Functional studies of the PreP peptidasome in Arabidopsis thaliana

........................................................................................................ vii Publications in the thesis.............................................................................. viii Additional publications...................................................................................................viii Abbreviations ................................................................................................. ix Mitochondrial and chloroplast biogenesis .....................................................11 Origin and evolution .................................................................................................11 Mitochondrial genome..............................................................................................12 Organization and function of mitochondria ..............................................................13 Chloroplast genome.................................................................................................14 Organization and function of chloroplasts................................................................14 Protein targeting to mitochondria and chloroplasts.......................................................15 Targeting peptides ...................................................................................................15 Mitochondrial protein import machinery ........................................................................17 Chaperone assisted import into mitochondria .........................................................18 The translocase of the outer mitochondrial membrane ...........................................19 Protein insertion into the outer mitochondrial membrane........................................20 The intermembrane space.......................................................................................21 The translocases of the inner mitochondrial membrane..........................................22 The mitochondrial processing peptidases ...............................................................23 Chloroplast protein import machinery ...........................................................................25 Chaperone assisted import into chloroplasts...........................................................25 The translocase of the chloroplast outer envelope..................................................25 The translocase of the chloroplast inner envelope ..................................................26 The chloroplastic processing peptidases.................................................................28 Proteolysis in mitochondria and chloroplasts................................................29 The ATP dependent proteases .....................................................................................29 The Clp family of proteases .....................................................................................29 The FtsH family of proteases...................................................................................30 The Lon family of proteases.....................................................................................31 The ATP independent proteases ..................................................................................32 The rhomboid family of proteases ...........................................................................32 The Deg family of proteases....................................................................................33 PreP .........................................................................................................................34 The processing peptidases......................................................................................34 Additional proteases ................................................................................................34 PreP, the organellar peptidasome.................................................................................35 The discovery...........................................................................................................35 Evolution and origin of PreP ....................................................................................36 Dual localization of PreP..........................................................................................38 Intracellular function of PreP....................................................................................39 Crystal structure and proteolytic mechanism of PreP..............................................40 PreP and Alzheimer disease....................................................................................41 The PreP double knockout in A. thaliana ......................................................................42 The phenotype and morphological changes in the knockout plants........................42 Peptidolysis in the PreP double knockout................................................................43 Compensatory mechanisms ....................................................................................44 Future perspectives and concluding remarks ...............................................................46 Acknowledgements .......................................................................................................48 References ....................................................................................................................50