PHOTOMORPHOGENESIS IN PLANTS AND BACTERIA 3RD EDITION

Transcription

1 PHOTOMORPHOGENESIS IN PLANTS AND BACTERIA 3RD EDITION

2 Photomorphogenesis in Plants and Bacteria 3rd Edition Function and Signal Transduction Mechanisms Edited by EBERHARD SCHÄFER Albert-Ludwigs-Universität Freiburg, Germany and FERENC NAGY Institute of Plant Biology, Szeged, Hungary

3 A C.I.P. Catalogue record for this book is available from the Library of Congress. ISBN (PB) ISBN (PB) ISBN (HB) ISBN (HB) ISBN ( e-book) ISBN (e-book) Published by Springer, P.O. Box 17, 3300 AA Dordrecht, The Netherlands. Printed on acid-free paper All Rights Reserved 2006 Springer No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Printed in the Netherlands.

4 This book is dedicated to Hans Mohr, a founding member of the AESOP (Annual European Symposium of Photormorphogenesis), on the occasion of his 75 th anniversary (May 11 th 2005).

5 PREFACE Plants as sessile organisms have evolved fascinating capacities to adapt to changes in their natural environment. Arguably, light is by far the most important and variable environmental factor. The quality, quantity, direction and duration of light is monitored by a series of photoreceptors covering spectral information from UVB to near infrared. The response of the plants to light is called photomorphogenesis and it is regulated by the concerted action of photoreceptors. The combined techniques of action spectroscopy and biochemistry allowed one of the important photoreceptors phytochrome to be identified in the middle of the last century. An enormous number of physiological studies published in the last century describe the properties of phytochrome and its function and also the physiology of blue and UV-B photoreceptors, unidentified at the time. This knowledge was summarized in the advanced textbook Photomorphogenesis in Plants (Kendrick and Kronenberg, eds., 1986, 1994). With the advent of molecular biology, genetics and new molecular, cellular techniques, our knowledge in the field of photomorphogenesis has dramatically increased over the last 15 years. In 2002 the publisher approached us with a suggestion to start a new edition of this advanced textbook. After several discussions we came to the conclusion that a new edition containing only the novel observations would no longer be useful as a textbook. Clearly, all the new molecular information has not erased the validity of the old physiological and biochemical data. Even more importantly, it is most unfortunate that in the new generation of researchers the knowledge of the old data starts to get lost. Consequently, ample evidence can be found in the literature for over or underinterpretation of results obtained by applying state of art methodologies which can be traced back to lack of in-depth knowledge of classical physiological data. Therefore, in agreement with the publisher we decided to edit a new textbook focusing on the novel observations and at the same time suggesting the 2 nd edition of Photomorphogenesis in Plants (Kendrick and Kronenberg, eds.) to be still available for the interested and motivated reader. In this new textbook the basis of the physiology and molecular biology of photomorphogenesis is once again summarized in a few intorductory chapters, to support the reading of the new chapters. Nevertheless, reading the 2 nd edition is strongly recommended. The world s leading experts from Europe, Japan, South America and the USA were invited to contribute to this advanced textbook and we are very pleased that almost all of them immediately accepted our invitation. Despite enormous advances the primary molecular function of photoreceptors is still not known and the UV-B photoreceptor still remains to be identified. Nevertheless, this book attempts to guide the reader through the approaches made with the aim of elucidating how absorption of light by the photoreceptors will be converted into a biochemical signal which then triggers molecular events at cellular level leading to characteristic physiological responses underlying photomorphogenesis of the plant.

6 viii Molecular biology, transgenic work, genetics, biochemistry and cell biology techniques have dramatically increased our knowledge in the field of photomorphogenesis. We hope that students, postdocs and academic teachers, like in the past, will again favourably respond to the fascination of photomorphogenesis research and that reading the book in the post-genomic era will stimulate new creative research in this field. Last but not least we would like to thank the publisher, especially Jacco Flipsen, for his strong support and interest, Prof. Govindjee for invitation and encouragement for this project and Dr. Erzsebet Fejes and Birgit Eiter for excellent assistance in editing. REFERENCES Kendrick, R. E. and Kronenberg, G. H. M., Photomorphogenesis in Plants, Dordrecht: Martinus Nijhoff Publishers, 1986 (ISBN ). Kendrick, R. E. and Kronenberg, G. H. M., Photomorphogenesis in Plants, 2 nd edition, Dordrecht: Kluwer Academic Publishers, 1994 (ISBN ). E. Schäfer 1 and F. Nagy 2 1 University of Freiburg Institute of Biology II/ Botany Schänzlestr. 1 D Freiburg Germany Eberhard.Schaefer@biologie.uni-freiburg.de 2 Biological Research Center Institute of Plant Biology P. O. Box 521 H-6701 Szeged Hungary nagyf@nucleus.szbk.u.szeged.hu

