CIRCADIAN RHYTHMS IN PLANTS

Uptake of uranium and thorium by native and cultivated plants

Large part of available literature on biogeochemistry of uranium and thorium refers to the studies performed either in highly contaminated areas or in nutrient solutions that have been artificially 'spiked' with radionuclides. Effects of background levels of natural radioactivity on soil-grown plants have not been studied to the same extent. In this paper, we summarised results of greenhouse and field experiments performed by the author from 2000 to 2006. We examined some of the factors affecting transfer of U and Th from soil to plants, differences in uptake of these radionuclides by different plants, relationships between U and Th in soil and in plants, and temporal variations of U and Th in different plant species. Concentrations of radionuclides (critical point for experimental studies on biogeochemistry of U and Th--rare trace elements in non-contaminated regions) and essential plant nutrients and trace elements were determined by instrumental neutron activation analysis.

Gene expression of DAM5 and DAM6 is suppressed by chilling temperatures and inversely correlated with bud break rate

We previously identified a cluster of d ormancy-a ssociated M ADS-box transcription factors (DAM genes) in peach [Prunus persica (L.) Batsch] as potential candidates for control of the non-dormant phenotype observed in the evg mutant. Of these genes, DAM3, DAM5 and DAM6 were winter expressed, suggesting a role for these genes during endodormancy. We used peach cultivars with contrasting chilling requirements (CR) for bud break to observe the expression of DAM3, DAM5 and DAM6 in response to chilling accumulation in the field and controlled environments. Vegetative terminal and floral buds were sampled weekly from field grown 'Contender' (1050 h CR), 'Rubyprince' (850 h CR) and 'Springprince' (650 h CR) peach cultivars through winter 2008-2009. Flower and vegetative terminal bud break potential was evaluated at each sampling by forcing cuttings in a growth-permissive environment. We also measured vegetative terminal bud break and DAM gene expression in potted 'Contender' and 'Peen-To' (450 h CR) trees under controlled-environment cold exposure. DAM3, DAM5 and DAM6 are all suppressed by exposure to chilling temperatures in the field and in controlled conditions. Expression of DAM5 and DAM6 are higher in high chill cultivars prior to chilling accumulation and their expression level reaches a minimum in each cultivar coincident with acquisition of bud break competence. Expression levels of DAM5 and DAM6 in vegetative tips in controlled environment conditions were negatively correlated with the time required for bud break in forcing conditions. The expression patterns of DAM5 and DAM6 are consistent with a role as quantitative repressors of bud break.

The 5'UTR of CCA1 includes an autoregulatory cis element that segregates between light and circadian regulation of CCA1 and LHY

The transcription factor CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) participates in both light and circadian clock regulation in Arabidopsis. Two sets of transgenic plants in which GFP was fused to the CCA1 promoter with (1.3-kb fragment) or without (1.01-kb fragment) its 5'UTR were engineered. The transgenic plants transformed with the promoter including the 5'UTR had altered circadian regulation resulting in elongated hypocotyls, a bushy appearance and delayed flowering. In contrast, the transgenic plants transformed with the promoter without the 5'UTR showed earlier flowering than the wild type. Changes in CCA1, LHY and TOC1 gene expression were investigated under light-dark (L:D) fluctuations, continuous darkness (D:D) and continuous light (L:L). The circadian expression of CCA1 was altered in both sets of transgenic plants, being repressed in the plants transformed with the 1.01-kb fragment and constitutively overexpressed in those transformed with the 1.3-kb fragment. Under L:D conditions, regulation of LHY and TOC1 expression was separated from CCA1 regulation in both sets of transgenic plants, with intact rhythmic expression of both LHY and TOC1. Under D:D conditions, the rhythmic expression of LHY and TOC1 was lost in the 1.3 plants but retained with some erratic pattern under L:L conditions. In the 1.01 plants, under both D:D and L:L conditions the rhythmic expression was retained. These results indicate separate light-induced signal-transmission pathways for LHY and CCA1.

Phototropism: mechanism and outcomes

Plants have evolved a wide variety of responses that allow them to adapt to the variable environmental conditions in which they find themselves growing. One such response is the phototropic response - the bending of a plant organ toward (stems and leaves) or away from (roots) a directional blue light source. Phototropism is one of several photoresponses of plants that afford mechanisms to alter their growth and development to changes in light intensity, quality and direction. Over recent decades much has been learned about the genetic, molecular and cell biological components involved in sensing and responding to phototropic stimuli. Many of these advances have been made through the utilization of Arabidopsis as a model for phototropic studies. Here we discuss such advances, as well as studies in other plant species where appropriate to the discussion of work in Arabidopsis.

Electrical signals in avocado trees: responses to light and water availability conditions

Plant responses to environmental changes are associated with electrical excitability and signaling; automatic and continuous measurements of electrical potential differences (DeltaEP) between plant tissues can be effectively used to study information transport mechanisms and physiological responses that result from external stimuli on plants. The generation and conduction of electrochemical impulses within plant different tissues and organs, resulting from abiotic and biotic changes in environmental conditions is reported. In this work, electrical potential differences are monitored continuously using Ag/AgCl microelectrodes, inserted 5 mm deep into sapwood at two positions in the trunks of several Avocado trees. Electrodes are referenced to a non polarisable Ag/AgCl microelectrode installed 20 cm deep in the soil. Systematic patterns of DeltaEP during absolute darkness, day-night cycles and different conditions of soil water availability are discussed as alternative tools to assess early plant stress conditions.

Lifetimes of mRNAs for Clock‐Regulated Proteins in a Dinoflagellate

Both pulsed and continuous applications of the RNA polymerase II inhibitor thiolutin cause a dramatic but reversible loss of bioluminescence and its overt rhythmicity in cells of the dinoflagellate Lingulodinium polyedrum (formerly Gonyaulax polyedra). Such cells remain alive, and the rhythm resumes after an interval, the length of which depends on the concentration of thiolutin used. The period and phase of the resumed rhythm were not systematically altered following such treatments, and the effects were not different at different circadian phases. For three different genes, luciferin binding protein (lbp), luciferase (lcf), and glyceraldehyde-3-phosphate dehydrogenase (gapdh), which are circadian-regulated at the level of translation, the amounts of their mRNAs were determined by Northern blots for times up to 12.5 h following the addition of 1.5 microM thiolutin. Consistent with previous reports that their abundances do not change with circadian time, their levels remained high for several hours after thiolutin addition, but then did diminish.

