CELL BIOLOGY: GENETIC STRUCTURE AND REPLICATION
KEVIN PYKE ABSTRACT 1 INTRODUCTION 2 PROPLASTIDS 3 THE MORPHOLOGY AND STRUCTURE OF DIFFERENT PLASTID TYPES 3 1 CHLOROPLAST STRUCTURE AND MORPHOLOGY 3 2 AMYLOPLAST STRUCTURE AND MORPHOLOGY 3 3 CHROMOPLAST STRUCTURE AND MORPHOLOGY 3 4 LEUCOPLASTS AND ROOT PLASTIDS 3 5 OTHER TYPES OF STORAGE PLASTIDS 4 THE CONTROL OF PLASTID DIFFERENTIATION 4 1 PLASTID INTERCONVERSIONS 5 PLASTID DIVISION 6 STROMULES 7 CONCLUSION ACKNOWLEDGEMENT REFERENCES STRUCTURE, FUNCTION, AND INHERITANCE OF PLASTID GENOMES RALPH BOCK 2 PHYSICAL PROPERTIES OF PLASTID GENOMES 2 1 COPY NUMBER OF PLASTID GENOMES 2 2 ORGANIZATION OF PLASTID GENOMES IN NUCLEOIDS 2 3 STRUCTURAL CONFORMATIONS OF PLASTID GENOMES 3 FINE STRUCTURE OF PLASTID GENOMES 3 1 INVERTED REPEATS AND SINGLE-COPY REGIONS 3 2 INFORMATION CONTENT OF PLASTID GENOMES 4 INHERITANCE OF PLASTID GENOMES 4 1 MATERNAL INHERITANCE 4 2 BIPARENTAL INHERITANCE 4 3 PATERNAL INHERITANCE 4 4 PATERNAL LEAKAGE 4 5 BIOTECHNOLOGICAL IMPLICATIONS OF PLASTID INHERITANCE LIST OF ABBREVIATIONS DNA REPLICATION, RECOMBINATION, AND REPAIR IN PLASTIDS ANIL DAY AND PANAGIOTIS MADESIS 1 THE IMPORTANCE OF DNA REPLICATION, RECOMBINATION, AND REPAIR PATHWAYS IN PLASTIDS 1 1 PROTEINS AND DNA TARGETS OF PLASTID DNA-RRR PATHWAYS 2 PLASTID DNA POLYPLOIDY, PACKAGING, AND SEGREGATION 2 1 PLASTID DNA COPY NUMBER 2 2 PACKAGING OF PLASTID DNA 2 3 SEGREGATION OF PLASTID GENOMES 3 TOPOLOGICAL FORMS OF PLASTID DNA 3 1 LINEAR HAIRPIN DNA MOLECULES IN PLASTIDS 3 2 LINEAR PLASTID DNA MOLECULES WITH DISCRETE ENDS IN WT PLASTIDS 4 A REPLICON MODEL FOR PLASTID GENOME MAINTENANCE 4 1 REPLICATION ORIGINS MAPPED TO THE LARGE INVERTED REPEAT 4 2 REPLICATION ORIGINS LOCATED IN THE SINGLE COPY REGIONS 5 MAINTENANCE OF SMALL DNA MOLECULES IN PLASTIDS 6 DELETION MAPPING DELIMITS DNA SEQUENCES CAPABLE OF SELF-REPLICATION IN PLASTIDS 7 A RECOMBINATION-DEPENDENT DNA REPLICATION MODEL OF PLASTID DNA 8 DNA RECOMBINATION IN PLASTIDS 8 1 INTEGRATION OF FOREIGN GENES BY HOMOLOGOUS RECOMBINATION 8 2 HOMOLOGOUS RECOMBINATION BETWEEN SHORT DNA REPEATS 9 RECOMBINATION AND PLASTID GENOME STABILITY 10 HOMEOLOGOUS RECOMBINATION IN PLASTIDS 11 REPLICATION SLIPPAGE IN PLASTIDS 12 DNA REPAIR IN PLASTIDS 13 IDENTIFICATION OF PROTEINS INVOLVED IN PLASTID DNA RRR-PATHWAYS 13 1 PLASTID DNA POLYMERASES 13 2 DNA PRIMASE ACTIVITIES