7 CONTENTS Preface VII Abbreviations XXVII Color plates.... XXXI PART 1: GENERAL INTRODUCTION AND HISTORICAL OVERVIEW OF PHOTOMORPHOGENESIS Chapter 1 HISTORICAL OVERVIEW Eberhard Schäfer and Ferenc Nagy 1. Introduction Phytochrome Induction Responses The High Irradiance Responses... Very Low Fluence Responses Further reading References 10 Chapter 2 PHYSIOLOGICAL BASIS OF PHOTOMORPHOGENESIS Eberhard Schäfer and Ferenc Nagy 1. Introduction Classical action spectroscopy Mode of function of phytochrome Correlations between in vivo spectroscopical measurements and physiological responses Phytochrome response types Summary References 22 Chapter 3 HISTORICAL OVERVIEW OF MOLECULAR BIOLOGY AND GENETICS IN PHOTOMORPHOGENESIS Eberhard Schäfer and Ferenc Nagy References... 30

8 x Chapter 4 GENETIC BASIS AND MOLECULAR MECHANISMS OF SIGNAL TRANSDUCTION FOR PHOTOMORPHOGENESIS Eberhard Schäfer and Ferenc Nagy 1. Introduction Phototropism mutants.. Photomorphogenic mutants. Circadian mutants Genetic variation, mutants identified by QTL mapping Signal transduction mutants Signal transduction at the molecular level... Summary.. References PART 2: THE PHYTOCHROME Chapter 5 THE PHYTOCHROME CHROMOPHORE Seth J. Davis 1. Introduction Structure of the phytochrome chromophore.... Phytochromobilin synthesis. 3.1 Heme Oxygenases Phytochromobilin Synthase Holo assembly.. Biophysics of the chromophore... Personal Perspectives Phy chromophore structure Phy chromophore synthesis Holo-phy assembly and structure References

9 xi Chapter 6 STRUCTURE, FUNCTION, AND EVOLUTION OF MICROBIAL PHYTOCHROMES Baruch Karniol and Richard D. Vierstra 1. Introduction Higher plant phys The Discovery of microbial Phys Phylogeny 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 Directing phototaxis Enhancement of photosynthetic potential Photocontrol of pigmentation Evolution of the phy superfamily..... Perspectives References Chapter 7 PHYTOCHROME GENES IN HIGHER PLANTS: STRUCTURE, EXPRESSION, AND EVOLUTION Robert A. Sharrock and Sarah Mathews 1. Introduction Phytochrome gene structures and protein sequences The first phytochrome sequences Phytochrome is a family of related photoreceptors encoded by multiple PHY genes in higher plants Phytochrome nomenclature Heterodimerization of type II phytochromes Expression patterns of phytochromes in plants How important are phytochrome expression patterns? Assaying phytochromes Early Expression Studies Patterns of PHY gene expression mrna levels and promoter fusion experiments The levels and distributions of phytochromes in plants. 112

10 xii 3.6 Circadian regulation of PHY gene expression Evolution of the PHY gene family in seed plants Phytochrome phylogeny in seed plants Phytochrome functional evolution in seed plants Angiosperm phyb and Gymnosperm phyp Angiosperm phya and Gymnosperm phyn and phyo Conclusions References 126 Chapter 8 PHYTOCHROME DEGRADATION AND DARK REVERSION Lars Hennig 1. Introduction Phytochrome degradation Kinetic properties of phytochrome degradation Mechanisms of phytochrome degradation Physiological functions of phytochrome degradation Dark reversion Kinetic properties of dark reversion Determinants of dark reversion Functional aspects of dark reversion Concluding remarks Further reading References 150 Chapter 9 INTRACELLULAR LOCALIZATION OF PHYTOCHROMES Eberhard Schäfer, Stefan Kircher and Ferenc Nagy 1. Introduction The classical methods Spectroscopic methods Cell biological methods Immunocytochemical methods The novel methods Intracellular localisation of PHYB in dark and light Intracellular localisation of PHYA in dark and light Intracellular localisation of PHYC, PHYD and PHYE in dark and light Intracellular localisation of intragenic mutant phytochromes Hyposensitive, loss-of-function mutants. 162

11 7.2 Hypersensitive mutants Protein composition of nuclear speckles associated with phyb The function of phytochromes localised in nuclei and cytosol Concluding remarks References PART 3: BLUE-LIGHT AND UV-RECEPTORS Chapter 10 BLUE/UV-A RECEPTORS: HISTORICAL OVERVIEW Winslow R. Briggs 1. Introduction Early history Phototropism: action spectra can be fickle The LIAC: a frustrating digression The cryptochrome story The phototropin story Stomatal opening in blue light Chloroplast movements induced by blue light Leaf expansion The rapid inhibition of growth Solar tracking The ZTL/ADO family Conclusions References 192 Chapter 11 CRYPTOCHROMES Anthony R. Cashmore 1. Introduction Photolyases The discovery of cryptochrome Cryptochromes of Arabidopsis Cryptochromes of algae, mosses and ferns Drosophila cryptochrome Mammalian cryptochromes Bacterial and related cryptochromes Cryptochromes and plant photomorphogenesis xiii

