A STUDY OF THE EFFECT OF LIGHT UPON PLANTS
MICROBIAL RHODOPSINS: PHYLOGENETIC AND FUNCTIONAL DIVERSITY INTRODUCTION ARCHAEAL RHODOPSINS CLUES TO NEWFOUND MICROBIAL RHODOPSIN FUNCTION FROM PRIMARY SEQUENCE COMPARISON TO ARCHAEAL RHODOPSINS BACTERIAL RHODOPSINS GREEN-ABSORBING PROTEORHODOPSIN (“GPR”) FROM MONTEREY BAY SURFACE PLANKTON BLUE-ABSORBING PROTEORHODOPSIN (“BPR”) FROM HAWAIIAN DEEP SEA PLANKTON ANABAENA SENSORY RHODOPSIN OTHER BACTERIAL RHODOPSINS EUKARYOTIC MICROBIAL RHODOPSINS FUNGAL RHODOPSINS ALGAL RHODOPSINS SPECTRAL TUNING A UNIFIED MECHANISM FOR MOLECULAR FUNCTION? OPSIN-RELATED PROTEINS WITHOUT THE RETINAL-BINDING SITE PERSPECTIVE REFERENCES SENSORY RHODOPSIN SIGNALING IN GREEN FLAGELLATE ALGAE RETINYLIDENE RECEPTORS 2 1 2 PHYSIOLOGY OF ALGAL PHOTOTAXIS AND THE PHOTOPHOBIC RESPONSE PHOTOELECTRICAL CURRENTS AND THEIR RELATIONSHIP TO SWIMMING BEHAVIOR THE PHOTOSENSORY RECEPTORS: CSRA AND CSRB GENOMICS, SEQUENCE, AND PREDICTED STRUCTURE CELLULAR CONTENT AND ROLES IN PHOTOTAXIS AND PHOTOPHOBIC BEHAVIOR MOLECULAR MECHANISM OF ACTION OTHER ALGAE CONCLUSION AND FUTURE PERSPECTIVES ACKNOWLEDGEMENTS VISUAL PIGMENTS AS PHOTORECEPTORS GENERAL CONSIDERATIONS PHOTORECEPTORS AND PIGMENTS NON-PHOTORECEPTOR OR “NON-ROD”, “NON-CONE” RETINAL PIGMENTS RETINAL PHOTOISOMERASES THE UNPHOTOLYZED STATE OF VERTEBRATE VISUAL PIGMENTS STRUCTURE OF VISUAL PIGMENTS: THE CHROMOPHORE OVERALL TOPOLOGY OF THE PIGMENT CYTOPLASMIC DOMAIN THE HYDROPHOBIC CORE OF RHODOPSIN AND THE RETINAL BINDING POCKET THE EXTRACELLULAR DOMAIN OF RHODOPSIN STRUCTURE OF OTHER VISUAL PIGMENTS PROTONATION STATE OF SOME OF THE CARBOXYLIC ACIDS OF RHODOPSIN INTERNAL WATERS IN VISUAL PIGMENTS IS RHODOPSIN A DIMER IN VIVO? FUNCTIONAL PROPERTIES OF THE UNPHOTOLYZED STATE OF A “GOOD” VISUAL PIGMENT QUANTUM EFFICIENCY OF VISUAL PIGMENT PHOTOCHEMISTRY DARK NOISE ORIGINATING FROM THE PHOTORECEPTOR PIGMENT ACTIVATION OF VERTEBRATE VISUAL PIGMENTS THE PRIMARY EVENT, PHOTOISOMERIZATION THE META I } META II TRANSITION MOLECULAR CHANGES UPON THE FORMATION OF META I AND META II INTERNAL WATER MOLECULES REQUIRED STEPS FOR RHODOPSIN ACTIVATION THE TRANSMEMBRANE SIGNALING PATHWAY THE UNPHOTOLYZED STATE OF INVERTEBRATE VISUAL PIGMENTS WAVELENGTH REGULATION OF INVERTEBRATE PIGMENTS MECHANISM OF ACTIVATION OF INVERTEBRATE VISUAL PIGMENTS THE INITIAL PHOTOCHEMICAL EVENTS FORMATION OF ACID METARHODOPSIN