Note: Intro -- Handbook of Photosensory Receptors -- Table of Contents -- Preface -- List of Authors -- 1 Microbial Rhodopsins: Phylogenetic and Functional Diversity -- 1.1 Introduction -- 1.2 Archaeal Rhodopsins -- 1.3 Clues to Newfound Microbial Rhodopsin Function from Primary Sequence Comparison to Archaeal Rhodopsins -- 1.4 Bacterial Rhodopsins -- 1.4.1 Green-absorbing Proteorhodopsin ("GPR") from Monterey Bay Surface Plankton -- 1.4.2 Blue-absorbing Proteorhodopsin ("BPR") from Hawaiian Deep Sea Plankton -- 1.4.3 Anabaena Sensory Rhodopsin -- 1.4.4 Other Bacterial Rhodopsins -- 1.5 Eukaryotic Microbial Rhodopsins -- 1.5.1 Fungal Rhodopsins -- 1.5.2 Algal Rhodopsins -- 1.6 Spectral Tuning -- 1.7 A Unified Mechanism for Molecular Function? -- 1.8 Opsin-related Proteins without the Retinal-binding Site -- 1.9 Perspective -- References -- 2 Sensory Rhodopsin Signaling in Green Flagellate Algae -- 2.1 Introduction -- 2.1.1 Retinylidene Receptors -- 2.1.2. Physiology of Algal Phototaxis and the Photophobic Response -- 2.1.3 Photoelectrical Currents and their Relationship to Swimming Behavior -- 2.2 The Photosensory Receptors: CSRA and CSRB -- 2.2.1 Genomics, Sequence, and Predicted Structure -- 2.2.2 Cellular Content and Roles in Phototaxis and Photophobic Behavior -- 2.2.3 Molecular Mechanism of Action -- 2.3 Other Algae -- 2.4 Conclusion and Future Perspectives -- Acknowledgements -- References -- 3 Visual Pigments as Photoreceptors -- 3.1 Introduction -- 3.1.1 General Considerations -- 3.1.2 Photoreceptors and Pigments -- 3.1.3 Non-photoreceptor or "Non-rod", "Non-cone" Retinal Pigments -- 3.1.4 Retinal Photoisomerases -- 3.2 The Unphotolyzed State of Vertebrate Visual Pigments -- 3.2.1 Structure of Visual Pigments: the Chromophore -- 3.2.2 Overall Topology of the Pigment -- 3.2.3 Cytoplasmic Domain. , 3.2.4 The Hydrophobic Core of Rhodopsin and the Retinal Binding Pocket -- 3.2.5 The Extracellular Domain of Rhodopsin -- 3.2.6 Structure of Other Visual Pigments -- 3.2.7 Protonation State of Some of the Carboxylic Acids of Rhodopsin -- 3.2.8 Internal Waters in Visual Pigments -- 3.2.9 Is Rhodopsin a Dimer in vivo? -- 3.2.10 Functional Properties of the Unphotolyzed State of a "Good" Visual Pigment -- 3.2.11 Quantum Efficiency of Visual Pigment Photochemistry -- 3.2.12 Dark Noise Originating from the Photoreceptor Pigment -- 3.3 Activation of Vertebrate Visual Pigments -- 3.3.1 Introduction -- 3.3.2 The Primary Event, Photoisomerization -- 3.3.3 The Meta I ↔ Meta II Transition -- 3.3.4 Molecular Changes upon the Formation of Meta I and Meta II -- 3.3.5 Internal Water Molecules -- 3.3.6 Required Steps for Rhodopsin Activation -- 3.3.7 The Transmembrane Signaling Pathway -- 3.4 The Unphotolyzed State of Invertebrate Visual Pigments -- 3.4.1 Introduction -- 3.4.2 Wavelength Regulation of Invertebrate Pigments -- 3.5 Mechanism of Activation of Invertebrate Visual Pigments -- 3.5.1 The Initial Photochemical Events -- 3.5.2 Formation of Acid Metarhodopsin -- 3.5.3 Required Steps for Photolyzed Octopus Rhodopsin to Activate its G-protein -- 3.5.4 Purification of the