12 xiv 5. Cryptochrome and flowering Plant cryptochromes and circadian rhythms Arabidopsis cryptochrome and gene expression Cryptochromes and circadian rhythms in animals Drosophila circadian rhythms are entrained through cryptochrome Mammalian cryptochromes: Negative transcriptional regulators and essential components of the circadian oscillator The mode of action of cryptochrome..... Chapter The Arabidopsis cryptochrome C-terminal domain mediates a constitutive light response COP1: A signalling partner of Arabidopsis cryptochromes Intracellular localization of Arabidopsis CRYs Phosphorylation of Arabidopsis cryptochromes Photochemical properties of Arabidopsis cryptochromes Drosophila cryptochrome interacts with PER and TIM in a light-dependent manner Mouse cryptochromes negatively regulate transcription in a PHOTOTROPINS Winslow R. Briggs, John M. Christie and Trevor E. Swartz light-independent manner Cryptochrome evolution Conclusions and future studies References Introduction Blue light-activated phosphorylation of a plasma-membrane protein The protein is likely ubiquitous in higher plants Subcellular localization of photl Distribution of the phototropins in relation to function Biochemical properties of the phosphorylation reaction in vitro Correlation of phot1 phosphorylation with phototropism Autophosphorylation occurs on multiple sites Cloning and molecular characterization of phototropin The initial discovery of phototropin LOV domains function as light sensors Why two LOV domains? Structural and photochemical properties of the LOV domains LOV domain photochemistry LOV-domain structure The LOV-domain photocycle Mechanism of FMN-cysteinyl adduct formation

13 xv 5.5 The LOV domain back reaction Protein conformational change on photoexcitation The ZTL/ADO family LOV domains in other systems A return to physiology: a model for phototropism Future prospects Note added in proof References Chapter 13 BLUE LIGHT PHOTORECEPTORS -BEYOND PHOTOTROPINS AND CRYPTOCHROMES Jay Dunlap 1. Introduction Historical antecedents The photobiology of Neurospora Light perception -the nature of the blue light photoreceptor Flavins as chromophores Genetic dissection of the blue light response Cloning of the white collar genes WHITE COLLAR-1 is the blue light photoreceptor WC-1 and WC-2 -positive elements in the circadian feedback loop How light resets the clock VIVID, a second photoreceptor that modulates light responses Complexities in light regulatory pathways Other Neurospora photoreceptors Flavin binding domain proteins as photoreceptors in photosynthetic eukaryotes Summary and conclusion References Chapter 14 UV-B PERCEPTION AND SIGNALLING IN HIGHER PLANTS Roman Ulm Introduction DNA damage and repair Photomorphogenic responses to UV-B Synthesis of sunscreen metabolites Inhibition of hypocotyl growth Cotyledon opening and expansion

14 xvi 4. UV-B perception Supporting evidence and possible nature of a specific UV-B photoreceptor Possible importance of specific UV-B perception? UV-B signalling Reactive oxygen species Plant hormones Calcium Phosphorylation Nitric oxide Transcriptional response to UV-B radiation Conclusions and perspectives References... Chapter 15 SIGNAL TRANSDUCTION IN BLUE LIGHT-MEDIATED RESPONSES Vera Quecini and Emmanuel Liscum 1. Introduction Cryptochrome signalling Cryptochromes and photomorphogenesis Cryptochrome signalling and photomorphogenic growth responses Cryptochrome signalling and electrophysiological processes Cryptochrome signalling and the regulation of gene expression Phototropin signaling Phototropins and plant movement responses Phototropins and phototropism Phototropins and stomatal aperture control Phototropins and chloroplast movement Phototropin signalling and electrophysiological processes Concluding remarks References

15 xvii PART 4: SIGNAL TRANSDUCTION IN PHOTOMORPHOGENESIS Chapter 16 GENERAL INTRODUCTION Peter H. Quail References Chapter 17 PHYTOCHROME SIGNAL TRANSDUCTION NETWORK Peter H. Quail 1. Introduction Genetically-identified signalling-intermediate candidates Phytochrome-Interacting Factors PIF PKS NDPK Other phy interactors... Transcription-factor genes are early targets of PHY signalling Biochemical mechanism of signal transfer References Chapter 18 THE FUNCTION OF THE COP/DET/FUS PROTEINS IN CONTROLLING PHOTOMORPHOGENESIS: A ROLE FOR REGULATED PROTEOLYSIS Elizabeth Strickland, Vicente Rubio and Xing Wang Deng 1. Introduction Genetic analysis of photomorphogenesis A brief summary of the ubiquitin-proteasome system Properties and functions of the pleiotropic COP/DET/FUS proteins COP Nuclear localization of COP Light regulation of COP Molecular role of COP The E3 ubiquitin-protein ligase activity of COP COP1 interactors

16 xviii 3.2 The COP9 signalosome Interactions and similarities between the CSN and the ubiquitin-proteasome system Biochemical activities of the CSN Derubylation Deubiquitination Protein phosphorylation Control of nucleocytoplasmic localization Independent roles for CSN subunits Non-photomorphogenic roles of the CSN The CDD complex COP DET COP10, DDB1, and DET1 are components of the same CDD complex Concluding remarks References... Chapter 19 BIOCHEMICAL AND MOLECULAR ANALYSIS OF SIGNALLING COMPONENTS Christian Fankhauser and Chris Bowler 1. Introduction Is phytochrome a light-regulated protein kinase? Phosphorylation in phy mediated signalling G-proteins Rapid ion fluxes Cytoplasmic movements Forward and reverse Genetics Interactions with internal cues (growth regulators, circadian clock) Conclusions References..... Chapter 20 THE PHOTORECEPTOR INTERACTION NETWORK Jorge José Casal Introduction Light signals and photoreceptors Shared and specific control of light responses by different photoreceptors.. 408

