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Table of Contents  
 
Preface XVII
List of Authors XIX
1 Microbial Rhodopsins: Phylogenetic and Functional Diversity
John L. Spudich and Kwang-Hwan Jung 		1
1.1 Introduction 1
1.2 Archaeal Rhodopsins 2
1.3 Clues to Newfound Microbial Rhodopsin Function from Primary Sequence Comparison to Archaeal Rhodopsins 7
1.4 Bacterial Rhodopsins 10
1.4.1 Green-absorbing Proteorhodopsin (“GPR”) from Monterey Bay Surface Plankton 10
1.4.2 Blue-absorbing Proteorhodopsin (“BPR”) from Hawaiian Deep Sea Plankton 12
1.4.3 Anabaena Sensory Rhodopsin 13
1.4.4 Other Bacterial Rhodopsins 15
1.5 Eukaryotic Microbial Rhodopsins 16
1.5.1 Fungal Rhodopsins 16
1.5.2 Algal Rhodopsins 17
1.6 Spectral Tuning 18
1.7 A Unified Mechanism for Molecular Function? 19
1.8 Opsin-related Proteins without the Retinal-binding Site 20
1.9 Perspective 20
References 21
2 Sensory Rhodopsin Signaling in Green Flagellate Algae
Oleg A. Sineshchekov and John L. Spudich 		25
2.1 Introduction 25
2.1.1 Retinylidene Receptors 25
2.1.2. Physiology of Algal Phototaxis and the Photophobic Response 26
2.1.3 Photoelectrical Currents and their Relationship to Swimming Behavior 27
2.2 The Photosensory Receptors: CSRA and CSRB 30
2.2.1 Genomics, Sequence, and Predicted Structure 31
2.2.2 Cellular Content and Roles in Phototaxis and Photophobic Behavior 32
2.2.3 Molecular Mechanism of Action 36
2.3 Other Algae 39
2.4 Conclusion and Future Perspectives 40
Acknowledgements 41
References 41
3 Visual Pigments as Photoreceptors
Masato Kumauchi and Thomas Ebrey 		43
3.1 Introduction 43
3.1.1 General Considerations 43
3.1.2 Photoreceptors and Pigments 49
3.1.3 Non-photoreceptor or “Non-rod”, “Non-cone” Retinal Pigments 50
3.1.4 Retinal Photoisomerases 51
3.2 The Unphotolyzed State of Vertebrate Visual Pigments 51
3.2.1 Structure of Visual Pigments: the Chromophore 51
3.2.2 Overall Topology of the Pigment 52
3.2.3 Cytoplasmic Domain 54
3.2.4 The Hydrophobic Core of Rhodopsin and the Retinal Binding Pocket 55
3.2.5 The Extracellular Domain of Rhodopsin 56
3.2.6 Structure of Other Visual Pigments 56
3.2.7 Protonation State of Some of the Carboxylic Acids of Rhodopsin 57
3.2.8 Internal Waters in Visual Pigments 57
3.2.9 Is Rhodopsin a Dimer in vivo? 58
3.2.10 Functional Properties of the Unphotolyzed State of a “Good” Visual Pigment 58
3.2.11 Quantum Efficiency of Visual Pigment Photochemistry 62
3.2.12 Dark Noise Originating from the Photoreceptor Pigment 63
3.3 Activation of Vertebrate Visual Pigments 65
3.3.1 Introduction 65
3.3.2 The Primary Event, Photoisomerization 65
3.3.3 The Meta I Meta II Transition 66
3.3.4 Molecular Changes upon the Formation of Meta I and Meta II 67
3.3.5 Internal Water Molecules 67
3.3.6 Required Steps for Rhodopsin Activation 67
3.3.7 The Transmembrane Signaling Pathway 68
3.4 The Unphotolyzed State of Invertebrate Visual Pigments 69
3.4.1 Introduction 69
3.4.2 Wavelength Regulation of Invertebrate Pigments 70
3.5 Mechanism of Activation of Invertebrate Visual Pigments 71
3.5.1 The Initial Photochemical Events 71
3.5.2 Formation of Acid Metarhodopsin 71
3.5.3 Required Steps for Photolyzed Octopus Rhodopsin to Activate its G-protein 71
3.5.4 Purification of the Active Form of an Invertebrate Visual Pigment 72
Acknowledgements 72
References 72
4 Structural and Functional Aspects of the Mammalian Rod-Cell Photoreceptor Rhodopsin