IN PLASTIDS 13 3 PLASTID LOCALISED RECA 13 4 DNA TOPOISOMERASES 13 5 DNA HELICASES 14 IDENTIFYING DNA-RRR PROTEINS BY COMPLEMENTATION OF E COLI MUTANTS 15 CONCLUSIONS AND OUTLOOK TRANSCRIPTION AND TRANSCRIPTIONAL REGULATION IN PLASTIDS KARSTEN LIERE AND THOMAS BÖRNER 2 RNA POLYMERASES 2 1 NEP: NUCLEAR-ENCODED PLASTID RNA POLYMERASE 2 2 PEP: PLASTID-ENCODED PLASTID RNA POLYMERASE 3 PLASTIDIAL PROMOTERS 3 1 NEP PROMOTERS 3 2 PEP PROMOTERS 3 3 INTERNAL PROMOTERS OF TRNAS 4 REGULATION OF TRANSCRIPTION IN PLASTIDS 4 1 ROLE OF MULTIPLE AND DIVERSE PROMOTERS 4 2 TRANSCRIPTION FACTORS INVOLVED IN PROMOTER RECOGNITION IN PLASTIDS 4 3 EXOGENOUS AND ENDOGENOUS FACTORS CONTROLLING PLASTIDIAL TRANSCRIPTION PROCESSING, DEGRADATION, AND POLYADENYLATION OF CHLOROPLAST TRANSCRIPTS THOMAS J BOLLENBACH, GADI SCHUSTER, VICTORIA PORTNOY, AND DAVID B STERN 2 THE ENZYMES OF RNA DEGRADATION AND MATURATION 2 1 ENDORIBONUCLEASES 2 2 EXORIBONUCLEASES 3 POLYADENYLATION 3 1 HISTORICAL PERSPECTIVE ON POLYADENYLATION 3 2 THE POLYADENYLATION-STIMULATED DEGRADATION PATHWAY IN BACTERIA 3 3 PNPASE AS THE MAJOR POLYADENYLATING ENZYME: VARIATIONS FROM E COLI 3 4 POLYADENYLATION IN THE CHLOROPLAST 4 RNA MATURATION 4 1 5’ END MATURATION 4 2 INTERCISTRONIC PROCESSING 4 4 NON-CODING RNAS 5 REGULATORY FACTORS 5 1 MUTATIONS AFFECTING SINGLE CHLOROPLAST LOCI 5 2 PLEIOTROPIC MUTATIONS 5 3 THE PPR/TPR PROTEIN SUPERFAMILIES 6 CONCLUSIONS ACKNOWLEDGEMENTS RNA SPLICING AND RNA EDITING IN CHLOROPLASTS CHRISTIAN SCHMITZ-LINNEWEBER AND ALICE BARKAN 2 PLASTID RNA SPLICING 2 1 INTRON CLASSES AND SPLICING MECHANISMS 2 2 INTRON DISTRIBUTION 2 3 PROTEINS INVOLVED IN THE SPLICING OF CHLOROPLAST INTRONS 2 4 THE REGULATION OF CHLOROPLAST RNA SPLICING 2 5 PERSPECTIVE 3 PLASTID RNA EDITING 3 1 EDITING SITES IMPACT PROTEIN FUNCTION 3 2 MECHANISM OF RNA EDITING 3 3 CIS-ELEMENTS INVOLVED IN PLASTID RNA EDITING 3 4 TRANS-FACTORS INVOLVED IN PLASTID RNA EDITING 3 5 MODELS FOR THE EDITOSOME 3 6 FUNCTION AND EVOLUTION OF PLASTID RNA EDITING 3 7 PERSPECTIVES TRANSLATION AND TRANSLATIONAL REGULATION IN CHLOROPLASTS HADAS PELED-ZEHAVI AND AVIHAI DANON 2 CHLOROPLAST TRANSLATION MACHINERY 3 MECHANISMS OF TRANSLATION INITIATION 4 TRANSLATION INITIATION REGULATION – INTRICATE INTERPLAY BETWEEN CIS- AND TRANS-ACTING ELEMENTS 4 1 CIS-ELEMENTS IN CHLOROPLAST 5’UTRS 4 2 STRUCTURAL ELEMENTS IN 5’UTRS 4 