Active Form of an Invertebrate Visual Pigment -- Acknowledgements -- References -- 4 Structural and Functional Aspects of the Mammalian Rod-Cell Photoreceptor Rhodopsin -- 4.1 Introduction -- 4.2 Rhodopsin and Mammalian Visual Phototransduction -- 4.2.1 Signal Amplification by Light-activated Rhodopsin -- 4.2.2 Inactivation of Light-activated Rhodopsin -- 4.3 Properties of Rhodopsin -- 4.3.1 Isolation of Rhodopsin -- 4.3.2 Biochemical and Physicochemical Properties of Rhodopsin -- 4.3.3 Post-translational Modifications in Rhodopsin -- 4.3.4 Membrane Topology of Rhodopsin and Functional Domains. , 4.4 Chromophore Binding Pocket and Photolysis of Rhodopsin -- 4.5 Structure of Rhodopsin -- 4.5.1 Crystal Structure of Rhodopsin -- 4.5.2 Atomic Force Microscopy of Rhodopsin in the Disk Membrane -- 4.6 Activation Mechanism of Rhodopsin -- 4.7 Conclusions -- Acknowledgements -- References -- 5 A Novel Light Sensing Pathway in the Eye: Conserved Features of Inner Retinal Photoreception in Rodents, Man and Teleost Fish -- Summary -- 5.1 Introduction -- 5.1.1 A Novel Photoreceptor within the Eye -- 5.1.2 Biological Clocks and their Regulation by Light -- 5.2 Non-rod, Non-cone Photoreception in Rodents -- 5.2.1 An Irradiance Detection Pathway in the Eye -- 5.2.2 The Discovery of a Novel Ocular Photopigment in Mice (OP(480)) -- 5.2.3 Melanopsin and Non-rod, Non-cone Photoreception -- 5.2.4 A Functional Syncitium of Directly Light-sensitive Ganglion Cells -- 5.3 Non-rod, Non-cone Photoreception in Humans -- 5.3.1 Introduction -- 5.3.2 Novel Photoreceptors Regulate Melatonin -- 5.3.3 Novel Photoreceptors Regulate the Primary Visual Cone Pathway -- 5.4 Non-rod, Non-cone Photoreception in Teleost Fish -- 5.4.1 Background -- 5.4.2 Vertebrate Ancient (VA) Opsin and Inner Retinal Photoreception in Teleost Fish -- 5.4.3 A Novel Light Response from VA-opsin- and Melanopsin-expressing Horizontal Cells -- 5.4.4 Action Spectra for the HC-RSD Light Response Identify a Novel Photopigment -- 5.4.5 The Possible Function of HC-RSD Neurones -- 5.5 Opsins can be Photosensors or Photoisomerases -- 5.6 Placing Candidate Genes and Photopigments into Context -- 5.7 Conclusions -- References -- 6 The Phytochromes -- 6.1 Introduction -- 6.1.1 Photomorphogenesis and Phytochromes -- 6.1.2 The Central Dogma of Phytochrome Action -- 6.2 Molecular Properties of Eukaryotic and Prokaryotic Phytochromes -- 6.2.1 Molecular Properties of Plant Phytochromes. , 6.2.2 Molecular Properties of Cyanobacterial Phytochromes -- 6.3 Photochemical and Nonphotochemical Conversions of Phytochrome -- 6.3.1 The Phytochrome Chromophore -- 6.3.2 Phytochrome Photointerconversions -- 6.3.3 Dark Reversion -- 6.4 Phytochrome Biosynthesis and Turnover -- 6.4.1 Phytobilin Biosynthesis in Plants and Cyanobacteria -- 6.4.2 Apophytochrome Biosynthesis and Holophytochrome Assembly -- 6.4.3 Phytochrome Turnover -- 6.5 Molecular Mechanism of Phytochrome Signaling: Future Perspective -- 6.5.1 Regulation of Protein-Protein Interactions by Phosphorylation -- 6.5.2 Regulation of Tetrapyrrole Metabolism -- Acknowledgements -- References -- 7 