Unstable, self-limiting thermochemical temperature oscillations in Macrozamia cycads

Field measurements and laboratory experiments on the Australian cycads Macrozamia lucida and Macrozamia macleayi demonstrate that their cones' diel peak thermogenic temperature increase varies systematically with cone stage, with single thermogenic temperature peaks occurring daily for up to 2 weeks and reaching 12 degrees C above ambient at midstage. The initiation, magnitude and timing of those peaks are strongly modulated by ambient temperature; the period between successive thermogenic temperature peaks is not circadian, and light is neither necessary nor sufficient to initiate a thermogenic event. A mathematical analysis is developed that provides a unified explanation of the experimental results. It describes these unstable, self-limiting thermogenic events in terms of conservation of energy and a first-order chemical reaction rate model that includes an Arrhenius equation dependence of the cone's metabolic heating rate on the cone temperature.

Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1

Understanding how nutrients affect gene expression will help us to understand the mechanisms controlling plant growth and development as a function of nutrient availability. Nitrate has been shown to serve as a signal for the control of gene expression in Arabidopsis. There is also evidence, on a gene-by-gene basis, that downstream products of nitrogen (N) assimilation such as glutamate (Glu) or glutamine (Gln) might serve as signals of organic N status that in turn regulate gene expression. To identify genome-wide responses to such organic N signals, Arabidopsis seedlings were transiently treated with ammonium nitrate in the presence or absence of MSX, an inhibitor of glutamine synthetase, resulting in a block of Glu/Gln synthesis. Genes that responded to organic N were identified as those whose response to ammonium nitrate treatment was blocked in the presence of MSX. We showed that some genes previously identified to be regulated by nitrate are under the control of an organic N-metabolite. Using an integrated network model of molecular interactions, we uncovered a subnetwork regulated by organic N that included CCA1 and target genes involved in N-assimilation. We validated some of the predicted interactions and showed that regulation of the master clock control gene CCA1 by Glu or a Glu-derived metabolite in turn regulates the expression of key N-assimilatory genes. Phase response curve analysis shows that distinct N-metabolites can advance or delay the CCA1 phase. Regulation of CCA1 by organic N signals may represent a novel input mechanism for N-nutrients to affect plant circadian clock function.

Expression analyses of casein kinase 2alpha and casein kinase 2beta in the silkmoth, Bombyx mori

A period-timeless (per-tim) based feedback loop is considered to be essential in generating circadian rhythms in Drosophila melanogaster. In addition to transcriptional regulation, the post-transcriptional modification is essential to the circadian oscillation of core clock proteins in the circadian system. Here we present expression profiles of the catalytic subunit of casein kinase 2alpha (ck2alpha) and casein kinase 2beta (ck2beta) in Bombyx mori. Southern blot analyses showed that ck2alpha and ck2beta of B. mori were single copy genes. Northern blot analyses demonstrated that both subunits were expressed in eggs, larval heads, adult heads, testes and ovaries. In situ hybridization analyses indicated that subunits were expressed in brain neurons expressing PER-like protein. Surprisingly, antisense RNAs of ck2alpha and ck2beta were also detected in the putative clock neurons. Temporal expressions of ck2alpha and ck2beta mRNAs were constant in adult heads under LD12:12. The core clock genes per and tim showed daily fluctuations of mRNA abundance in the embryonic stage that is photoperiod sensitive period to determine egg diapause in the next generation whereas the expression of ck2alpha and ck2beta was constant. No evidence supports that ck2alpha and ck2beta of B. mori were transcriptionally regulated by circadian oscillation, but histological data show a close association of ck2alpha and ck2beta with circadian system in B. mori.

Pentatricopeptide repeat proteins and their emerging roles in plants

Several protein families with tandem repeat motifs play a very important role in plant development and defense. The pentatricopeptide repeat (PPR) protein family, one of the largest families, is the most perplexing one in plants. PPR proteins have been implicated in many crucial functions broadly involving organelle biogenesis and plant development. PPR motifs are degenerate motifs, each with 35-amino-acid sequences and are present in tandem arrays of 2-27 repeats per protein. Although PPR proteins are found in other eukaryotes, their large number is probably required in plants to meet the specific needs of organellar gene expression. The repeats of PPR proteins form a superhelical structure to bind a specific ligand, probably a single-stranded RNA molecule, and modulate its expression. Functional studies on different PPR proteins have revealed their role in organellar RNA processing, fertility restoration in CMS plants, embryogenesis, and plant development. Functional genomic techniques can help identify the diverse roles of the PPR family of proteins in nucleus-organelle interaction and in plant development.

Cryptochrome signaling in plants

Cryptochromes are blue light receptors that mediate various light-induced responses in plants and animals. They share sequence similarity to photolyases, flavoproteins that catalyze the repair of UV light-damaged DNA, but do not have photolyase activity. Arabidopsis cryptochromes work together with the red/far-red light receptor phytochromes to regulate various light responses, including the regulation of cell elongation and photoperiodic flowering, and are also found to act together with the blue light receptor phototropins to mediate blue light regulation of stomatal opening. The signaling mechanism of Arabidopsis cryptochromes is mediated through negative regulation of COP1 by direct CRY-COP1 interaction through CRY C-terminal domain. Arabidopsis CRY dimerized through its N-terminal domain and dimerization of CRY is required for light activation of the photoreceptor activity. Recently, significant progresses have been made in our understanding of cryptochrome functions in other dicots such as pea and tomato and lower plants including moss and fern. This review will focus on recent advances in functional and mechanism characterization of cryptochromes in plants. It is not intended to cover every aspect of the field; readers are referred to other review articles for historical perspectives and a more comprehensive understanding of this photoreceptor.

Interplay of circadian clocks and metabolic rhythms

This review examines the connections between circadian and metabolic rhythms. Examples from a wide variety of well-studied organisms are used to illustrate some of the genetic and molecular pathways linking circadian timekeeping to metabolism. The principles underlying biological timekeeping by intrinsic circadian clocks are discussed briefly. Genetic and molecular studies have unambiguously identified the importance of gene expression feedback circuits to the generation of overt circadian rhythms. This is illustrated particularly well by the results of genome-wide expression studies, which have uncovered hundreds of clock-controlled genes in cyanobacteria, fungi, plants, and animals. The potential connections between circadian oscillations in gene expression and circadian oscillations in metabolic activity are a major focus of this review.