17 2. Photoreceptor interaction during de-etiolation Multiple photoreceptors control de-etiolation Redundancy The potential action of a photoreceptor can be hidden by the action of others Definition of redundancy The mechanisms of redundancy Redundant photoreceptors are not equally important Synergism between phytochromes and cryptochromes Blue light-mediated responsivity amplification towards phytochrome cryl amplifies responsitivity towards phyb The synergism between cry1 and phyb is conditional Other manifestations of synergism between phytochromes and cryptochromes Synergistic or antagonistic interaction between phya and phyb Synergism between phyb and phyc Interactive signalling under sunlight reduces noise/ signal ratio Photoreceptor interaction during adult plant body shape formation Redundant control of normal progression of vegetative development by phytochromes and cryptochromes The response to R:FR Photoreceptor interaction in phototropism Phototropins perceive the unilateral stimulus Phytochromes enhance the responses mediated by phototropins The role of cryptochromes Photoreceptor interaction in clock entrainment... Photoreceptor interaction controlling flowering Different light signals control the transition between vegetative and reproductive growth Roles of cry2, cry1 and phya in the photoperiodic response Roles of phyb, phyd and phye in the response to low R:FR Integration of the responses to photoperiod and R:FR Points of convergence in the photoreceptor signalling network The occurrence of interactions is an emergent property of the signalling network Direct convergence: Physical interaction between photoreceptor pigments Convergence in the control of transcription: HFR Post-transcriptional convergence accounts for the interaction between phyb and phyc Convergence in the control of protein stability: COP Photoreceptor sub-cellular partitioning SUB Overview... xix

18 xx 8.1 Redundancy Hierarchical action Synergism Sensitivity and homeostasis Connectivity References... Chapter 21 INTERACTION OF LIGHT AND HORMONE SIGNALLING TO MEDIATE PHOTOMORPHOGENESIS Michael M. Neff, Ian H. Street, Edward M. Turk and Jason M. Ward Introduction Gibberellins Gibberellin biosynthetic genes and seed germination Gibberellins and de-etiolation The SPY and PHOR1 genes A possible role for protein degradation Interactions with other hormone signalling pathways Auxin Auxin transport Auxin and phototropism Auxin and shade avoidance Auxin responsive genes involved in photomorphogenesis Auxin and protein degradation Interaction of auxin with other hormone signalling pathways Brassinosteroids Brassinosteroid-deficient mutants Brassinosteroids and gene expression Further genetic connections between brassinosteroids and light Brassinosteroids and light signalling: three speculative models Ethylene Genetic connections between ethylene and photomorphogenesis Ethylene mutants and shade-avoidance Ethylene and fruit ripening Cytokinins Summary Further reading References

19 xxi PART 5: SELECTED TOPICS Chapter 22 THE ROLES OF PHYTOCHROMES IN ADULT PLANTS Keara A. Franklin and Garry C. Whitelam 1. Introduction The natural light environment R:FR ratio and shade avoidance Roles of different phytochromes in shade avoidance Roles for phytochrome A in adult plants Molecular mechanisms controlling shade avoidance responses The acceleration of flowering Early events in R:FR ratio signalling References... Chapter 23 A ROLE FOR CHLOROPHYLL PRECURSORS IN PLASTID-TO-NUCLEUS SIGNALING Robert M. Larkin and Joanne Chory 1. Introduction Chlorophyll biosynthetic mutant, inhibitor, and feeding studies Plastid-to-nucleus signaling mutants inhibit Mg-porphyrin accumulation Mechanism of Mg-Proto/Mg-ProtoMe signaling Plastid and light signaling pathways appear to interact Conclusions and perspectives Further Reading References Chapter 24 PHOTOMORPHOGENESIS OF FERNS Takeshi Kanegae and Masamitsu Wada Introduction Photoreceptors in Adiantum Cryptochromes Phototropins Phytochromes

20 xxii Phytochrome Phytochrome Phytochrome Phytochrome Mutant analyses Methods of mutant selection Red light aphototropic mutants Mutants deficient in the chloroplast avoidance response Dark position-deficient mutants Function of phytochrome Phytochrome3-dependent chloroplast movement Phytochrome3-dependent phototropism Function of phototropin Phototropin2-dependent chloroplast movement Physiological estimation of the lifetime of phot signals Germination-related genes Concluding remarks References Chapter 25 PHOTOMORPHOGENESIS OF MOSSES Tilman Lamparter 1. Introduction Effects of light on moss development Spore germination Cell differentiation Phototropism and polarotropism Lights effects on gravitropism Chloroplast movement Chlorophyll synthesis Protoplast regeneration Different photoreceptors in mosses Phytochromes Phytochrome genes and proteins Mutants... Ceratodon Class 1 mutants... Ceratodon class 2 mutants... Physcomitrella phytochrome knockout mutants Light direction and polarization Cryptochromes and phototropin Signal transduction Ca Cytoskeleton