Najmoutin G. Abdulaev and Kevin D. Ridge 		77
4.1 Introduction 77
4.2 Rhodopsin and Mammalian Visual Phototransduction 79
4.2.1 Signal Amplification by Light-activated Rhodopsin 79
4.2.2 Inactivation of Light-activated Rhodopsin 79
4.3 Properties of Rhodopsin 80
4.3.1 Isolation of Rhodopsin 80
4.3.2 Biochemical and Physicochemical Properties of Rhodopsin 81
4.3.3 Post-translational Modifications in Rhodopsin 82
4.3.4 Membrane Topology of Rhodopsin and Functional Domains 82
4.4 Chromophore Binding Pocket and Photolysis of Rhodopsin 85
4.5 Structure of Rhodopsin 86
4.5.1 Crystal Structure of Rhodopsin 86
4.5.2 Atomic Force Microscopy of Rhodopsin in the Disk Membrane 88
4.6 Activation Mechanism of Rhodopsin 88
4.7 Conclusions 89
Acknowledgements 90
References 90
5 A Novel Light Sensing Pathway in the Eye: Conserved Features of Inner Retinal Photoreception in Rodents, Man and Teleost Fish
Mark W. Hankins and Russell G. Foster 		93
Summary 93
5.1 Introduction 94
5.1.1 A Novel Photoreceptor within the Eye 94
5.1.2 Biological Clocks and their Regulation by Light 95
5.2 Non-rod, Non-cone Photoreception in Rodents 96
5.2.1 An Irradiance Detection Pathway in the Eye 96
5.2.2 The Discovery of a Novel Ocular Photopigment in Mice (OP480) 97
5.2.3 Melanopsin and Non-rod, Non-cone Photoreception 99
5.2.4 A Functional Syncitium of Directly Light-sensitive Ganglion Cells 101
5.3 Non-rod, Non-cone Photoreception in Humans 104
5.3.1 Introduction 104
5.3.2 Novel Photoreceptors Regulate Melatonin 105
5.3.3 Novel Photoreceptors Regulate the Primary Visual Cone Pathway 105
5.4 Non-rod, Non-cone Photoreception in Teleost Fish 107
5.4.1 Background 107
5.4.2 Vertebrate Ancient (VA) Opsin and Inner Retinal Photoreception in Teleost Fish 108
5.4.3 A Novel Light Response from VA-opsin- and Melanopsin-expressing Horizontal Cells 108
5.4.4 Action Spectra for the HC–RSD Light Response Identify a Novel Photopigment 109
5.4.5 The Possible Function of HC–RSD Neurones 111
5.5 Opsins can be Photosensors or Photoisomerases 112
5.6 Placing Candidate Genes and Photopigments into Context 113
5.7 Conclusions 114
References 115
6 The Phytochromes
Shih-Long Tu and J. Clark Lagarias 		121
6.1 Introduction 121
6.1.1 Photomorphogenesis and Phytochromes 121
6.1.2 The Central Dogma of Phytochrome Action 122
6.2 Molecular Properties of Eukaryotic and Prokaryotic Phytochromes 123
6.2.1 Molecular Properties of Plant Phytochromes 123
6.2.2 Molecular Properties of Cyanobacterial Phytochromes 125
6.3 Photochemical and Nonphotochemical Conversions of Phytochrome 127
6.3.1 The Phytochrome Chromophore 127
6.3.2 Phytochrome Photointerconversions 129
6.3.3 Dark Reversion 132
6.4 Phytochrome Biosynthesis and Turnover 133
6.4.1 Phytobilin Biosynthesis in Plants and Cyanobacteria 133
6.4.2 Apophytochrome Biosynthesis and Holophytochrome Assembly 138
6.4.3 Phytochrome Turnover 141
6.5 Molecular Mechanism of Phytochrome Signaling: Future Perspective 142
6.5.1 Regulation of Protein–Protein Interactions by Phosphorylation 142
6.5.2 Regulation of Tetrapyrrole Metabolism 143
Acknowledgements 145
References 145
7 Phytochrome Signaling
Enamul Huq and Peter H. Quail 		151
7.1 Introduction 151
7.2 Photosensory and Biological Functions of Individual Phytochromes 152
7.3 phy Domains Involved in Signaling 154
7.4 phy Signaling Components 155
7.4.1 Second Messenger Hypothesis 155
7.4.2 Genetically Identified Signaling Components 156