Circadian control of isoprene emissions from oil palm (Elaeis guineensis)

The emission of isoprene from the biosphere to the atmosphere has a profound effect on the Earth's atmospheric system. Until now, it has been assumed that the primary short-term controls on isoprene emission are photosynthetically active radiation and temperature. Here we show that isoprene emissions from a tropical tree (oil palm, Elaeis guineensis) are under strong circadian control, and that the circadian clock is potentially able to gate light-induced isoprene emissions. These rhythms are robustly temperature compensated with isoprene emissions still under circadian control at 38 degrees C. This is well beyond the acknowledged temperature range of all previously described circadian phenomena in plants. Furthermore, rhythmic expression of LHY/CCA1, a genetic component of the central clock in Arabidopsis thaliana, is still maintained at these elevated temperatures in oil palm. Maintenance of the CCA1/LHY-TOC1 molecular oscillator at these temperatures in oil palm allows for the possibility that this system is involved in the control of isoprene emission rhythms. This study contradicts the accepted theory that isoprene emissions are primarily light-induced.

The Arabidopsis SPA1 gene is required for circadian clock function and photoperiodic flowering

Arabidopsis phytochrome A (phyA) regulates not only seed germination and seedling de-etiolation but also circadian rhythms and flowering time in adult plants. The SUPPRESSOR OF PHYA-105 (SPA1) acts as a negative regulator of phyA-mediated de-etiolation of young seedlings, but its roles in adult plants have not yet been described. Here, we show that SPA1 is involved in regulating circadian rhythms and flowering time in plants. Under constant light, the abundance of SPA1 protein exhibited circadian regulation, whereas under constant darkness, SPA1 protein levels remained unchanged. These results indicate that the SPA1 protein is controlled by the circadian clock and light signals. In addition, the spa1-3 mutation slightly shortened the circadian period of CCA1, TOC1/PRR1 and SPA1 transcript accumulation under constant light. Phenotypic analysis showed that the spa1-3 mutant flowers early under short-day (SD) but not long-day (LD) conditions. Consistent with this finding, transcripts encoding flowering locus T (FT), which promotes flowering, increased in spa1-3 under only SD conditions, although the CONSTANS (CO) transcript level was not affected under either SD nor LD conditions. Our results indicate that SPA1 not only negatively controls phyA-mediated signaling in seedlings, but also regulates circadian rhythms and flowering time in plants.

FLOWERING LOCUS C-dependent and -independent regulation of the circadian clock by the autonomous and vernalization pathways

BACKGROUND

The circadian system drives pervasive biological rhythms in plants. Circadian clocks integrate endogenous timing information with environmental signals, in order to match rhythmic outputs to the local day/night cycle. Multiple signaling pathways affect the circadian system, in ways that are likely to be adaptively significant. Our previous studies of natural genetic variation in Arabidopsis thaliana accessions implicated FLOWERING LOCUS C (FLC) as a circadian-clock regulator. The MADS-box transcription factor FLC is best known as a regulator of flowering time. Its activity is regulated by many regulatory genes in the "autonomous" and vernalization-dependent flowering pathways. We tested whether these same pathways affect the circadian system.

RESULTS

Genes in the autonomous flowering pathway, including FLC, were found to regulate circadian period in Arabidopsis. The mechanisms involved are similar, but not identical, to the control of flowering time. By mutant analyses, we demonstrate a graded effect of FLC expression upon circadian period. Related MADS-box genes had less effect on clock function. We also reveal an unexpected vernalization-dependent alteration of periodicity.

CONCLUSION

This study has aided in the understanding of FLC's role in the clock, as it reveals that the network affecting circadian timing is partially overlapping with the floral-regulatory network. We also show a link between vernalization and circadian period. This finding may be of ecological relevance for developmental programming in other plant species.

Diurnal regulation of the brassinosteroid-biosynthetic CPD gene in Arabidopsis

Plant steroid hormones, brassinosteroids (BRs), are essential for normal photomorphogenesis. However, the mechanism by which light controls physiological functions via BRs is not well understood. Using transgenic plants carrying promoter-luciferase reporter gene fusions, we show that in Arabidopsis (Arabidopsis thaliana) the BR-biosynthetic CPD and CYP85A2 genes are under diurnal regulation. The complex diurnal expression profile of CPD is determined by dual, light-dependent, and circadian control. The severely decreased expression level of CPD in phytochrome-deficient background and the red light-specific induction in wild-type plants suggest that light regulation of CPD is primarily mediated by phytochrome signaling. The diurnal rhythmicity of CPD expression is maintained in brassinosteroid insensitive 1 transgenic seedlings, indicating that its transcriptional control is independent of hormonal feedback regulation. Diurnal changes in the expression of CPD and CYP85A2 are accompanied by changes of the endogenous BR content during the day, leading to brassinolide accumulation at the middle of the light phase. We also show that CPD expression is repressed in extended darkness in a BR feedback-dependent manner. In the dark the level of the bioactive hormone did not increase; therefore, our data strongly suggest that light also influences the sensitivity of plants to BRs.

The importance of maltose in transitory starch breakdown

Starch content of leaves responds to environmental stresses in various ways. Understanding these environmental effects on starch metabolism has been difficult in the past because the pathways of transitory starch synthesis and degradation are not completely known. Over the past two years there has been a significant increase in our understanding of transitory starch breakdown. The discovery of a maltose transporter (MEX1) and the studies of a cytosolic disproportionating enzyme (D-enzyme, DPE2) confirmed that maltose is the predominant form of carbon exported from chloroplasts at night. Maltose increases in leaves when starch breakdown is induced during the day under photorespiratory conditions. Maltose metabolism is regulated by a circadian clock, day length and temperature. The expression of maltose-metabolizing genes shows a pronounced circadian rhythm indicating maltose metabolism is clock regulated. Indeed, the maltose level oscillates under continuous light. The transcript of a beta-amylase gene (BAM3) peaks during the day in long days and peaks at night in short days. This could provide a mechanism for adjusting starch breakdown rates to day length. Under cold-stress conditions, maltose increases and BAM3 expression is induced. We hypothesize that maltose metabolism is a bridge between transitory starch breakdown and the plants' adaptation to changes in environmental conditions.

Organ specificity in the circadian control of plant gene expression

Of the many plant genes whose expressions are controlled by the circadian clock, one of the phosphoenolpyruvate carboxylase kinase genes in soya bean (Glycine max) exhibits the unusual property that its control is organ-specific – it is under circadian control in leaves but not in roots. Preliminary experiments suggest that the same is true for at least one gene in Arabidopsis thaliana. It will be important to define the extent and function of this phenomenon and the underlying mechanism.

PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock

Previously, we screened 50 000 seedlings of Arabidopsis thaliana carrying a P(GI)::LUC+ bioluminescence reporter gene mutagenized with ethylmethanesulfonate for mutants with phenotypes of extensively altered circadian rhythms, and identified three loci, PHYTOCLOCK 1 (PCL1), PCL2 and PCL3, whose mutations cause arrhythmia. Here we succeeded to clone the PCL1 gene and show that the PCL1 gene encodes a novel DNA binding protein belonging to the GARP protein family and is essential for a functional clock oscillator in A. thaliana. The PCL1 gene satisfies the requirements for the clock oscillator gene: (i) pcl1 null mutations caused arrhythmia in multiple circadian outputs, including expression of potential clock genes TOC1, CCA1 and LHY, and flowering lacked a photoperiodic response; (ii) PCL1 expression showed circadian rhythm in both constant light and constant dark; (iii) over-expression of the PCL1 gene gradually caused arrhythmicity in all the multiple circadian outputs examined; and (iv) the PCL1 gene controlled its own expression via negative feedback. Therefore, the PCL1 gene is the clock oscillator gene essential to the generation of clock oscillation in the higher plant.

Circadian control of messenger RNA stability. Association with a sequence-specific messenger RNA decay pathway

Transcriptional and posttranscriptional regulation are well-established mechanisms for circadian gene expression. Among the latter, differential messenger RNA (mRNA) stability has been hypothesized to control gene expression in response to the clock. However, direct proof that the rate of mRNA turnover can be regulated by the clock is lacking. Previous microarray expression data for unstable mRNAs in Arabidopsis (Arabidopsis thaliana) revealed that mRNA instability is associated with a group of genes controlled by the circadian clock. Here, we show that CCR-LIKE (CCL) and SENESCENCE ASSOCIATED GENE 1 transcripts are differentially regulated at the level of mRNA stability at different times of day. In addition, the changes in CCL mRNA stability continue under free-running conditions, indicating that it is controlled by the Arabidopsis circadian clock. Furthermore, we show that these mRNAs are targets of the mRNA degradation pathway mediated by the downstream (DST) instability determinant. Disruption of the DST-mediated decay pathway in the dst1 mutant leads to aberrant circadian mRNA oscillations that correlate with alterations of the half-life of CCL mRNA relative to parental plants in the morning and afternoon. That this is due to an effect on the circadian control is evidenced by mRNA decay experiments carried out in continuous light. Finally, we show that the defects exhibited by dst mutants are reflected by an impact on circadian regulation at the whole plant level. Together, these results demonstrate that regulation of mRNA stability is important for clock-controlled expression of specific genes in Arabidopsis. Moreover, these data uncover a connection between circadian rhythms and a sequence-specific mRNA decay pathway.

Daylength and circadian effects on starch degradation and maltose metabolism

Transitory starch is stored during the day inside chloroplasts and broken down at night for export. Maltose is the primary form of carbon export from chloroplasts at night. We investigated the influence of daylength and circadian rhythms on starch degradation and maltose metabolism. Starch breakdown was faster in plants of Arabidopsis (Arabidopsis thaliana) ecotype Wassilewskija growing in long days. Transcript levels of genes encoding enzymes involved in starch degradation and maltose metabolism showed a strong diurnal rhythm. Under altered photoperiods, the transcript levels and the rate of starch degradation changed within one day/night cycle. However, the amount of proteins involved in starch degradation was maintained relatively constant throughout the day/night cycle. To investigate whether the diurnal cycling of the transcript levels is only a response to light or is also regulated by a circadian clock, we measured the amount of messenger RNAs in Arabidopsis leaves under continuous light and continuous darkness. The expression of genes encoding starch degradation-related enzymes was under very strong circadian control in continuous light. Under continuous light, the amount of maltose also showed a strong endogenous rhythm close to 24 h, indicating that maltose metabolism is under circadian control. Light is necessary for the cycling of transcript levels and maltose levels. Under continuous darkness, these genes were barely expressed, and no cycling of maltose levels was observed.

Identifying Eucalyptus expressed sequence tags related to Arabidopsis flowering-time pathway genes

Flowering initiation depends on the balanced expression of a complex network of genes that is regulated by both endogenous and environmental factors. The timing of the initiation of flowering is crucial for the reproductive success of plants; therefore, they have developed conserved molecular mechanisms to integrate both environmental and endogenous cues to regulate flowering time precisely. Extensive advances in plant biology are possible now that the complete genome sequences of flowering plants is available and plant genomes can be comprehensively compared. Thus, association studies are emerging as powerful tools for the functional identification of genes involved on the regulation of flowering pathways. In this paper we report the results of our search in the Eucalyptus Genome Sequencing Project Consortium (FORESTS) database for expressed sequence tags (ESTs) showing sequence homology with known elements of flowering-time pathways. We have searched the 33,080 sequence clusters in the FORESTS database and identified Eucalyptus sequences that codify putative conserved elements of the autonomous, vernalization-, photoperiod response- and gibberellic acid-controlled flowering-time pathways. Additionally, we have characterized in silico ten putative members of the Eucalyptus homologs to the Arabidopsis CONSTANS family of transcription factors.

LdpA: a component of the circadian clock senses redox state of the cell

The endogenous 24-h (circadian) rhythms exhibited by the cyanobacterium Synechococcus elongatus PCC 7942 and other organisms are entrained by a variety of environmental factors. In cyanobacteria, the mechanism that transduces environmental input signals to the central oscillator of the clock is not known. An earlier study identified ldpA as a gene involved in light-dependent modulation of the circadian period, and a candidate member of a clock-entraining input pathway. Here, we report that the LdpA protein is sensitive to the redox state of the cell and exhibits electron paramagnetic resonance spectra consistent with the presence of two Fe4S4 clusters. Moreover, LdpA copurifies with proteins previously shown to be integral parts of the circadian mechanism. We also demonstrate that LdpA affects both the absolute level and light-dependent variation in abundance of CikA, a key input pathway component. The data suggest a novel input pathway to the circadian oscillator in which LdpA is a component of the clock protein complex that senses the redox state of a cell.