3 GENERAL AND SPECIFIC TRANSLATION FACTORS 4 4 MULTIPLE PROTEINS INTERACT WITH SINGLE MRNA 5 TRANSLATION REGULATION EXAMPLES 5 1 TRANSLATION REGULATION OF D1 SYNTHESIS 5 2 NEGATIVE FEEDBACK LOOPS: ASSEMBLY-CONTROLLED REGULATION OF TRANSLATION 6 REGULATION OF TRANSLATION ELONGATION 7 INTERACTIONS OF 5’ AND 3’ ENDS OF CHLOROPLAST MRNA 8 SUBCHLOROPLAST LOCATION OF TRANSLATION 9 CONCLUDING REMARKS ASSEMBLY OF PROTEIN COMPLEXES IN PLASTIDS EIRA KANERVO, MARJAANA SUORSA, AND EVA-MARI ARO 2 ASSEMBLY OF THE PROTEIN COMPLEXES 2 1 ASSEMBLY OF PSII 2 2 ASSEMBLY OF THE PSI COMPLEX 2 3 ASSEMBLY OF THE CYT B6 F COMPLEX 2 4 ASSEMBLY OF SOLUBLE COMPLEXES 3 INSERTION OF PROTEINS TO THE THYLAKOID MEMBRANE - THYLAKOID TRANSLOCASE COMPLEXES AND CHAPERONES 3 1 THYLAKOID TRANSLOCASES 3 2 CHAPERONES 4 POSTTRANSLATIONAL MODIFICATIONS OF CHLOROPLAST PROTEINS 4 1 N-TERMINAL METHIONINE EXCISION 4 2 PROTEIN PHOSPHORYLATION 5 CONCLUDING REMARKS PROTEIN STABILITY AND DEGRADATION IN PLASTIDS ZACH ADAM 2 MAJOR CHLOROPLAST PROTEASES 2 1 CLP PROTEASE 2 2 FTSH PROTEASE 2 3 LON PROTEASE 2 4 DEG PROTEASE 2 5 INTRAMEMBRANE PROTEASES 3 PROTEOLYTIC PROCESSES IN CHLOROPLASTS AND THE ENZYMES INVOLVED 3 1 MATURATION OF PRE-PROTEINS 3 2 ADAPTATION TO CHANGING LIGHT INTENSITIES 3 3 PROTEIN QUALITY CONTROL 3 4 OXIDATIVELY DAMAGED PROTEINS 4 OTHER FUNCTIONS 4 1 NUTRIENT STRESS AND SENESCENCE 4 2 THERMOTOLERANCE 5 IDENTIFICATION OF SPECIFIC SUBSTRATES 6 DETERMINANTS OF PROTEIN INSTABILITY 7 FUTURE PROSPECTS PROTEIN IMPORT INTO PLASTIDS BIRGIT AGNE AND FELIX KESSLER 1 PLASTIDS 1 1 PLASTID BIOGENESIS 2 CHLOROPLAST TARGETING SIGNALS 2 1 STRUCTURE OF TRANSIT PEPTIDES 3 ENERGY REQUIREMENTS OF IN VITRO CHLOROPLAST PROTEIN IMPORT 3 1 PRECURSOR PROTEIN RECOGNITION AT THE CHLOROPLAST SURFACE 3 2 THE EARLY TRANSLOCATION INTERMEDIATE 3 3 THE LATE TRANSLOCATION INTERMEDIATE 4 IDENTIFICATION OF COMPONENTS OF THE TRANSLOCATION MACHINERY 4 1 COMPONENTS OF THE TOC COMPLEX 4 2 COMPONENTS OF THE TIC COMPLEX 5 REGULATION AT THE TOC AND TIC COMPLEXES 5 1 GTP-REGULATED PROTEIN RECOGNITION AT THE TOC COMPLEX 5 2 REGULATION BY PHOSPHORYLATION 5 3 REDOX-REGULATION 5 4 CALCIUM/CALMODULIN REGULATION 6 FUNCTIONAL SPECIALIZATION IN THE GENERAL IMPORT PATHWAY 6 1 PLASTID PROTEIN IMPORT MUTANTS AND PHENOTYPES 6 2 EXPRESSION PATTERNS OF TOC GTPASES 6 3 BIOCHEMICAL EVIDENCE FOR FUNCTIONAL SPECIALIZATION