21 5. Summary References Chapter 26 CIRCADIAN REGULATION OF PHOTOMORPHOGENESIS Paul Devlin 1. Introduction The Circadian Clock Circadian rhythms The circadian clock in plants Setting the plant circadian clock Driven vs Endogenous Rhythms Gating Circadian Regulation of Photomorphogenesis Circadian regulation of light-induced changes in gene expression Circadian regulation of light-mediated inhibition of hypocotyl elongation Circadian regulation of light-mediated stimulation of hypocotyl hook opening Circadian regulation of light-mediated stimulation of stomatal opening 8.5 Circadian regulation of sensitivity to light allows daylength perception 9. Mechanism of circadian regulation of photomorphogenesis Mutants affecting circadian regulation of photomorphogenesis early flowering 3 (elf3) time for coffee (tic) Other possible components involved gating Circadian regulation of photoreceptor levels Circadian regulation of photoreceptor subcellular localisation Circadian regulation of photoreceptor signal transduction components GIGANTEA (GI) ZEITLUPE (ZTL) Suppressor of phya 1 (SPA1) early phytochrome responsive 1 (epr1) A twist in the tale: Is there just one circadian clock regulating photomorphogenesis? Conclusion: Concerns for photomorphogenic study Epilogue Further suggested reading References... xxiii

22 xxiv Chapter 27 THE MOLECULAR GENETICS OF PHOTO-PERIODIC RESPONSES: COMPARISONS BETWEEN LONG-DAY AND SHORT-DAY SPECIES George Coupland 1. Introduction Genetic model systems A molecular pathway that controls flowering-time in response to day length in Arabidopsis by generating a long-distance signal from the leaf An external coincidence model for the day-length response in Arabidopsis Genetic analysis of the photoperiodic control of flowering in rice, a short-day plant Relationships between photoperiodic control and other environmental cues regulating flowering Photoperiodic responses other than flowering Perspectives References Chapter 28 COMMERCIAL APPLICATIONS OF PHOTOMORPHOGENESIS RESEARCH Ganga Rao Davuluri and Chris Bowler 1. Introduction Light-mediated responses in the natural environment Manipulation of light responses in agriculture Modulation of day length perception Modulation of shade avoidance responses Modulation of fruit ripening Light-based biological engineering Conclusions and perspectives References... Chapter 29 PHOTOMORPHOGENESIS WHERE NOW? Harry Smith Where are we going, Dad? Where are we now, Dad?

23 xxv So what, Dad? Is that all, Dad? Why, Dad? What use is it, Dad? Are we nearly there yet? Race you to the beach, Dad! References Conclusions Index

24 Abbreviations AFLP amplified fragment-length polymorphism APRR Arabidopsis pseudo response regulator ATP adenosine triphosphate B blue light BBP bilin-binding pocket Bch bacteriochlorophyll BHF blue light high fluence BLF blue light low fluence BphPs bacteriophytochrome photoreceptors BV biliverdin IXa CAB chlorophyll a/b binding proteins CAT3 catalase 3 CCA complementary chromatic adaptation CCA1 circadian clock-associated 1 CCR2 cold circadian clock-regulated CCT cryptochrome C-terminal domain CFB cytophaga-flexibacter-bacterioides Chl chloroplast CHS chalcone synthase CNT cryptochrome N-terminal domain CO constans COP1 constitutively photomorphogenic 1 CPD cyclobutane pyrimidine dimmers Cphs cyanobacterial Phys Crt carotenoids CRY cryptochrome Cry1/ hy4 cryptochrome1/ hypocotyl4 CT circadian Time Cyto cytoplasm DBD DNA-binding domain DDB1 UV-damaged DNA binding protein DET1 de-etiolated 1 DET2 de-etiolated 2 DUF ELF3 domain of unknown function early flowering 3 ELF4 EPR1 early-flowering 4 early phytochrome responsive 1 FAD flavin adenine dinucleotide FDD fluorescence differential display FKF1 flavin-binding kelch repeat F-box 1 FLC flowering locus C Fphs fungal Phys FR far-red FSBA fluorosulfonylbenzoyladenosine FT flowering locus T G green light GA gibberelin acid GAF cgmp phosphodiesterase/adenyl cyclase/fhla GAI GA-insensitive GFP green fluorescent protein GGDEF Gly/Gly/Asp/Gly/Phe motif GI gigantea GRAS GAI/RGA and SCARECROW HAMP HK/adenyl cyclases/methyl-binding proteins/phophatases domain Hd heading date HIR high irradiance response HKD histidine kinase domain