Conservation and divergence of circadian clock operation in a stress-inducible Crassulacean acid metabolism species reveals clock compensation against stress

One of the best-characterized physiological rhythms in plants is the circadian rhythm of CO(2) metabolism in Crassulacean acid metabolism (CAM) plants, which is the focus here. The central components of the plant circadian clock have been studied in detail only in Arabidopsis (Arabidopsis thaliana). Full-length cDNAs have been obtained encoding orthologs of CIRCADIAN CLOCK-ASSOCIATED1 (CCA1)/LATE ELONGATED HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION1 (TOC1), EARLY FLOWERING4 (ELF4), ZEITLUPE (ZTL), FLAVIN-BINDING KELCH REPEAT F-BOX1 (FKF1), EARLY FLOWERING3 (ELF3), and a partial cDNA encoding GIGANTEA in the model stress-inducible CAM plant, Mesembryanthemum crystallinum (Common Ice Plant). TOC1 and LHY/CCA1 are under reciprocal circadian control in a manner similar to their regulation in Arabidopsis. ELF4, FKF1, ZTL, GIGANTEA, and ELF3 are under circadian control in C(3) and CAM leaves. ELF4 transcripts peak in the evening and are unaffected by CAM induction. FKF1 shows an abrupt transcript peak 3 h before subjective dusk. ELF3 transcripts appear in the evening, consistent with their role in gating light input to the circadian clock. Intriguingly, ZTL transcripts do not oscillate in Arabidopsis, but do in M. crystallinum. The transcript abundance of the clock-associated genes in M. crystallinum is largely unaffected by development and salt stress, revealing compensation of the central circadian clock against development and abiotic stress in addition to the well-known temperature compensation. Importantly, the clock in M. crystallinum is very similar to that in Arabidopsis, indicating that such a clock could control CAM without requiring additional components of the central oscillator or a novel CAM oscillator.

A nitrate-induced frq-less oscillator in Neurospora crassa

When nitrate is the only nitrogen source, Neurospora crassa's nitrate reductase (NR) shows endogenous oscillations in its nitrate reductase activity (NRA) on a circadian time scale. These NRA oscillations can be observed in darkness or continuous light conditions and also in a frq(9) mutant in which no functional FRQ protein is formed. Even in a white-collar-1 knockout mutant, NRA oscillations have been observed, although with a highly reduced amplitude. This indicates that the NRA oscillations are not a simple output rhythm of the white-collar-driven frq oscillator but may be generated by another oscillator that contains the nit-3 autoregulatory negative feedback loop as a part. In this negative feedback loop, a product in the reaction chain catalyzed by nitrate reductase, probably glutamine, induces repression of the nitrate reductase gene and thus downregulates its own production. This is the first example of an endogenous, nutritionally induced daily rhythm with known molecular components that is observed in the absence of an intact FRQ protein.

Flowering time control: gene network modelling and the link to quantitative genetics

Flowering is a key stage in plant development that initiates grain production and is vulnerable to stress. The genes controlling flowering time in the model plant Arabidopsis thaliana are reviewed. Interactions between these genes have been described previously by qualitative network diagrams. We mathematically relate environmentally dependent transcription, RNA processing, translation, and protein–protein interaction rates to resultant phenotypes. We have developed models (reported elsewhere) based on these concepts that simulate flowering times for novel A. thaliana genotype–environment combinations. Here we draw 12 contrasts between genetic network (GN) models of this type and quantitative genetics (QG), showing that both have equal contributions to make to an ideal theory. Physiological dominance and additivity are examined as emergent properties in the context of feed-forwards networks, an instance of which is the signal-integration portion of the A. thaliana flowering time network. Additivity is seen to be a complex, multi-gene property with contributions from mass balance in transcript production, the feed-forwards structure itself, and downstream promoter reaction thermodynamics. Higher level emergent properties are exemplified by critical short daylength (CSDL), which we relate to gene expression dynamics in rice (Oryza sativa). Next to be discussed are synergies between QG and GN relating to the quantitative trait locus (QTL) mapping of model coefficients. This suggests a new verification test useful in GN model development and in identifying needed updates to existing crop models. Finally, the utility of simple models is evinced by 80 years of QG theory and mathematical ecology.

Signaling mechanisms of higher plant photoreceptors: a structure-function perspective

Higher plants monitor changes in the ambient light environment using three major classes of photoreceptors: the red/far-red-absorbing phytochromes, the blue/UV-A-absorbing cryptochromes, and phototropins. These photoreceptors mediate various photoresponses, ranging from seed germination, to seedling de-etiolation, stem elongation, leaf expansion, floral initiation, phototropic bending of organs, intracellular movement of chloroplast, and stomata opening. Here I briefly review the distinct and overlapping physiological functions of these photoreceptors and highlight recent progress that provided significant insights into their signaling mechanisms, particularly from a structure-function perspective. This review focuses on the early photochemical and biochemical events that lead to photoreceptor activation and signaling initiation.

Circadian rhythms of ethylene emission in Arabidopsis

Ethylene controls multiple physiological processes in plants, including cell elongation. Consequently, ethylene synthesis is regulated by internal and external signals. We show that a light-entrained circadian clock regulates ethylene release from unstressed, wild-type Arabidopsis (Arabidopsis thaliana) seedlings, with a peak in the mid-subjective day. The circadian clock drives the expression of multiple ACC SYNTHASE genes, resulting in peak RNA levels at the phase of maximal ethylene synthesis. Ethylene production levels are tightly correlated with ACC SYNTHASE 8 steady-state transcript levels. The expression of this gene is controlled by light, by the circadian clock, and by negative feedback regulation through ethylene signaling. In addition, ethylene production is controlled by the TIMING OF CAB EXPRESSION 1 and CIRCADIAN CLOCK ASSOCIATED 1 genes, which are critical for all circadian rhythms yet tested in Arabidopsis. Mutation of ethylene signaling pathways did not alter the phase or period of circadian rhythms. Mutants with altered ethylene production or signaling also retained normal rhythmicity of leaf movement. We conclude that circadian rhythms of ethylene production are not critical for rhythmic growth.

Plant response regulators implicated in signal transduction and circadian rhythm

The so-called 'response regulators' were originally discovered as common components of the widespread histidine (His)-->aspartate (Asp) phosphorelay signal transduction system in prokaryotes. Through the course of evolution, higher plants have also come to employ such prokaryotic response regulators (RRs) for their own signal transduction, such as the elicitation of plant hormone (e.g. cytokinin) responses. Furthermore, plants have evolved their own atypical variants of response regulators, pseudo response regulators (PRRs), which are used to modulate sophisticated biological processes, including circadian rhythms and other light-signal responses. Recent studies using the model plant Arabidopsis thaliana have begun to shed light on the interesting functions of these plant response regulators.