REQUIRED STEPS FOR PHOTOLYZED OCTOPUS RHODOPSIN TO ACTIVATE ITS G-PROTEIN PURIFICATION OF THE ACTIVE FORM OF AN INVERTEBRATE VISUAL PIGMENT STRUCTURAL AND FUNCTIONAL ASPECTS OF THE MAMMALIAN ROD-CELL PHOTORECEPTOR RHODOPSIN RHODOPSIN AND MAMMALIAN VISUAL PHOTOTRANSDUCTION SIGNAL AMPLIFICATION BY LIGHT-ACTIVATED RHODOPSIN INACTIVATION OF LIGHT-ACTIVATED RHODOPSIN PROPERTIES OF RHODOPSIN ISOLATION OF RHODOPSIN BIOCHEMICAL AND PHYSICOCHEMICAL PROPERTIES OF RHODOPSIN POST-TRANSLATIONAL MODIFICATIONS IN RHODOPSIN MEMBRANE TOPOLOGY OF RHODOPSIN AND FUNCTIONAL DOMAINS CHROMOPHORE BINDING POCKET AND PHOTOLYSIS OF RHODOPSIN STRUCTURE OF RHODOPSIN CRYSTAL STRUCTURE OF RHODOPSIN ATOMIC FORCE MICROSCOPY OF RHODOPSIN IN THE DISK MEMBRANE ACTIVATION MECHANISM OF RHODOPSIN CONCLUSIONS A NOVEL LIGHT SENSING PATHWAY IN THE EYE: CONSERVED FEATURES OF INNER RETINAL PHOTORECEPTION IN RODENTS, MAN AND TELEOST FISH SUMMARY A NOVEL PHOTORECEPTOR WITHIN THE EYE BIOLOGICAL CLOCKS AND THEIR REGULATION BY LIGHT NON-ROD, NON-CONE PHOTORECEPTION IN RODENTS AN IRRADIANCE DETECTION PATHWAY IN THE EYE THE DISCOVERY OF A NOVEL OCULAR PHOTOPIGMENT IN MICE (OP480) MELANOPSIN AND NON-ROD, NON-CONE PHOTORECEPTION A FUNCTIONAL SYNCITIUM OF DIRECTLY LIGHT-SENSITIVE GANGLION CELLS NON-ROD, NON-CONE PHOTORECEPTION IN HUMANS NOVEL PHOTORECEPTORS REGULATE MELATONIN NOVEL PHOTORECEPTORS REGULATE THE PRIMARY VISUAL CONE PATHWAY NON-ROD, NON-CONE PHOTORECEPTION IN TELEOST FISH BACKGROUND VERTEBRATE ANCIENT (VA) OPSIN AND INNER RETINAL PHOTORECEPTION IN TELEOST FISH A NOVEL LIGHT RESPONSE FROM VA-OPSIN- AND MELANOPSIN-EXPRESSING HORIZONTAL CELLS ACTION SPECTRA FOR THE HC–RSD LIGHT RESPONSE IDENTIFY A NOVEL PHOTOPIGMENT THE POSSIBLE FUNCTION OF HC–RSD NEURONES OPSINS CAN BE PHOTOSENSORS OR PHOTOISOMERASES PLACING CANDIDATE GENES AND PHOTOPIGMENTS INTO CONTEXT THE PHYTOCHROMES PHOTOMORPHOGENESIS AND PHYTOCHROMES THE CENTRAL DOGMA OF PHYTOCHROME ACTION MOLECULAR PROPERTIES OF EUKARYOTIC AND PROKARYOTIC PHYTOCHROMES MOLECULAR PROPERTIES OF PLANT PHYTOCHROMES MOLECULAR PROPERTIES OF CYANOBACTERIAL PHYTOCHROMES PHOTOCHEMICAL AND NONPHOTOCHEMICAL CONVERSIONS OF PHYTOCHROME THE PHYTOCHROME CHROMOPHORE PHYTOCHROME PHOTOINTERCONVERSIONS DARK REVERSION PHYTOCHROME BIOSYNTHESIS AND TURNOVER PHYTOBILIN BIOSYNTHESIS IN PLANTS AND CYANOBACTERIA APOPHYTOCHROME BIOSYNTHESIS AND HOLOPHYTOCHROME