25 xxviii HKRD histidine kinase-related domain HO heme oxygenase HPT histidine phosphotransferase HWE His/Try/Asp HY5 hypocotyl 5 ICGs interchromatin granual clusters LFR LHCB LHY low Fluence Response light harvesting chlorophyll a/b-binding protein late elongated hypocotyl LIAC light-induced absorbance change LKP2 LOV kelch protein 2 LRE light-responsive regulatory element LUC luciferase Me-Ac methyl-accepting chemotaxis protein domain Mg-ProtoMe Mg-Protoporphyrin IX monomethyl ester MS mass Spectroscopic analysis MTHF methenyltetrahydrofolate NAI2 nitrate reductase NDPK2 nucleoside diphosphate kinase 2 NLS nuclear localisation signal NMR nuclear magnetic resonance NO nictric oxide NOE nuclear overhauser effect NPA NPH 1-naphthylphthalamic acid non-phototropic hypocotyl Nuc nucleus ORF open reading frame PAC PAS-like domain C-terminal to PAS PAS Per/Arndt/Sim PCB 3(Z)-phycocyanobilin Pchlide protochlorophyllide PEB phycoerythrobilin PER period PFT1 phytochrome flowering time 1 Phy phytochrome PIF3 phytochrome interacting factor 3 PIL1 PIF3-like 1 PIL2 PIF3- like 2 PIL4 PIF3- like 4 PIL6 PIF3- like 6 PIN1 pinformed 1 PKS1 phytochrome kinase substrate 1 PKS2 phytochrome kinase substrate 2 PLD PAS-like domain PM plasma membrane PP pyrimidine-pyrimidinone dimers PP2C protein phosphatase-2c Proto protoporphyrin IX PYP photoactive yellow protein P B 3(Z)-phytochromobilin QTL quantitative trait loci R red light RAP2 red light aphototropic 2 RGA repressor of ga 1-3 RGL RGA-like RNAi RNA interference

26 xxix ROS reactive oxygen species RR response regulator Rubisco ribulose-1,5-bisphosphate carboxylase/oxygenase SAP sequestered areas of phytochrome SCF complex Skp1 cullin F-box protein SCN suprachiasmatic nucleus SOC1 suppressor of overexpression of co 1 SPA1 suppressor of phya 1 SPY spindly SRD serine-rich domain SRR1 sensitivity to red light reduced TC-HK TIC two-component histidine kinase time for coffee TIM timeless TIR3 toll interleukin resistance domain cotaining protein toc1 ULI timing of cab expression 1 UV-B light insensitive ULI3 UV-B light insensitive 3 UV ultra violet light UV-A nm UV UV-B nm UV UV-C <280 nm UV VLFR very low fluence response ZT zeitgeber time ZTL zeitlupe

27 Color plate section Chapter 7, Figure 5. Histochemical localization of the expression patterns of PHYB::GUS (a-c) and PHYD::GUS (d-f ) promoter-reporter fusion genes in Arabidopsis. (a, d) seven day old dark-grown seedlings; (b, e) seven day old light-grown seedlings; (c, f ) flowers.

28 xxxii hook area Chapter 9, Figure 1. Localisation of PHYA-GFP fusion proteins in Arabidopsis seedlings. 4d old dark-grown Arabidopsis seedlings expressing fusion proteins of Arabidopsis PhyA and GFPcontrolled by the Arabidopsis promoter were irradiated briefly with white light. Subsequently bright-field images (greyscale) and confocal images of GFP (green channel) and chlorophyll (red channel) fluorescence have been recorded with a Zeiss LSM510 microscope. The colour- combined images are showing the hook area and an area of the rim of a cotyledon (inlet). Bar= 25 µm. Chapter 9, Figure 2. Model of the light-driven intracellular dynamics of phytochrome A. In dark-grown seedlings phya is synthesized in its physiological inactive Pr-form (Pr) and stays in the cytosolic compartment. Irradiation establishes a wavelength-dependent equilibrium of the Pr to the active Pfr form. Red light (R) leads to formation of about 80% of Pfr, far-red light (FR) to about 3% Pfr. PhyA Pfr localises to sequestered areas of phytochrome (SAP) in the cytosol and is imported into the nucleus where it forms nuclear speckles. The light-requirements for these intracellular processes overlap with the light requirements for typical physiological responses of phytochrome A. While pulses of light can promote very low fluence response (VLFR, here the effect of a red pulse is shown), continuous irradiation with far-red light (cfr) leads to high irradiance responses (HIR). Due to the instability of the Pfr form of PHYA, continuous red-light (cr) leads to a rapid destruction of the photoreceptor.

29 xxxiii Chapter 9, Figure 3. Co-localisation of Phytochrome B with the bhlh factor PIF3. 4d old dark-grown Arabidopsis seedlings simultaneously expressing fusion proteins of PhyB with YFP and PIF3 with CFP each controlled by the 35S promoter were irradiated briefly with white light. Subsequently, confocal images of YFP (green channel) and CFP (red channel) fluorescence have been recorded with a Zeiss LSM510 microscope. The images are showing epidermal cells of the base of a cotyledon, either representing the PhyB-YFP or PIF3-CFP signals, an overlay of these images resulting in yellow colour for co-localisation of PhyB and PIF3 or an additional co-localisation analysis of both factors using ImageJ software package (NIH). Chapter 9, Figure 4. Localisation of a fusion protein consisting of Arabidopsis PhyB, GFP and a nuclear localisation sequence. 4d old dark-grown Arabidopsis seedlings expressing fusion proteins of Arabidopsis PhyB, GFP and the SV 40 NLS under the control of the Arabidopsis promoter were analysed either after incubation for 24 hours in red light (R) or darkness (cd). Subsequently, bright-field images (greyscale) and confocal images of GFP (green channel) and chlorophyll (red channel) fluorescence have been recorded with a Zeiss LSM510 microscope. The colour-combined images are showing the hook area or an area of a cotyledon. Bar = 25 µm.

