRIA AT COMPLEXES I AND III SEE CHAP 6 1 2 MITOCHONDRIA A GENETICALLY INDEPENDENT CELL ORGANELLE ACCORDING TO THE GENERALLY ACCEPTED ENDOSYMBIOTIC THEORY WALLIN 1923 MARGULIS 1975 ZIMMER 2009 RICHARDS AND ARCHIBALD 2011 MITOCHONDRIA ORIGINATED FROM SYMBIOSIS OF AN OXIDATIVE A PROTEOBACTERIUM WITH AN ANAEROBIC PRE EUKARYOTIC HOST CELL 1 5 2 BILLION YEARS AGO THE RESULTING EUKARYOTIC CELL GENERATES ATP MAINLY BY OXPHOS IN THE MITOCHONDRIA WHICH YIELDS ABOUT 15 TIMES MORE ATP FROM GLUCOSE COMPARED TO GLYCOLYSIS UNDER ANAEROBIC CONDITIONS DURING EVOLUTION MOST OF THE GENETIC MATERIAL OF THE ANCESTRAL OXIDATIVE A PROTEOBACTERIUM WAS TRANSFERRED TO THE NUCLEUS OF THE HOST CELL FURTHERMORE DURING EVOLUTION EUKARYOTIC CELLS ACCU MULATED ADDITIONAL GENES AND FUNCTIONS A GENOME REMAINED IN MITOCHONDRIA WHICH IS INDEPENDENT OF NUCLEAR DNA MITOCHONDRIAL DNA MTDNA OF MAMMALS CODES FOR 2 RIBOSOMAL AND 22 TRANSFER RNAS BUT ONLY FOR 13 PROTEINS ALL REPRESENTING SUB UNITS OF THE 4 PROTON PUMPS OF OXPHOS 7 OF COMPLEX I 1 OF COMPLEX III 3 OF COM PLEX IV AND 2 OF COMPLEX V THE TRANSCRIPTION AND TRANSLATION OF MTDNA DIFFERS FROM THE NUCLEAR SYSTEM AND REQUIRES MORE THAN 100 NUCLEAR ENCODED PROTEINS 2 PROTEIN PHOSPHATASE WHICH IN ADDITION TO ABOUT 1 000 OTHER NUCLEAR ENCODED PROTEINS HAVE TO BE TRANSPORTED INTO MITOCHONDRIA BY A COMPLEX PROTEIN TRANSPORT SYSTEM SCHMIDT ET AL 2010 SEE CHAP 3 HUMAN MTDNA IS INHERITED ONLY BY THE MOTHER AND HAS AN ABOUT TEN TIMES HIGHER MUTATION RATE THAN NUCLEAR DNA POSSIBLY LEADING TO MATER NALLY INHERITED MITOCHONDRIAL DISEASES SHOUBRIDGE 2001 KRISHNAN ET AL 2008 DIMAURO AND SCHON 2008 SEE CHAP 14 IT HAS BEEN PROPOSED THAT AGING IS PARTLY DUE TO SOMATIC MUTATIONS OF MTDNA FREQUENTLY CAUSING DEFECTIVE COX M LLER H CKER ET AL 1992 1993 CONCOMITANT WITH IMPAIRED SYNTHESIS OF ATP AND A DECLINE IN CELL ENERGETICS WITH INCREASING AGE WALLACE 2010 1 3 THE MITOCHONDRIAL PROTEOME A RECENT FUNCTIONAL CLASSI CATION OF THE MITOCHONDRIAL PROTEOME OF SACCHAROMYCES CEREVISIAE BY SCHMIDT ET AL 2010 COMPRISING ABOUT 850 PROTEINS HAVE ASSIGNED ONLY 15 OF THE PROTEOME TO ENERGY METABOLISM OTHER PARTS OF THE PROTEOME INVOLVE PROTEIN SYNTHESIS 13 3 AND GENOME MAINTENANCE AND TRANSCRIPTION 11 9 A TOTAL OF 7 4 ARE ASSIGNED TO PROTEIN TRANSPORT AND FOLDING AND THE KNOWLEDGE OF THESE TRANSPORT PROTEINS INCREASED CONSIDERABLY DURING RECENT YEARS SCHMIDT ET AL 2010 SEE CHAP 3 A TOTAL OF 5 8 OF THE YEAST PROTEOME ARE PROTEINS INVOLVED IN THE TRANSPORT OF METABOLITES MITOCHONDRIAL CARRIER PROTEINS ARE WIDELY DISTRIBUTED IN ALL EUKARYOTES AND ARE INVOLVED IN NUMEROUS METABOLIC PATHWAYS IN A RECENT STUDY 35 GENES FOR MITOCHONDRIAL CARRIERS HAVE BEEN IDENTI ED IN YEAST AND 53 IN THE HUMAN GENOME AND THE NUMBER OF MITOCHONDRIAL CARRIER GENES VARIED IN DIFFERENT SPECIES BETWEEN 35 AND 125 PALMIERI ET AL 2011 UNTIL NOW 22 MITOCHONDRIAL CARRIER SUBFAMILIES HAVE BEEN FUNCTIONALLY CHARACTERIZED PALMIERI AND PIERRI 2010 AND SEVERAL DIS EASES BASED ON MUTATIONS OF THE CARRIER GENES HAVE BEEN DESCRIBED PALMIERI 2008 THE RST CRYSTAL STRUCTURE OF A MITOCHONDRIAL CARRIER WAS PRESENTED FOR THE ADP ATP CARRIER PEBAY PEYROULA ET AL 2003 AND IT WAS SHOWN TO FUNCTION AS A MONOMER BAMBER ET AL 2007 KUNJI AND ROBINSON 2010 IN CONTRAST TO PREVIOUS ASSUMP TIONS THE OBSERVED DIMERIC STRUCTURE OF THE ADP ATP CARRIER IN THE MEMBRANE COULD HAVE ADDITIONAL REGULATORY ROLES KLINGENBERG 2008 ONLY VERY FEW PROTEINS INVOLVED IN SIGNALING 4 1 OF THE PROTEOME HAVE BEEN IDENTI ED AND RESEARCH IN MITOCHONDRIAL SIGNALING REPRESENTS A CURRENT CHALLENGE PROTEINS OF AMINO ACID 4 2 AND LIPID METABOLISM 3 4 ARE ALSO INVOLVED IN ENERGY METABOLISM SINCE THEY PRODUCE THE SUBSTRATES FOR OXIDATIVE METABOLISM FOR 19 3 OF THE PROTEOME NO FUNCTIONS COULD BE ASSIGNED YET MITOCHONDRIA ALSO CON TAIN PROTEINS INVOLVED IN OTHER FUNCTIONS SUCH AS SSION AND FUSION OF THE ORGANELLE SEE CHAP 2 INDUCTION OF APOPTOSIS BRENNER AND MAK 2009 MARTINOU AND YOULE 2011 INDRAN ET AL 2011 GENERATION AND DETOXI CATION OF ROS SEE CHAP 6 AND REGULATION OF CYTOPLASMIC AND MITOCHONDRIAL MATRIX CALCIUM PIVOVAROVA AND ANDREWS 2010 IN ADDITION MITOCHONDRIA ARE PARTLY INVOLVED IN THE BIOSYNTHESIS OF HEME SCHULTZ ET AL 2010 AND IRON SULFUR PROTEINS LILL 2009 SHEFTEL ET AL 2010 3 PROTEIN PHOSPHATASE