Phytochrome Signaling -- 7.1 Introduction -- 7.2 Photosensory and Biological Functions of Individual Phytochromes -- 7.3 phy Domains Involved in Signaling -- 7.4 phy Signaling Components -- 7.4.1 Second Messenger Hypothesis -- 7.4.2 Genetically Identified Signaling Components -- 7.4.3 phy-Interacting Factors -- 7.4.4 Early phy-Responsive Genes -- 7.5 Biochemical Mechanism of Signal Transfer -- 7.6 phy Signaling and Circadian Rhythms -- 7.7 Future Prospects -- Acknowledgements -- References -- 8 Phytochromes in Microorganisms -- 8.1 Introduction -- 8.2 Higher Plant Phys -- 8.3 The Discovery of Microbial Phys -- 8.4 Phylogenetic Analysis of the Phy Superfamily -- 8.4.1 Cyanobacterial Phy (Cph) Family -- 8.4.2 Bacteriophytochrome (BphP) Family -- 8.4.3 Fungal Phy (Fph) Family -- 8.4.4 Phy-like Sequences -- 8.5 Downstream Signal-Transduction Cascades -- 8.6 Physiological Roles of Microbial Phys -- 8.6.1 Regulation of Phototaxis -- 8.6.2 Enhancement of Photosynthetic Potential -- 8.6.3 Photocontrol of Pigmentation -- 8.7 Evolution of the Phy Superfamily -- 8.8 Perspectives -- Acknowledgements -- References -- 9 Light-activated Intracellular Movement of Phytochrome -- 9.1 Introduction. , 9.2 The Classical Methods -- 9.2.1 Spectroscopic Methods -- 9.2.2 Cell Biological Methods -- 9.2.3 Immunocytochemical Methods -- 9.3 Novel Methods -- 9.4 Intracellular Localization of PHYB in Dark and Light -- 9.5 Intracellular Localization of PHYA in Dark and Light -- 9.6 Intracellular Localization of PHYC, PHYD and PHYE in Dark and Light -- 9.7 Intracellular Localization of Intragenic Mutant Phytochromes -- 9.7.1 Hyposensitive, Loss-of-function Mutants -- 9.7.2 Hypersensitive Mutants -- 9.8 Protein Composition of Nuclear Speckles Associated with phyB -- 9.9 The Function of Phytochromes Localized in Nuclei and Cytosol -- 9.10 Concluding Remarks -- References -- 10 Plant Cryptochromes: Their Genes, Biochemistry, and Physiological Roles -- Summary -- 10.1 Cryptochrome Genes and Evolution -- 10.1.1 The Discovery of Cryptochromes -- 10.1.2 Distribution of Cryptochromes and their Evolution -- 10.2 Cryptochrome Domains, Cofactors and Similarities with Photolyase -- 10.3 Biological Function of Plant Cryptochromes -- 10.3.1 Control of Growth -- 10.3.2 Role of Cryptochromes in Circadian Clock Entrainment and Photoperiodism -- 10.3.3 Regulation of Gene Expression -- 10.4 Localization of Cryptochromes -- 10.5 Biochemical Properties of Cryptochromes -- 10.5.1 Protein Stability -- 10.5.2 Phosphorylation -- 10.5.3 DNA Binding -- 10.5.4 Electron Transfer -- 10.6 Summary -- Acknowledgements -- References -- 11 Plant Cryptochromes and Signaling -- 11.1 Introduction -- 11.2 Photolyases -- 11.3 Cryptochrome Photochemistry -- 11.4 Cryptochrome Action Spectra -- 11.5 Cryptochromes and Blue Light-dependent Inhibition of Cell Expansion -- 11.6 Signaling Mutants -- 11.7 Signaling by Cryptochrome CNT and CCT Domains -- 11.8 Arabidopsis Cryptochromes Exist as Dimers -- 11.9 COP1, a Signaling Partner of Arabidopsis Cryptochromes -- 11.10 Cryptochrome and Phosphorylation. , 11.11 Cryptochrome and Gene Expression.