30 xxxiv Chapter 12, Figure 1. Domain structures for phototropins 1 and 2. Chapter 12, Figure 2. Localization of phot1-green fluorescent protein (GFP) in guard cells and leaf epidermal cells. Red fluorescence is from chloroplasts. See Sakamoto and Briggs (2002).

31 xxxv Chapter 12, Figure 6. Structural model of the phytochrome3 LOV domain from Adiantum capillus veneris (after Crosson and Moffat, 2001). FMN and cysteine 39 are highlighted. Chapter 12, Figure 7. LOV2-domain absorption of ground state and intermediates and photocycle (see Swartz et al., 2001). Details in text.

32 xxxvi Chapter 12, Figure 8. Domain structure of the ZTL/ADO family of putative Arabidopsis blue light receptors. Chapter 13, Figure 2. Real and putative photoreceptors in Neurospora. The identity and approximate location of various functional domains in Neurospora proteins are shown. In the list, only WC-1 and VVD are known to bind chromophores and to be true photores- ponse mediators, although WC-2 is required for the function of WC-1.

33 xxxvii Chapter 13, Figure 3. Two light regulatory sequences within the frq promoter in Neurosto FAD as the chromophore, and the small oval represents WC-2. See text for details (Figure pora bind to complexes of WC-1 and WC-2. The large oval represents WC-1 binding courtesy of A. Froehlich). Chapter 13, Figure 6. Known molecular components in the circadian feedback loop of Neuros- pora. Light lines represents effects of light, grey or dark lines actions that take place in the dark. Within the cell, the WCC drives expression of FRQ which does three things: (1) Its first and dominant action is to bind to the WCC to block its function, thus constituting a negative feedback loop that is the clock. (2) It promotes the synthesis of WC-1 posttrans- criptionally and wc-2 mrna, actions that promote robustness in the feedback loop; (3) It becomes phosphorylated which eventually leads to its turnover. When this happens, the bolus of WCC whose synthesis was promoted by FRQ is released to start the cycle again (Lee et al., 2000; Loros and Dunlap, 2001). The result of these feedback loops are daily rhythms in expression of frq mrna, FRQ, and WC-1 whose timing within the day defines biological time; for instance, high frq mrna doesn t just occur in mid-day, high frq degfines mid-day for the organism (adapted form Dunlap, 2003).

34 xxxviii Chapter 13, Figure 7. Light resetting of the Neurospora clock. At the top is shown a Northern: Absent light on the left, frq expression levels are seen to rise and fall with a circadian rhythm whereas on the right, light exposure at any time of day results in a rapid large induction of frq. In the middle panel is shown a schematic of how this light induction resets the clock: the dark curve represents the control rhythm of frq in the dark. Light exposure when frq is falling (evening) delays the clock whereas light exposure when frq is rising (late night to early morning) advances the clock. The bottom panel shows hour by hour through the day how light induction of frq will reset the clock, by plotting the daily rhythm in frq mrna on top of the amount of clock resetting elicited by light exposure (adapted from Dunlap, 1999). Chapter 13, Figure 8. vvd is rapidly light induced, and loss of vvd slows the rate of decay of light-induced transcripts. On the right, P and S stand for two alleles, P which makes no transcript and S that makes transcript but no protein; W denotes wild type. (From (Heintzen et al., 2001) with permission).

35 xxxix Chapter 13, Figure 9. Summary of light responses in Neurospora (Figure courtesy of C. Schwerdtfeger; all rights reserved). Light Phy s Cry s ZTL LKP2 TOC1 CCA1 LHY Outputs FKF1 Flowering ELF3 Chapter 13, Figure 10. Placement of LOV domain-associated protein turnover photoreceptors within the circadian system in Arabidopsis. The feedback loop formed by TOC1 and LHY/CCA1 is at the core of the clock. ZTL and LKP2 are associate with light input and FKF1 with output in the regulation of CO in the context of flowering. Clock-regulated ELF3 regulates light signalling pathways. Figure courtesy of Thomas Schulz and Steven Kay; all rights reserved.

36 xl Chapter 15, Figure 1. Depiction of the cryptochrome-associated signalling events discussed in the text. Dark and lit-states of cry2 and cry2 are shown together as they relate to intracellular localization and function. Question marks refer to inferred, but still unidentified, molecules.

37 xli Chapter 15, Figure 2. Depiction of the phototropin 1 signaling events associated with phototropism. In darkness (top panel) phot1 is in its resting-state, and as such, its signaling is not activated. In the absence of phot1 signaling basipetal polar auxin (IAA) transport predominates, as mediated by passive uptake of IAAH from the cell wall space and active efflux of the IAA anion via action of the PIN1-MDR1 (PGP1, not shown) complex. Also inactive in the dark is the ARF7 transcriptional machinery, as the ARF7 inhibitor, IAA19, persists. Upon unilateral B irradiation phot1 signaling is activated and a dramatic redistribution of auxin occurs. Although it is not clear at present how phot1 activates this process at least two events appear likely: 1) disruption of the the PIN1-MDR1 complex on the shaded side that thus disrupts efflux in that side, and 2) activation of laterally localized PIN3 that results in directional lateral flow of auxin. Both of these events lead to accumulation of auxin on the shaded side of the plant that in turn stimulate the degradation of IAA19 and subsequent activation of ARF7-dependent transcription.