Formation of an SCF(ZTL) complex is required for proper regulation of circadian timing

The circadian timing system involves an autoregulatory transcription/translation feedback loop that incorporates a diverse array of factors to maintain a 24-h periodicity. In Arabidopsis a novel F-box protein, ZEITLUPE (ZTL), plays an important role in the control of the free-running period of the circadian clock. As a class, F-box proteins are well-established components of the Skp/Cullin/F-box (SCF) class of E3 ubiquitin ligases that link the target substrates to the core ubiquitinating activity of the ligase complex via direct association with the Skp protein. Here we identify and characterize the SCFZTL complex in detail. Yeast two-hybrid tests demonstrate the sufficiency and necessity of the F-box domain for Arabidopsis Skp-like protein (ASK) interactions and the dispensability of the unique N-terminal LOV domain in this association. Co-immunoprecipitation of full-length (FL) ZTL with the three known core components of SCF complexes (ASK1, AtCUL1 and AtRBX1) demonstrates that ZTL can assemble into an SCF complex in vivo. F-box-containing truncated versions of ZTL (LOV-F and F-kelch) can complex with SCF components in vivo, whereas stably expressed LOV or kelch domains alone cannot. Stable expression of F-box-mutated FL ZTL eliminates the shortened period caused by mild ZTL overexpression and also abolishes ASK1 interaction in vivo. Reduced levels of the core SCF component AtRBX1 phenocopy the long period phenotype of ztl loss-of-function mutations, demonstrating the functional significance of the SCFZTL complex. Taken together, our data establish SCFZTL as an essential SCF class E3 ligase controlling circadian period in plants.

Large-scale screening of Arabidopsis circadian clock mutants by a high-throughput real-time bioluminescence monitoring system

Using a high-throughput real-time bioluminescence monitoring system, we screened large numbers of Arabidopsis thaliana mutants for extensively altered circadian rhythms. We constructed reporter genes by fusing a promoter of an Arabidopsis flowering-time gene - either GIGANTEA (GI) or FLOWERING LOCUS T (FT) - to a modified firefly luciferase gene (LUC(+)), and we transferred the fusion gene (P(GI)::LUC(+) or P(FT)::LUC(+)) into the Arabidopsis genome. After mutagenesis with ethyl methanesulfonate, 50 000 M(2) seedlings carrying the P(GI)::LUC(+) and 50 000 carrying P(FT)::LUC(+) were screened their bioluminescence rhythms. We isolated six arrhythmic (AR) mutants and 29 other mutants that showed more than 3 h difference in the period length or phase of rhythms compared with the wild-type strains. The shortest period length was 16 h, the longest 27 h. Five of the six AR mutants carrying P(GI)::LUC(+) showed arrhythmia in bioluminescence rhythms in both constant light and constant dark. These five AR mutants also showed arrhythmia in leaf movement rhythms in constant light. Genetic analysis revealed that each of the five AR mutants carried a recessive mutation in a nuclear gene and the mutations belonged to three complementation groups, and at least one of which was mapped on a novel locus. Our results suggest that the three loci identified here may contain central clock or clock-related genes, at least one of which may be a novel.

Graft transmission of a floral stimulant derived from CONSTANS

Photoperiod in plants is perceived by leaves and in many species influences the transition to reproductive growth through long-distance signaling. CONSTANS (CO) is implicated as a mediator between photoperiod perception and the transition to flowering in Arabidopsis. To test the role of CO in long-distance signaling, CO was expressed from a promoter specific to the companion cells of the smallest veins of mature leaves. This expression in tissues at the inception of the phloem translocation stream was sufficient to accelerate flowering at the apical meristem under noninductive (short-day) conditions. Grafts that conjoined the vegetative stems of plants with different flower-timing phenotypes demonstrated that minor-vein expression of CO is able to substitute for photoperiod in generating a mobile flowering signal. Our results suggest that a CO-derived signal(s), or possibly CO itself, fits the definition of the hypothetical flowering stimulant, florigen.

Genomic structure of a novel Arabidopsis clock-controlled gene, AtC401, which encodes a pentatricopeptide repeat protein

We isolated and characterized AtC401, a novel Arabidopsis clock-controlled gene that encodes a protein containing the pentatricopeptide repeat (PPR) motif. AtC401 was isolated as an Arabidopsis homolog of Pharbitis nil C401 (PnC401), a gene that encodes a leaf protein closely related to the photoperiodic induction of flowering and displays a circadian rhythm at the transcriptional level. The AtC401 gene spans 5.6 kb and contains 12 exons. Comparisons of the sequences and genomic organization of AtC401 and PnC401 revealed that each has two exons near the 3'-end, which encode a highly conserved domain consisting of 12 repeats of the PPR motif. Phylogenetic analysis of at least 450 Arabidopsis proteins containing PPR motifs revealed that AtC401 and related proteins form a distinct group. Moreover, the position of the intron between the two exons that encode the PPR domain has been conserved exactly in other C401-like genes. Using a reporter assay, we found a fragment (-174 to +73) of AtC401 that was sufficient to regulate circadian rhythmic expression. These results suggest that the conserved domain of AtC401 has a function similar to that of PnC401, and that the expression of C401 genes according to a circadian rhythm is important for protein function.

Characterization of Transcriptional Oscillation of an Arabidopsis Homolog of PnC401 Related to Photoperiodic Induction of Flowering in Pharbitis nil

AtC401 is an Arabidopsis homolog of PnC401 that is related to photoperiodic induction of flowering in Pharbitis nil. These genes show free-running rhythms. To study the free-running rhythm of AtC401, we fused a firefly luciferase reporter to the AtC401 promoter and transformed it into Arabidopsis plants. The observed bioluminescence oscillated under continuous light and continuous dark only with sucrose supplementation. The free-running period of bioluminescence was temperature-compensated between 22 degrees C and 30 degrees C. Light-pulse experiments under continuous darkness produced a phase-response curve typical of circadian rhythms. We conclude that rhythmic expression of AtC401 is controlled by a circadian oscillator.

Occurrence of circadian rhythms in hairy root cultures grown under controlled conditions

Hairy roots obtained by transformation via Agrobacterium rhizogenes provide an artificial plant material devoid of aerial parts with high growth on hormone-free media. Fundamental knowledge of hairy root physiology is essential to develop and control its culture. In contrast to shake-flask cultures, a bioreactor set-up combined with on-line data logging provides an efficient tool to study rapid physiological variations in hairy root cultures. Datura innoxia hairy roots were grown in a bioreactor equipped with on-line data analyses of pH, dissolved oxygen (pO2), conductivity, oxygen, and carbon dioxide. The experiments were done at a constant temperature and in the absence of light cues. The results obtained showed that the carbon dioxide evolution rate (CER) presented regular oscillations during the culture. Similar oscillations were also observed for the oxygen uptake rate (OUR). These signals were treated mathematically to look for the existence of a rhythm. An autocorrelation function was used to detect any periodic components. The results demonstrate that hairy root respiration exhibited peaks of 1 day. These oscillations, having a period of about 24 h, were also observed in pH and conductivity signals, although not for the pO2 signal. The data acquired in the absence of hairy roots showed that the observed periodic behavior was not an artifact. No effect on rhythms was observed by the imposition of an external "day/night" cycle. The fact that oscillations persisted in the absence of external stimuli, with a free-running period of 24 h, suggests that a circadian rhythm exists in hairy roots of D. innoxia.