ASSEMBLY PHYTOCHROME TURNOVER MOLECULAR MECHANISM OF PHYTOCHROME SIGNALING: FUTURE PERSPECTIVE REGULATION OF PROTEIN–PROTEIN INTERACTIONS BY PHOSPHORYLATION REGULATION OF TETRAPYRROLE METABOLISM PHYTOCHROME SIGNALING PHOTOSENSORY AND BIOLOGICAL FUNCTIONS OF INDIVIDUAL PHYTOCHROMES PHY DOMAINS INVOLVED IN SIGNALING PHY SIGNALING COMPONENTS SECOND MESSENGER HYPOTHESIS GENETICALLY IDENTIFIED SIGNALING COMPONENTS PHY-INTERACTING FACTORS EARLY PHY-RESPONSIVE GENES BIOCHEMICAL MECHANISM OF SIGNAL TRANSFER PHY SIGNALING AND CIRCADIAN RHYTHMS FUTURE PROSPECTS PHYTOCHROMES IN MICROORGANISMS HIGHER PLANT PHYS THE DISCOVERY OF MICROBIAL PHYS PHYLOGENETIC ANALYSIS OF THE PHY SUPERFAMILY CYANOBACTERIAL PHY (CPH) FAMILY BACTERIOPHYTOCHROME (BPHP) FAMILY FUNGAL PHY (FPH) FAMILY PHY-LIKE SEQUENCES DOWNSTREAM SIGNAL-TRANSDUCTION CASCADES PHYSIOLOGICAL ROLES OF MICROBIAL PHYS REGULATION OF PHOTOTAXIS ENHANCEMENT OF PHOTOSYNTHETIC POTENTIAL PHOTOCONTROL OF PIGMENTATION EVOLUTION OF THE PHY SUPERFAMILY PERSPECTIVES LIGHT-ACTIVATED INTRACELLULAR MOVEMENT OF PHYTOCHROME THE CLASSICAL METHODS SPECTROSCOPIC METHODS CELL BIOLOGICAL METHODS IMMUNOCYTOCHEMICAL METHODS NOVEL METHODS INTRACELLULAR LOCALIZATION OF PHYB IN DARK AND LIGHT INTRACELLULAR LOCALIZATION OF PHYA IN DARK AND LIGHT INTRACELLULAR LOCALIZATION OF PHYC, PHYD AND PHYE IN DARK AND LIGHT INTRACELLULAR LOCALIZATION OF INTRAGENIC MUTANT PHYTOCHROMES HYPOSENSITIVE, LOSS-OF-FUNCTION MUTANTS HYPERSENSITIVE MUTANTS PROTEIN COMPOSITION OF NUCLEAR SPECKLES ASSOCIATED WITH PHYB THE FUNCTION OF PHYTOCHROMES LOCALIZED IN NUCLEI AND CYTOSOL CONCLUDING REMARKS PLANT CRYPTOCHROMES: THEIR GENES, BIOCHEMISTRY, AND PHYSIOLOGICAL ROLES CRYPTOCHROME GENES AND EVOLUTION THE DISCOVERY OF CRYPTOCHROMES DISTRIBUTION OF CRYPTOCHROMES AND THEIR EVOLUTION CRYPTOCHROME DOMAINS, COFACTORS AND SIMILARITIES WITH PHOTOLYASE BIOLOGICAL FUNCTION OF PLANT CRYPTOCHROMES CONTROL OF GROWTH ROLE OF CRYPTOCHROMES IN CIRCADIAN CLOCK ENTRAINMENT AND PHOTOPERIODISM REGULATION OF GENE EXPRESSION LOCALIZATION OF CRYPTOCHROMES BIOCHEMICAL PROPERTIES OF CRYPTOCHROMES PROTEIN STABILITY PHOSPHORYLATION DNA BINDING ELECTRON TRANSFER PLANT CRYPTOCHROMES AND SIGNALING PHOTOLYASES CRYPTOCHROME PHOTOCHEMISTRY CRYPTOCHROME ACTION SPECTRA CRYPTOCHROMES AND BLUE LIGHT-DEPENDENT INHIBITION OF CELL EXPANSION SIGNALING MUTANTS SIGNALING BY CRYPTOCHROME