Annual Plant Reviews, Endogenous Plant Rhythms

, by Hall, Anthony J. W.; McWatters, Harriet G.

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ISBN: 9781405123761 | 1405123761
Cover: Hardcover
Copyright: 1/9/2006

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Our knowledge of the circadian clock in plants has advanced considerably in recent years and we now have a clearer view of the biochemical processes making up its mechanism. Recent work provides insight into the central role played by the circadian system in the regulation of many aspects of metabolism. The multiple systems involved in photoreception have been determined, leading to an understanding of how light entrains the internal biological clock to the natural cycle of day and night, and how this impacts on key events in the plant lifecycle, such as the photoperiodic regulation of flowering. This book provides a contemporary overview of endogenous plant rhythms for researchers and professionals in the plant sciences. It will also serve as a valuable source of reference for the wider circadian community.

Contributors

xiii

Preface

xvii

The plant circadian clock: review of a clockwork Arabidopsis

(24)

Frank G. Harmon

Takato Imaizumi

Steve A. Kay

Introduction

(1)

How plant circadian biology got to where it is today

(5)

Forward genetics

(1)

Direct circadian screens -- TOCI, ZTL, TEJ, TIC, LUX

(3)

Non-circadian forward genetic screens -- LHY, ELF3, ELF4

(1)

Reverse genetics -- CCA1, PRR3-PRR9

(1)

How the components were placed in the plant clock?

(4)

CCA1, LHY, and TOC1 contribute to a feedback loop at the core of the oscillator

(2)

The interplay between TOCI and ZTL sets circadian period

(1)

PRR7 and PRR9 form a feedback loop that affects CCA1 and LHY expression

(1)

Current framework for understanding the Arabidopsis clock

(2)

What may pave the way to greater understanding of the clock

(6)

Forward genetics

(2)

Genomics and functional genomics

(2)

Transient functional assays

(1)

Characterizing protein modification

(1)

Conclusion

(7)

References

(7)

Pseudo-response regulator genes `tell' the time of day: multiple feedbacks in the circadian system of higher plants

(32)

Shigeru Hanano

Seth J. Davis

Introduction

(1)

History of the circadian system

(3)

The CCA1/LHY - TOCI model for the Arabidopsis clock

(1)

An overview of the phosphorelay two-component system in Arabidopsis

(3)

AHK and AHP genes involved in the phosphorelay system of Arabidopsis

(2)

Arabidopsis response regulators

(1)

Pseudo-response regulators

(1)

Circadian regulation of TOCI/PRR family: CCA1/LHY-TOCI feedback model and circadian wave form of the TOCI/PRR family

(4)

Regulation of TOCI expression

(1)

Interactions between TOC1 and other PRR family members

(1)

The role of the evening element in PRR9 regulation

(1)

Interactions between PRRs and clock components

(1)

A detailed description of signal convergence in the PRR genes

(6)

TOCI/PRRI, At5g61380

(1)

Toc 1-2 and TOC1 mini-gene mutants

(2)

TOC1 and phytochrome

(1)

TOC1 and flowering time

(1)

PRR9, At2g46790

(2)

PRR7, At5g02810

(1)

PRR5, At5g24470

(1)

PRR3, At5g60100

(1)

Phylogenetic and epistatic relations between the PRRs

(2)

Partners of PRR proteins

(1)

PIF3-like family

(1)

ZTL family

(1)

Other interactions

(1)

A brief overview of PRRs in other plants

(1)

Perspective

(11)

Limitations of the current model

(2)

Acknowledgements

(1)

References

(7)

Multiple and slave oscillators

(28)

Dorothee Staiger

Corinna Streitner

Fabian Rudolf

Xi Huang

Introduction

(1)

Central and peripheral oscillators in the mammalian timing

(2)

Organization of the timing system in plants

(6)

Are clocks localized in different parts of the plant?

(1)

Does the same type of clock control rhythms in distinct parts of the plant?

(2)

Do individual clocks interact with each other?

(1)

Do chloroplasts retain remnants of a clock of an endosymbiontic ancestor?

(1)

Molecular organization of the clock within a plant cell

(1)

Linking gene expression to the clockwork -- how output genes are regulated

(7)

Transcriptional control of output genes

(1)

Identification of cycling transcription factors mediating rhythmic output

(1)

Post-transcriptional control

(2)

RNA stability

(1)

Polyadenylation

(1)

Splicing

(1)

Translational control mediated by a new class of RNA-binding proteins

(1)

RNA-based regulation: The role of an antisense RNA

(1)

Control by second messengers: do Ca2+ ions mediate rhythmic output?

(1)

Slave oscillators

(3)

The clock-regulated RNA-binding protein ATGRP7 in Arabidopsis thaliana

(2)

Transcriptional feedback loop as slave oscillator: EPR1

(1)

Summary

(9)

References

(7)

Entrainment of the circadian clock

(22)

Dave Somers

Introduction

(1)

Light perception and entrainment

(6)

Phytochromes

(2)

Cryptochromes

(2)

A novel family of blue light photoreceptors?