Possible involvement of leaf gibberellins in the clock-controlled expression of XSP30, a gene encoding a xylem sap lectin, in cucumber roots

Root-produced organic compounds in xylem sap, such as hormones and amino acids, are known to be important in plant development. Recently, biochemical approaches have revealed the identities of several xylem sap proteins, but the biological functions and the regulation of the production of these proteins are not fully understood. XYLEM SAP PROTEIN 30 kD (XSP30), which is specifically expressed in the roots of cucumber (Cucumis sativus), encodes a lectin and is hypothesized as affecting the development of above-ground organs. In this report, we demonstrate that XSP30 gene expression and the level of XSP30 protein fluctuate in a diurnal rhythm in cucumber roots. The rhythmic gene expression continues for at least two or three cycles, even under continuous light or dark conditions, demonstrating that the expression of this gene is controlled by a circadian clock. Removal of mature leaves or treatment of shoots with uniconazole-P, an inhibitor of gibberellic acid (GA) biosynthesis, dampens the amplitude of the rhythmic expression; the application of GA negates these effects. These results suggest that light signals perceived by above-ground organs, as well as GA that is produced, possibly, in mature leaves, are important for the rhythmic expression of XSP30 in roots. This is the first demonstration of the regulation of the expression of a clock-controlled gene by GA.

Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana

The underlying mechanism of circadian rhythmicity appears to be conserved among organisms, and is based on negative transcriptional feedback loops forming a cellular oscillator (or 'clock'). Circadian changes in protein stability, phosphorylation and subcellular localization also contribute to the generation and maintenance of this clock. In plants, several genes have been shown to be closely associated with the circadian system. However, the molecular mechanisms proposed to regulate the plant clock are mostly based on regulation at the transcriptional level. Here we provide genetic and molecular evidence for a role of ZEITLUPE (ZTL) in the targeted degradation of TIMING OF CAB EXPRESSION 1 (TOC1) in Arabidopsis thaliana (thale cress). The physical interaction of TOC1 with ZTL is abolished by the ztl-1 mutation, resulting in constitutive levels of TOC1 protein expression. The dark-dependent degradation of TOC1 protein requires functional ZTL, and is prevented by inhibiting the proteosome pathway. Our results show that the TOC1-ZTL interaction is important in the control of TOC1 protein stability, and is probably responsible for the regulation of circadian period by the clock.

No photoperiodoc control of the formation of turions in eight clones of Spirodela polyrhiza

The influence of daily photoperiod (8, 16, 24 h) on eight clones of Spirodela polyrhiza was tested in two different nutrient media. The number of vegetative fronds and resting turions formed after 50 days of cultivation were scored. The specific turion yield (STY; number of turions formed per vegetative frond) was used to evaluate the effectiveness of turion formation of the tested clones. All clones formed turions in both nutrient media. The STY varied substantially between the different clones, ranging from 0.22 +/- 0.03 (clone SC from Cuba) to 3.9 +/- 0.3 (clone 9256 from Finland) in continuous light. The STY increased with increasing duration of the photoperiod. This increase may have been due to the extended period of photosynthesis rather than that of a photoperiodic long-day response. Shorter photoperiods did not stimulate turion formation in any of the clones. S. polyrhiza is a day-neutral plant with respect to turion formation, as noted previously (Appenroth et al. 1990. Annals of Botany 66: 163-168). In accordance with this conclusion, no correlation was detected between the STY and the latitude at which the clones occur naturally. Environmental factors other than shortening of photoperiods seem to be effective in signalling seasonal changes of growth conditions in advance to S. polyrhiza.

Surface plasmon resonance spectroscopy (SPR) interaction studies of the circadian-controlled tomato LHCa4*1 (CAB 11) protein with its promoter

Feedback regulation is an important biochemical mechanism which is also able to direct the circadian timing at the transcriptional level. Independent investigations highlighted a conserved ca. 10 nucleotide motif present in many circadian regulated Lhc genes. Two of such nucleotide motifs exist within 119 nucleotides of the Lhca4*1 promoter from tomato. This promoter fragment was used as a bait in a yeast one hybrid screen and interestingly a clone encoding with sequence identity to the LHCa4*1 protein was isolated as an interaction partner. The LHCa4*1 protein was heterologous expressed and binding to the 119bp promoter fragment was demonstrated by surface plasmon resonance spectroscopy (SPR, Biacore). This result allows to postulate an autoregulatory feedback loop involved in expression of the Lhca4*1 gene.

Ethylene modulates root-wave responses in Arabidopsis

When stimulated to bend downward by being held at 45 degrees off vertical but unable to penetrate into agar-based media, Arabidopsis roots develop waving and looping growth patterns. Here, we demonstrate that ethylene modulates these responses. We determined that agar-containing plates sealed with low-porosity film generate abiotic ethylene concentrations of 0.1 to 0.3 microL L(-1), whereas in plates wrapped with porous tape, ethylene remains at trace levels. We demonstrate that exogenous ethylene at concentrations as low as a few nanoliters per liter modulates root waving, root growth direction, and looping but through partly different mechanisms. Nutrients and Suc modify the effects of ethylene on root waving. Thus, ethylene had little effect on temporal wave frequency when nutrients were omitted but reduced it significantly on nutrient-supplemented agar. Suc masked the ethylene response. Ethylene consistently suppressed the normal tendency for roots of Landsberg erecta to skew to the right as they grow against hard-agar surfaces and also generated righthanded petiole twisting. Furthermore, ethylene suppressed root looping, a gravity-dependent growth response that was enhanced by high nutrient and Suc availability. Our work demonstrates that cell file twisting is not essential for root waving or skewing to occur. Differential flank growth accounted for both the extreme root waving on zero-nutrient plates and for root skewing. Root twisting was nutrient-dependent and was thus strongly associated with the looping response. The possible role of auxin transport in these responses and the involvement of circadian rhythms are discussed.