CNT AND CCT DOMAINS ARABIDOPSIS CRYPTOCHROMES EXIST AS DIMERS COP1, A SIGNALING PARTNER OF ARABIDOPSIS CRYPTOCHROMES CRYPTOCHROME AND PHOSPHORYLATION CRYPTOCHROME AND GENE EXPRESSION CONCLUDING THOUGHTS ANIMAL CRYPTOCHROMES DISCOVERY OF ANIMAL CRYPTOCHROMES STRUCTURE–FUNCTION CONSIDERATIONS DROSOPHILA MELANOGASTER CRYPTOCHROME MAMMALIAN CRYPTOCHROMES, CIRCADIAN RHYTHMICITY, AND NONVISUAL PHOTORECEPTION CRYPTOCHROMES OF OTHER ANIMALS 12 7 CONCLUSIONS AND FUTURE DIRECTIONS BLUE LIGHT SENSING AND SIGNALING BY THE PHOTOTROPINS PHOTOTROPIN STRUCTURE AND FUNCTION DISCOVERY OF PHOTOTROPIN PHOT1: A BLUE LIGHT-ACTIVATED RECEPTOR KINASE PHOT2: A SECOND PHOTOTROPIC RECEPTOR PHOTOTROPINS: PHOTORECEPTORS FOR MOVEMENT AND MORE OVERVIEW OF PHOTOTROPIN ACTIVATION LOV DOMAIN STRUCTURE AND FUNCTION LIGHT SENSING BY THE LOV DOMAINS LOV IS ALL AROUND ARE TWO LOVS BETTER THAN ONE? FROM LIGHT SENSING TO RECEPTOR ACTIVATION LOV CONNECTION PHOTOTROPIN AUTOPHOSPHORYLATION PHOTOTROPIN RECOVERY PHOTOTROPIN SIGNALLING BEYOND PHOTORECEPTOR ACTIVATION PHOTOTROPISM STOMATAL OPENING CHLOROPLAST MOVEMENT RAPID INHIBITION OF HYPOCOTYL GROWTH BY BLUE LIGHT LOV-DOMAIN PHOTOCHEMISTRY THE CHROMOPROTEIN GROUND STATE STRUCTURE AND SPECTROSCOPY STRUCTURE OF THE CHROMOPROTEIN AND ITS CHROMOPHORE ENVIRONMENT FMN ELECTROSTATIC ENVIRONMENT WITHIN THE PROTEIN PHOTOCHEMISTRY PHOTOCYCLE KINETICS AND STRUCTURE OF ITS INTERMEDIATES PHOTO-BACKREACTION REACTION MECHANISMS ADDUCT FORMATION ADDUCT DECAY FUTURE PERSPECTIVES LOV-DOMAIN STRUCTURE, DYNAMICS, AND DIVERSITY OVERVIEW LOV DOMAIN ARCHITECTURE AND CHROMOPHORE ENVIRONMENT PHOTOEXCITED-STATE STRUCTURAL DYNAMICS OF LOV DOMAINS COMPARATIVE STRUCTURAL ANALYSIS OF LOV DOMAINS LOV-DOMAIN DIVERSITY THE ZEITLUPE FAMILY OF PUTATIVE PHOTORECEPTORS CIRCADIAN CLOCKS SCF UBIQUITIN LIGASES PHOTOPERCEPTION THE ZTL GENE FAMILY ZTL PHOTORECEPTOR GENE FAMILIES IN LOWER PLANTS CRYPTOCHROMES ADIANTUM CAPILLUS-VENERIS PHYSCOMITRELLA PATENS CHLAMYDOMONAS REINHARDTII PHOTOTROPINS PHYTOCHROMES IN LOWER PLANTS CONVENTIONAL PHYTOCHROMES PHYTOCHROME 3 IN POLYPODIACEOUS FERNS NEUROSPORA PHOTORECEPTORS INTRODUCTION AND OVERVIEW THE PHOTOBIOLOGY OF FUNGI IN GENERAL AND NEUROSPORA IN PARTICULAR PHOTORESPONSES ARE WIDESPREAD PHOTOBIOLOGY OF NEUROSPORA LIGHT PERCEPTION – THE NATURE OF THE PRIMARY BLUE LIGHT PHOTORECEPTOR FLAVINS AS CHROMOPHORES GENETIC DISSECTION