7.4.3 phy-Interacting Factors 159
7.4.4 Early phy-Responsive Genes 162
7.5 Biochemical Mechanism of Signal Transfer 164
7.6 phy Signaling and Circadian Rhythms 165
7.7 Future Prospects 166
Acknowledgements 167
References 168
8 Phytochromes in Microorganisms
Richard D. Vierstra and Baruch Karniol 		171
8.1 Introduction 171
8.2 Higher Plant Phys 172
8.3 The Discovery of Microbial Phys 174
8.4 Phylogenetic Analysis of the Phy Superfamily 176
8.4.1 Cyanobacterial Phy (Cph) Family 179
8.4.2 Bacteriophytochrome (BphP) Family 179
8.4.3 Fungal Phy (Fph) Family 184
8.4.4 Phy-like Sequences 185
8.5 Downstream Signal-Transduction Cascades 186
8.6 Physiological Roles of Microbial Phys 188
8.6.1 Regulation of Phototaxis 188
8.6.2 Enhancement of Photosynthetic Potential 189
8.6.3 Photocontrol of Pigmentation 191
8.7 Evolution of the Phy Superfamily 191
8.8 Perspectives 192
Acknowledgements 193
References 194
9 Light-activated Intracellular Movement of Phytochrome
Eberhard Schäfer and Ferenc Nagy 		197
9.1 Introduction 197
9.2 The Classical Methods 197
9.2.1 Spectroscopic Methods 197
9.2.2 Cell Biological Methods 198
9.2.3 Immunocytochemical Methods 198
9.3 Novel Methods 199
9.4 Intracellular Localization of PHYB in Dark and Light 200
9.5 Intracellular Localization of PHYA in Dark and Light 201
9.6 Intracellular Localization of PHYC, PHYD and PHYE in Dark and Light 202
9.7 Intracellular Localization of Intragenic Mutant Phytochromes 203
9.7.1 Hyposensitive, Loss-of-function Mutants 203
9.7.2 Hypersensitive Mutants 204
9.8 Protein Composition of Nuclear Speckles Associated with phyB 204
9.9 The Function of Phytochromes Localized in Nuclei and Cytosol 207
9.10 Concluding Remarks 208
References 209
10 Plant Cryptochromes: Their Genes, Biochemistry, and Physiological Roles
Alfred Batschauer 		211
Summary 211
10.1 Cryptochrome Genes and Evolution 212
10.1.1 The Discovery of Cryptochromes 212
10.1.2 Distribution of Cryptochromes and their Evolution 213
10.2 Cryptochrome Domains, Cofactors and Similarities with Photolyase 214
10.3 Biological Function of Plant Cryptochromes 219
10.3.1 Control of Growth 220
10.3.2 Role of Cryptochromes in Circadian Clock Entrainment and Photoperiodism 223
10.3.3 Regulation of Gene Expression 228
10.4 Localization of Cryptochromes 232
10.5 Biochemical Properties of Cryptochromes 234
10.5.1 Protein Stability 234
10.5.2 Phosphorylation 236
10.5.3 DNA Binding 239
10.5.4 Electron Transfer 240
10.6 Summary 241
Acknowledgements 241
References 242
11 Plant Cryptochromes and Signaling
Anthony R. Cashmore 		247
11.1 Introduction 247
11.2 Photolyases 247
11.3 Cryptochrome Photochemistry 248
11.4 Cryptochrome Action Spectra 249
11.5 Cryptochromes and Blue Light-dependent Inhibition of Cell Expansion 250
11.6 Signaling Mutants 251
11.7 Signaling by Cryptochrome CNT and CCT Domains 251
11.8 Arabidopsis Cryptochromes Exist as Dimers 252
11.9 COP1, a Signaling Partner of Arabidopsis Cryptochromes 253
11.10 Cryptochrome and Phosphorylation 253
11.11 Cryptochrome and Gene Expression 254
11.12 Concluding Thoughts 255
References 257
12 Animal Cryptochromes
Russell N. Van Gelder and Aziz Sancar 		259
12.1 Introduction 259
12.2 Discovery of Animal Cryptochromes 260
12.3 Structure–Function Considerations 260
12.4 Drosophila melanogaster Cryptochrome 263
12.5 Mammalian Cryptochromes, Circadian Rhythmicity, and Nonvisual Photoreception 266