OF CHLOROPLAST IMPORT RECEPTORS 6 4 SUBSTRATE SPECIFICITY OF TOC-GTPASE SUB-PATHWAYS 7 TOC/TIC INDEPENDENT “ALTERNATIVE” IMPORT PATHWAYS INTO THE CHLOROPLAST 7 1 IMPORT DEPENDING ON INTERNAL TARGETING SEQUENCES 7 2 SUBSTRATE DEPENDENT IMPORT 7 3 PROTEIN IMPORT VIA THE SECRETORY PATHWAY BIANCA NAUMANN AND MICHAEL HIPPLER 1 THE ART OF PROTEOMICS 1 1 PREREQUISITE FOR BIOMOLECULAR MASS SPECTROMETRY: MALDI AND ESI IONIZATION 1 2 PEPTIDE MASS FINGER PRINTING AND TANDEM MASS SPECTROMETRY 1 3 DATABASE SEARCHING 1 4 DE NOVO SEQUENCING 1 5 LINKING DATABASE SEARCHING AND DE NOVO SEQUENCING 1 6 STRATEGIES FOR THE ANALYSIS OF PROTEOME DYNAMICS 2 PROTEOMICS OF THE CHLOROPLAST AND ITS COMPARTMENTS 2 1 ENVELOPE MEMBRANES 2 2 STROMA AND CHLOROPLAST RIBOSOME 2 3 THYLAKOID MEMBRANE 2 4 THYLAKOID LUMEN 4 COMPARATIVE PROTEOMICS 4 1 PLANT AND CHLOROPLAST DEVELOPMENT 4 2 BIOTIC STRESS 4 3 ABIOTIC STRESS 5 CONCLUSION PLASTID-NUCLEUS COMMUNICATION: ANTEROGRADE AND RETROGRADE SIGNALLING IN THE DEVELOPMENT AND FUNCTION OF PLASTIDS KATHARINA BRÄUTIGAM, LARS DIETZEL, AND THOMAS PFANNSCHMIDT 2 MAJOR PROBLEMS OF COORDINATION AND COMMUNICATION BETWEEN PLASTIDS AND NUCLEUS 2 1 TISSUE SPECIFICITY OF PLASTID DEVELOPMENT 2 2 THE GENE COPY NUMBER PROBLEM 2 3 INTEGRATION OF PLASTID RESPONSES WITHIN THE CELL 3 ANTEROGRADE SIGNALLING 3 1 THE NUCLEAR CONTROL PRINCIPLE 3 2 DEVELOPMENTAL SIGNALS 3 3 ENVIRONMENTAL CONTROL OF PLASTID DEVELOPMENT 4 RETROGRADE SIGNALLING 4 1 SIGNALS DEPENDING ON PLASTID GENE EXPRESSION 4 2 RETROGRADE SIGNALS DEPENDING ON PIGMENT SYNTHESIS 4 3 REDOX SIGNALS FROM CHLOROPLASTS 4 4 PLASTID SIGNALS CONTROLLING TISSUE DEVELOPMENT 5 CONCLUSIONS AND PERSPECTIVES THE GENETIC TRANSFORMATION OF PLASTIDS HANS-ULRICH KOOP, STEFAN HERZ, TIMOTHY J GOLDS, AND JÖRG NICKELSEN 1 1 PLASTID BIOLOGY IN CHLAMYDOMONAS AND TOBACCO 2 GENERAL PROCEDURES 2 1 GENE TRANSFER METHODS 2 2 TRANSFORMATION VECTORS 2 3 MARKER GENE REMOVAL 3 PLASTID TRANSFORMATION IN ALGAE 3 1 EXPRESSION CONTROL ELEMENTS 3 2 RESISTANCE MARKER GENES 3 3 TARGETED INACTIVATION 3 4 INTRODUCED GENES, EXPRESSED PROTEINS 3 5 TRANSFORMED SPECIES 4 PLASTID TRANSFORMATION IN HIGHER PLANTS 4 1 EXPRESSION CONTROL ELEMENTS 4 2 INDUCIBLE GENE EXPRESSION 4 3 RESISTANCE MARKER GENES AND SELECTION SCHEMES 4 4 TARGETED INACTIVATION 4 5 INTRODUCED GENES, EXPRESSED PROTEINS 4 6 TRANSFORMED SPECIES 5 PERSPECTIVES