(2)

Signal transduction and interaction

(4)

ZTL and phototransduction: phy and cry photoreceptors

(1)

ZTL and phototransduction: ELF3

(3)

Other potential photoentrainment intermediates

(1)

Coupling to the central oscillator

(1)

Circadian gating of photic input

(2)

Thermal entrainment

(1)

Conclusion

100

(7)

References

101

(6)

Photoreceptors and light signaling pathways in plants

107

(26)

Victoria S. Larner

Keara A. Franklin

Garry C. Whitelam

Introduction

107

(1)

Photoreceptor structures

108

(3)

Phototropin structure

108

(1)

Cryptochrome structure

109

(1)

Phytochrome structure

110

(1)

Photoreceptor functions

111

(4)

Phototropin functions

111

(1)

Cryptochrome functions

112

(1)

Phytochrome functions

113

(2)

Cellular and sub-cellular localization of photoreceptors

115

(2)

Phototropin localization

115

(1)

Cryptochrome localization

115

(1)

Phytochrome localization

115

(2)

Photoreceptor signaling

117

(6)

Post-translational Phosphorylation

117

(1)

Cytosolic signaling mechanisms

118

(1)

Regulation of protein degradation

119

(1)

Photoreceptor interacting proteins

120

(3)

Crosstalk in photoreceptor signaling

123

(1)

Integration of environmental signals

123

(1)

Integration of light and endogenous signals

123

(1)

Conclusions

124

(9)

References

125

(8)

Circadian regulation of global gene expression and metabolism

133

(34)

Stacey L. Harmer

Michael F. Covington

Oliver Blasing

Mark Stitt

Circadian rhythms in transcription

133

(3)

Monitoring rhythms of transcription

133

(2)

Circadian regulation of the transcriptome

135

(1)

Post-transcriptional circadian regulation

136

(2)

Proteomics

137

(1)

Metabolomics

137

(1)

Circadian regulation of transcription -- what kinds of genes, and why?

138

(1)

Clock-associated genes

138

(1)

Slave oscillators

139

(1)

Genes encoding other regulatory proteins

139

(1)

Regulation of plant metabolism

139

(5)

Photosynthesis

140

(1)

Partitioning of fixed carbon

140

(1)

Nitrogen assimilation

141

(1)

Secondary metabolic pathways

142

(2)

Circadian regulation of plant growth and development

144

(2)

Plant growth

144

(1)

Hormone regulation

144

(2)

Control of flowering time

146

(1)

How is clock-regulation of gene expression achieved?

146

(2)

The evening element (EE)

146

(1)

Other circadian associated motifs

147

(1)

Cross-species comparisons

148

(3)

Are similar genes clock regulated in all organisms?

148

(1)

Rhythmic gene expression in photosynthetic species

149

(2)

Comparing gene expression in constant and diurnal conditions

151

(4)

Circadian rhythms vs. diurnal responses

151

(2)

Interactions between sugar and circadian regulation

153

(2)

Why have a clock rather than relying on driven rhythms?

155

(2)

Might anticipation be key?

155

(1)

Do transcript levels correlate with protein levels?

156

(1)

Why are the transcripts of stable proteins under circadian regulation?

156

(1)

Future prospects

157

(10)

Acknowledgements

157

(1)

References

158

(9)

Photoperiodic responses and the regulation of flowering

167

(24)

Isabelle Carre

George Coupland

Joanna Putterill

Introduction to photoperiodism

167

(1)

Models for the measurement of day length

168

(2)

The hourglass timer

168

(1)

The circadian clock

168

(2)

Internal and external coincidence models

170

(1)

Arabidopsis molecular genetics identifies a regulatory pathway that controls flowering in long photoperiods

170

(5)

The GI-CO-FT regulatory hierarchy

171

(3)

Role of CO and FT in long-distance day-length signaling

174

(1)

Regulation of the Arabidopsis photoperiod pathway: molecular evidence in favor of the coincidence model

175

(3)

CO: a major link between photoperiod and the circadian clock

175

(2)

How does light coincidence with CO mRNA expression result in the induction of FT transcription?

177

(1)

Summary of the evidence in support of the external coincidence model of the photoperiodic regulation of flowering and a role for CO

178

(1)

Interaction between photoperiod pathway and other flowering-time pathways in Arabidopsis

178

(2)

Convergence of the photoperiod and vernalization pathways

178

(2)

Other pathways converging with the photoperiod pathway?