12.6 Cryptochromes of Other Animals 273
12.7. Conclusions and Future Directions 274
References 274
13 Blue Light Sensing and Signaling by the Phototropins
John M. Christie and Winslow R. Briggs 		277
13.1 Introduction 277
13.2 Phototropin Structure and Function 278
13.2.1 Discovery of Phototropin 278
13.2.2 Phot1: a Blue Light-activated Receptor Kinase 279
13.2.3 Phot2: a Second Phototropic Receptor 280
13.2.4 Phototropins: Photoreceptors for Movement and More 281
13.2.5 Overview of Phototropin Activation 283
13.3 LOV Domain Structure and Function 284
13.3.1 Light Sensing by the LOV Domains 284
13.3.2 LOV is all Around 286
13.3.3 Are Two LOVs Better than One? 288
13.4 From Light Sensing to Receptor Activation 290
13.4.1 LOV Connection 290
13.4.2 Phototropin Autophosphorylation 291
13.4.3 Phototropin Recovery 292
13.5 Phototropin Signalling 294
13.5.1 Beyond Photoreceptor Activation 294
13.5.2 Phototropism 294
13.5.3 Stomatal Opening 296
13.5.4 Chloroplast Movement 297
13.5.5 Rapid Inhibition of Hypocotyl Growth by Blue Light 299
13.6 Future Prospects 300
References 300
14 LOV-domain Photochemistry
Trevor E. Swartz and Roberto A. Bogomolni 		305
14.1 Introduction 305
14.2 The Chromoprotein Ground State Structure and Spectroscopy 306
14.2.1 Structure of the Chromoprotein and its Chromophore Environment 306
14.2.2 FMN Electrostatic Environment within the Protein 307
14.3 Photochemistry 312
14.3.1 Photocycle Kinetics and Structure of its Intermediates 312
14.3.2 Photo-backreaction 316
14.4 Reaction Mechanisms 316
14.4.1 Adduct Formation 316
14.4.2 Adduct Decay 319
14.4 Future Perspectives 320
References 321
15 LOV-Domain Structure, Dynamics, and Diversity
Sean Crosson 		323
15.1 Overview 323
15.2 LOV Domain Architecture and Chromophore Environment 324
15.3 Photoexcited-State Structural Dynamics of LOV Domains 326
15.4 Comparative Structural Analysis of LOV Domains 328
15.5 LOV-Domain Diversity 330
Acknowledgements 334
References 335
16 The ZEITLUPE Family of Putative Photoreceptors
Thomas F. Schultz 		337
16.1 Introduction 337
16.2 Circadian Clocks 337
16.3 SCF Ubiquitin Ligases 340
16.4 Photoperception 341
16.5 The ZTL Gene Family 342
16.5.1 ZTL 343
16.5.2 FKF1 344
16.5.3 LKP2 345
16.6 Summary 346
References 346
17 Photoreceptor Gene Families in Lower Plants
Noriyuki Suetsugu and Masamitsu Wada 		349
17.1 Introduction 349
17.2 Cryptochromes 352
17.2.1 Adiantum capillus-veneris 352
17.2.2 Physcomitrella patens 354
17.2.3 Chlamydomonas reinhardtii 356
17.3 Phototropins 357
17.3.1 Adiantum capillus-veneris 357
17.3.2 Physcomitrella patens 358
17.3.3 Chlamydomonas reinhardtii 361
17.4 Phytochromes in Lower Plants 363
17.4.1 Conventional Phytochromes 363
17.4.2 Phytochrome 3 in Polypodiaceous Ferns 364
17.5 Concluding Remarks 366
Acknowledgements 366
References 367
18 Neurospora Photoreceptors
Jay C. Dunlap and Jennifer J. Loros 		371
18.1 Introduction and Overview 371
18.2 The Photobiology of Fungi in General and Neurospora in Particular 371
18.2.1 Photoresponses are Widespread 371
18.2.2 Photobiology of Neurospora 372
18.3 Light Perception – the Nature of the Primary Blue Light Photoreceptor 375
18.3.1 Flavins as Chromophores 375
18.3.2 Genetic Dissection of the Light Response 375
18.3.3 New Insights into Photoreceptors from Genomics 376
18.4 How do the Known Photoreceptors Work? 377
18.4.1 WC-1 and WC-2 contain PAS Domains and Act as a Complex 377