OF THE LIGHT RESPONSE NEW INSIGHTS INTO PHOTORECEPTORS FROM GENOMICS HOW DO THE KNOWN PHOTORECEPTORS WORK? WC-1 AND WC-2 CONTAIN PAS DOMAINS AND ACT AS A COMPLEX WC-1 IS THE BLUE LIGHT PHOTORECEPTOR A NON-PHOTOBIOLOGICAL ROLE FOR WC-1 AND THE WCC VIVID, A SECOND PHOTORECEPTOR THAT MODULATES LIGHT RESPONSES TYPES OF PHOTORESPONSE MODULATION PROOF OF VVD PHOTORECEPTOR FUNCTION COMPLEXITIES IN LIGHT REGULATORY PATHWAYS SUMMARY AND CONCLUSION PHOTOACTIVE YELLOW PROTEIN, THE XANTHOPSIN DISCOVERY OF THE PHOTOACTIVE YELLOW PROTEIN A FAMILY OF PHOTOACTIVE YELLOW PROTEINS: THE XANTHOPSINS DIFFERENTIATION OF FUNCTION AMONG THE XANTHOPSINS PYP: THE PROTOTYPE PAS DOMAIN STRUCTURE PRIMARY, SECONDARY, AND TERTIARY STRUCTURE SOLUTION STRUCTURE VS CRYSTAL STRUCTURE THE XANTHOPSINS COMPARED PHOTOACTIVITY OF THE XANTHOPSINS THE BASIC PHOTOCYCLE PHOTOCYCLE NOMENCLATURE EXPERIMENTAL OBSERVATION: CONTEXT DEPENDENCE MUTANTS AND HYBRIDS PHOTO-ACTIVATION IN THE DIFFERENT XANTHOPSINS COMPARED THE PHOTOCYCLE OF PHOTOACTIVE YELLOW PROTEIN INITIAL EVENTS SIGNALING STATE FORMATION AND GROUND STATE RECOVERY STRUCTURAL RELAXATION OF PR PROTONATION CHANGE UPON PB’ FORMATION STRUCTURAL CHANGE UPON PB FORMATION RECOVERY OF THE GROUND STATE SPECTRAL TUNING OF PHOTOACTIVE YELLOW PROTEIN GROUND STATE TUNING SPECTRAL TUNING IN PHOTOCYCLE INTERMEDIATES SUMMARY AND FUTURE PERSPECTIVE HYPERICIN-LIKE PHOTORECEPTORS ABSTRACT CILIATE PHOTORECEPTORS ACTION SPECTRA THE CHROMOPHORES PROTEINS AND LOCALIZATION PHOTOSENSITIZATION? PRIMARY PHOTOPROCESSES PHOTOSENSORY SIGNAL TRANSDUCTION SIGNAL GENERATION SIGNAL AMPLIFICATION SIGNAL TRANSDUCTION THE ANTIREPRESSOR APPA USES THE NOVEL FLAVIN-BINDING BLUF DOMAIN AS A BLUE-LIGHT-ABSORBING PHOTORECEPTOR TO CONTROL PHOTOSYSTEM SYNTHESIS OXYGEN AND LIGHT INTENSITY CONTROL SYNTHESIS OF THE BACTERIAL PHOTOSYSTEM PPSR IS A DNA-BINDING TRANSCRIPTION FACTOR THAT COORDINATES BOTH OXYGEN AND LIGHT REGULATION DISCOVERY OF APPA, A REDOX RESPONDING, BLUE LIGHT ABSORBING, ANTIREPRESSOR OF PPSR MECHANISM OF THE BLUF PHOTOCYCLE IN APPA OTHER BLUF CONTAINING PROTEINS ACKNOWLEDGEMENT DISCOVERY AND CHARACTERIZATION OF PHOTOACTIVATED ADENYLYL CYCLASE (PAC), A NOVEL BLUE-LIGHT RECEPTOR FLAVOPROTEIN, FROM EUGLENA GRACILIS ACTION SPECTROSCOPY PAC DISCOVERY AND ITS IDENTIFICATION AS THE BLUE-LIGHT RECEPTOR FOR PHOTOAVOIDANCE PAC INVOLVEMENT IN PHOTOTAXIS PAC ORIGIN