180

(1)

Comparative analysis of photoperiod regulation in rice and Arabidopsis

180

(3)

Perspectives

183

(8)

References

185

(6)

Circadian regulation of Ca2+ signaling

191

(20)

Michael J. Gardner

Antony N. Dodd

Carlos T. Hotta

Dale Sanders

Alex A. R. Webb

Introduction

191

(1)

Ca2+ signaling is ubiquitous and versatile

191

(4)

Transduction of extracellular signals

191

(1)

Spatio-temporal dynamics of [Ca2+]cyt increases

191

(2)

Circadian oscillations of cytosolic free calcium

193

(2)

The cellular basis of circadian oscillations of plant [Ca2+]cyt

195

(1)

Mechanisms controlling [Ca2+]cyt influx

195

(1)

So how does the clock control Ca2+ influx?

195

(1)

The cellular basis of circadian oscillations of [Ca2+]cyt in mammals

196

(2)

The mammalian circadian clock

196

(1)

A role for glutamate and cADPR-sensitive ryanodine receptor induced Ca2+ release in the entrainment of the mammalian clock

196

(2)

The source of [Ca2+]cyt influx

198

(1)

A comparison of the circadian regulation of Ca2+ homeostasis in both SCN and plant cells

198

(2)

cADPR is a key player in mammalian circadian behaviour

199

(1)

A role for nitric oxide in plant clock

199

(1)

Molecular regulation of circadian Ca2+ signaling

200

(3)

Circadian influx of Ca2+ to the cytosol

200

(2)

Circadian efflux of Ca2+ from the cytosol

202

(1)

Ca2+ sensor proteins

202

(1)

Physiological targets for circadian oscillations of [Ca2+]cyt

203

(2)

Difficulties in assigning of physiological function to oscillations in [Ca2+]cyt

203

(1)

A role for Ca2+ in the photoperiodic control of flowering

204

(1)

Conclusions and future prospects

205

(6)

Acknowledgements

205

(1)

References

205

(6)

The circadian clock in CAM plants

211

(26)

James Hartwell

Introduction

211

(1)

The daily cycle of metabolism in CAM plants

211

(4)

Discovery of a circadian rhythm of CO2 fixation in CAM species

212

(1)

CAM CO2 output rhythms in constant darkness, CO2-free air, 15°C

213

(1)

CAM CO2-assimilation rhythms in constant light and normal air

214

(1)

Phase responses of CAM CO2 rhythms

215

(2)

Light induced phase shifts

215

(1)

Temperature induced phase shifts

216

(1)

The biochemical basis for the circadian rhythm of CO2 fixation

217

(6)

PEPc phosphorylation rhythms

217

(1)

Regulation of PEPc phosphorylation

218

(1)

Regulation of PEPc kinase activity

218

(1)

The contribution of PEPc and Rubisco to CAM CO2 fixation rhythms

219

(1)

The influence of temperature on rhythms of PEPc activity

220

(1)

Cloning the PEPc kinase gene from CAM plants

221

(1)

Regulation of PPCK

222

(1)

Multiple points of clock control within the CAM pathway?

223

(1)

The molecular identity of the central oscillator in CAM species?

224

(5)

The tonoplast-as-oscillator?

225

(1)

Is the CCA1/LHY-TOCI oscillator controlling CAM rhythmicity?

226

(3)

Future perspectives and unanswered questions

229

(8)

Starch synthesis rhythms in CAM plants

230

(1)

Stomatal rhythms in CAM plants

231

(1)

Multiple origins of CAM

232

(1)

Insights from CAM plants

233

(1)

Acknowledgements

234

(1)

References

234

(3)

Clock evolution and adaptation: whence and whither?

237

(24)

Carl Hirschie Johnson

Charalambos P. Kyriacou

Introductory quotation

237

(1)

Setting the stage: the appearance of circadian clocks

237

(1)

Putative selective pressures

238

(3)

Temporal separation of metabolic events

239

(1)

`Escape from light'

239

(2)

Cyanobacteria and the first clock genes

241

(1)

The appearance of clocks in photosynthetic eukaryotes

242

(2)

Absence of clock gene homologues across taxa

243

(1)

Regulatory homologues do exist across taxa

244

(1)

Clocks are widespread in plants: mosses, gymnosperms and angiosperms

244

(1)

Clocks in `primitive' plants

245

(1)

Rhythms controlled by the `Clockwork Green'

245

(2)

Photoperiodic time measurement

246

(1)

Why not an hourglass timer?

247

(1)

Advantages of a self-sustained oscillator

247

(1)

The clock as an adaptation: past and present

248

(1)

The circadian clock as an adaptation

249

(1)

Experimental tests of adaptive significance before 1980

249

(2)

Laboratory studies of circadian clocks and reproductive fitness since 1980

251

(3)

Advantages of cycles that resonate with the environment

251

(2)

Testing clock conferred advantages in other species

253

(1)

Evidence that the clock is still adaptive from studies of organisms in natural environments

254

(1)

Environmental gradients

254

(1)

Quantitative trait locus analysis

255

(1)

Clocks: Where did they come from? What are they doing now?

255

(6)

Acknowledgements

256

(1)

References

256

(5)

Index

261

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Annual Plant Reviews, Endogenous Plant Rhythms

Summary

Author Biography

Table of Contents

Supplemental Materials