18.4.2 WC-1 is the Blue Light Photoreceptor 378
18.4.3 Post-activation Regulation of WC-1 382
18.4.4 A Non-photobiological Role for WC-1 and the WCC 383
18.5 VIVID, a Second Photoreceptor that Modulates Light Responses 384
18.5.1 Types of Photoresponse Modulation 384
18.5.2 Proof of VVD Photoreceptor Function 386
18.6 Complexities in Light Regulatory Pathways 387
18.7 Summary and Conclusion 387
References 388
19 Photoactive Yellow Protein, the Xanthopsin
Michael A. van der Horst, Johnny Hendriks, Jocelyne Vreede, Sergei Yeremenko, Wim Crielaard and Klaas J. Hellingwerf 		391
19.1 Introduction 391
19.1.1 Discovery of the Photoactive Yellow Protein 391
19.1.2 A Family of Photoactive Yellow Proteins: the Xanthopsins 392
19.1.3 Differentiation of Function among the Xanthopsins 392
19.1.4 PYP: The Prototype PAS Domain 393
19.2 Structure 394
19.2.1 Primary, Secondary, and Tertiary Structure 394
19.2.2 Solution Structure vs. Crystal Structure 395
19.2.3 The Xanthopsins Compared 396
19.3 Photoactivity of the Xanthopsins 397
19.3.1 The Basic Photocycle 397
19.3.2 Photocycle Nomenclature 399
19.3.3 Experimental Observation: Context Dependence 399
19.3.4 Mutants and Hybrids 400
19.3.5 Photo-activation in the Different Xanthopsins Compared 400
19.4 The Photocycle of Photoactive Yellow Protein 401
19.4.1 Initial Events 401
19.4.2 Signaling State Formation and Ground State Recovery 403
19.4.3 Structural Relaxation of pR 404
19.4.4 Protonation Change upon pB’ Formation 404
19.4.5 Structural Change upon pB Formation 405
19.4.6 Recovery of the Ground State 407
19.5 Spectral Tuning of Photoactive Yellow Protein 408
19.5.1 Ground State Tuning 409
19.5.2 Spectral Tuning in Photocycle Intermediates 410
19.6 Summary and Future Perspective 411
References 412
20 Hypericin-like Photoreceptors
Pill-Soon Song 		417
Abstract 417
20.1 Introduction 417
20.2 Ciliate Photoreceptors 420
20.2.1 Action Spectra 420
20.2.2 The Chromophores 421
20.2.3 Proteins and Localization 423
20.3 Photochemistry 425
20.3.1 Photosensitization? 425
20.3.2 Primary Photoprocesses 425
20.4 Photosensory Signal Transduction 427
20.4.1 Signal Generation 428
20.4.2 Signal Amplification 429
20.4.3 Signal Transduction 429
20.5 Concluding Remarks 430
Acknowledgements 430
References 431
21 The Antirepressor AppA uses the Novel Flavin-Binding BLUF Domain as a Blue-Light-Absorbing Photoreceptor to Control Photosystem Synthesis
Shinji Masuda and Carl E. Bauer 		433
21.1 Overview 433
21.2 Oxygen and Light Intensity Control Synthesis of the Bacterial Photosystem 434
21.2.1 PpsR is a DNA-binding Transcription Factor that Coordinates both Oxygen and Light Regulation 435
21.2.2 Discovery of AppA, a Redox Responding, Blue Light Absorbing, Antirepressor of PpsR 435
21.3 Mechanism of the BLUF Photocycle in AppA 438
21.4 Other BLUF Containing Proteins 441
21.5 Concluding Remarks 443
Acknowledgement 444
References 444
22 Discovery and Characterization of Photoactivated Adenylyl Cyclase (PAC), a Novel Blue-Light Receptor Flavoprotein, from Euglena gracilis
Masakatsu Watanabe and Mineo Iseki 		447
22.1 Introduction 447
22.2 Action Spectroscopy 447
22.3 PAC Discovery and its Identification as the Blue-light Receptor for Photoavoidance 449
22.4 PAC Involvement in Phototaxis 456
22.5 PAC Origin 457
22.6 Future Prospects 457
Acknowledgements 459
References 460

 
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