38 xlii Chapter 15, Figure 3. Depiction of the phototropin signaling events associated with B-dependent stomatal aperture control. In darkness (or B deficient light) the phot signaling system is in its off state and thus the guard cells exhibit no appreciable ion gradient across the plasma membrane (top panel). In the absence of such a gradient no water uptake occurs and a small stomatal pore is maintained. Upon exposure to B (bottom panel), the phot signaling is activated (activation is shown in only one cell for simplicity, but the mirror image processes + occur in the second guard cell) whereby the H -ATPase is activated leading to a membrane hyperpolarization that activates inward rectifying K + channels. The resultant K + gradient in turn drives the uptake of H2O and turgor driven cell expansion, which leads to an opening of the pore.

39 xliii Chapter 23, Figure 2. Model for Mg-Proto/ Mg-ProtoMe signalling. GUN5, which is also known as ChlH, two other Mg-chelatase subunits named ChlI ChlD insert Mg 2+ into the Proto ring with assistance from GUN4. GUN4 binds the substrate and product of the Mgtakes place in the plastid envelope, but for the sake of clarity, porphyrin trafficking is not chelatase reaction, Proto and Mg-Proto. Under conditions of Mg-Proto accumulation, Mg-Proto may be guided to a Tetrapyrrole transporter (Y) by GUN4, GUN5 or by another Mg-Proto-binding protein (X). After export from the plastid, a cytoplasmic factor (Z) binds Mg- Proto. Factor Z affects a signalling pathway that represses Lhcb transcription when chloroplast development is blocked; Mg-Proto regulates the activity of factor Z. Mg-ProtoMe signalling may function in a similar manner. This Proto and Mg-Proto trafficking probably shown to be associated with the envelope. The details of the model are explained in the text NE, nuclear envelope; PE plastid envelope.

40 xliv Chapter 27, Figure 1. Hierarchy of gene action within the photoperiodic flowering pathways of Arabidopsis and rice. A. The photoperiodic response pathway of Arabidopsis. The circadian clock, which is proposed to comprise of a feed-back loop between the LHY/CCA1 and TOC1 genes, regulates the expression of an output pathway including the GI, CO, SOC1 and FT genes. These four genes represent a transcriptional cascade as shown. Light has two roles in the pathway. Exposure to light entrains the circadian clock, and is required for activation of CO function under long photoperiods. The activation of CO involves postvia FKF1. ELF3 modulates entrainment of the clock by light input. B. The photoperiodic transcriptional regulation by the photoreceptors CRY2 and PHYA, and transcriptional regulation response pathway of rice. The logic of the pathway as for A. Hd1 function is activated under long photoperiods, and represses the expression of Hd3a, thereby delaying flowering.

41 xlv Chapter 27, Figure 2. Coincidence model for the activation of flowering under long photoperiods in Arabidopsis. Top: Under short days circadian clock regulation of CO causes its mrna to accumulate in the dark. CO protein does not accumulate, and FT expression is not activates. Bottom: Under long days circadian clock regulation and activation of CO transcription by light via FKF1 causes CO mrna to accumulate in the light. The CO protein is stabilised through the activity of the PhyA and Cry2 photoreceptors. The presence of the CO protein causes activation of FT transcription, which leads to flowering.

42 xlvi Chapter 27, Figure 3. Coincidence model for the activation of flowering under short photo- periods in rice. Top: Under short-day conditions, circadian clock regulation of Hd1 mrna causes it to accumulate in the dark. Hd3a is expressed and this leads to early flowering. Bottom: Under long-day conditions circadian clock regulation of Hd1 mrna causes it to accumulate in the light. This leads to activation of Hd1 function so that it represses Hd3a expression and delays flowering.

43 xlvii Chapter 28, Figure 1. Field trial of transgenic tobacco plants overexpressing the oat PHYA gene. Control plants are shown on the left, PHYA-overexpressing plants are shown on the right. Disabling of the shade avoidance response is clearly apparent in the transgenic PHYA-over expressing plants. The photograph was taken in 1994 in Rothamstead, UK, and was kindly provided by Harry Smith (University of Nottingham, UK). Chapter 28, Figure 2. Fruit truss phenotypes from a range of tomato photomorphogenic mutants. From left to right: (1) phyaphyb1, (2) phyaphyb1hp-1, (3) phyaphyb1phyb2, (4) phyaphyb1phyb2hp-1, (5) phyaphyb1cry1, (6) phyaphyb1cry1hp-1. Note that the triple phyaphyb1phyb2 mutant displays elongated truss phenotypes whereas the phyaphyb1cry1 mutant does not. However, both show reduced fruit pigmentation. In each mutant background the hp mutant is epistatic to the photoreceptor mutant phenotypes for fruit pigmentation, but not for the defects in truss architecture. Photograph kindly provided by Ageeth van Tuinen and Dick Kendrick (Wageningen University, NL).

44 xlviii Chapter 28, Figure 3. Immature fruit phenotype caused by the fruit-specific silencing of the tomoto DETI gene. The left panel shows fruit from a wild-type plant and the right panel shows fruit from a plant in which DET1 gene expression has been suppressed specifically in the fruits by RNAi.