The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA

The clock-regulated RNA-binding protein AtGRP7 is part of a negative feedback circuit through which the protein influences circadian oscillations of its own transcript. Constitutive overexpression of AtGRP7 in transgenic plants leads to the appearance of a low amount of an alternatively spliced Atgrp7 transcript with a premature stop codon. It is generated by the use of a 5' cryptic splice site in the middle of the intron at the expense of the fully spliced mRNA, indicating a role for AtGRP7 in splice site selection. Accelerated decay of this transcript accounts for its low steady state abundance. This implicates a mechanism for the AtGRP7 feedback loop: Atgrp7 expression is downregulated, as AtGRP7 protein accumulates over the circadian cycle, partly by the generation of an alternate transcript that due to its instability does not accumulate to high levels and does not produce a functional protein. Recombinant AtGRP7 protein specifically interacts with the 3' untranslated region and the intron of its transcript, suggesting that the shift in splice site selection and downregulation involves binding of AtGRP7 to its pre-mRNA. AtGRP7 also influences the choice of splice sites in the Atgrp8 transcript encoding a related RNA-binding protein, favoring the production of an alternatively spliced, unstable Atgrp8 transcript. This conservation points to the importance of this regulatory mechanism to control the level of the clock-regulated glycine-rich RNA-binding proteins and shows how AtGRP7 can control abundance of target transcripts.

Phosphorylation of the D1 photosystem II reaction center protein is controlled by an endogenous circadian rhythm

The light dependence of D1 phosphorylation is unique to higher plants, being constitutive in cyanobacteria and algae. In a photoautotrophic higher plant, Spirodela oligorrhiza, grown in greenhouse conditions under natural diurnal cycles of solar irradiation, the ratio of phosphorylated versus total D1 protein (D1-P index: [D1-P]/[D1] + [D1-P]) of photosystem II is shown to undergo reproducible diurnal oscillation. These oscillations were clearly out of phase with the period of maximum in light intensity. The timing of the D1-P index maximum was not affected by changes in temperature, the amount of D1 kinase activity present in the thylakoid membranes, the rate of D1 protein synthesis, or photoinhibition. However, when the dark period in a normal diurnal cycle was cut short artificially by transferring plants to continuous light conditions, the D1-P index timing shifted and reached a maximum within 4 to 5 h of light illumination. The resultant diurnal oscillation persisted for at least two cycles in continuous light, suggesting that the rhythm is endogenous (circadian) and is entrained by an external signal.

Temperature effect on entrainment, phase shifting, and amplitude of circadian clocks and its molecular bases

Effects of temperature and temperature changes on circadian clocks in cyanobacteria, unicellular algae, and plants, as well as fungi, arthropods, and vertebrates are reviewed. Periodic temperature with periods around 24 h even in the low range of 1-2 degrees C (strong Zeitgeber effect) can entrain all ectothermic (poikilothermic) organisms. This is also reflected by the phase shifts-recorded by phase response curves (PRCs)-that are elicited by step- or pulsewise changes in the temperature. The amount of phase shift (weak or strong type of PRC) depends on the amplitude of the temperature change and on its duration when applied as a pulse. Form and position of the PRC to temperature pulses are similar to those of the PRC to light pulses. A combined high/low temperature and light/dark cycle leads to a stabile phase and maximal amplitude of the circadian rhythm-when applied in phase (i.e., warm/light and cold/dark). When the two Zeitgeber cycles are phase-shifted against each other the phase of the circadian rhythm is determined by either Zeitgeber or by both, depending on the relative strength (amplitude) of both Zeitgeber signals and the sensitivity of the species/individual toward them. A phase jump of the circadian rhythm has been observed in several organisms at a certain phase relationship of the two Zeitgeber cycles. Ectothermic organisms show inter- and intraspecies plus seasonal variations in the temperature limits for the expression of the clock, either of the basic molecular mechanism, and/or the dependent variables. A step-down from higher temperatures or a step-up from lower temperatures to moderate temperatures often results in initiation of oscillations from phase positions that are about 180 degrees different. This may be explained by holding the clock at different phase positions (maximum or minimum of a clock component) or by significantly different levels of clock components at the higher or lower temperatures. Different permissive temperatures result in different circadian amplitudes, that usually show a species-specific optimum. In endothermic (homeothermic) organisms periodic temperature changes of about 24 h often cause entrainment, although with considerable individual differences, only if they are of rather high amplitudes (weak Zeitgeber effects). The same applies to the phase-shifting effects of temperature pulses. Isolated bird pineals and rat suprachiasmatic nuclei tissues on the other hand, respond to medium high temperature pulses and reveal PRCs similar to that of light signals. Therefore, one may speculate that the self-selected circadian rhythm of body temperature in reptiles or the endogenously controlled body temperature in homeotherms (some of which show temperature differences of more than 2 degrees C) may, in itself, serve as an internal entraining system. The so-called heterothermic mammals (undergoing low body temperature states in a daily or seasonal pattern) may be more sensitive to temperature changes. Effects of temperature elevation on the molecular clock mechanisms have been shown in Neurospora (induction of the frequency (FRQ) protein) and in Drosophila (degradation of the period (PER) and timeless (TIM) protein) and can explain observed phase shifts of rhythms in conidiation and locomotor activity, respectively. Temperature changes probably act directly on all processes of the clock mechanism some being more sensitive than the others. Temperature changes affect membrane properties, ion homeostasis, calcium influx, and other signal cascades (cAMP, cGMP, and the protein kinases A and C) (indirect effects) and may thus influence, in particular, protein phosphorylation processes of the clock mechanism. The temperature effects resemble to some degree those induced by light or by light-transducing neurons and their transmitters. In ectothermic vertebrates temperature changes significantly affect the melatonin rhythm, which in turn exerts entraining (phase shifting) functions.

The out of phase 1 mutant defines a role for PHYB in circadian phase control in Arabidopsis

Arabidopsis displays circadian rhythms in stomatal aperture, stomatal conductance, and CO(2) assimilation, each of which peaks around the middle of the day. The rhythmic opening and closing of stomata confers a rhythm in sensitivity and resistance, respectively, to the toxic gas sulfur dioxide. Using this physiological assay as a basis for a mutant screen, we isolated mutants with defects in circadian timing. Here, we characterize one mutant, out of phase 1 (oop1), with the circadian phenotype of altered phase. That is, the timing of the peak (acrophase) of multiple circadian rhythms (leaf movement, CO(2) assimilation, and LIGHT-HARVESTING CHLOROPHYLL a/b-BINDING PROTEIN transcription) is early with respect to wild type, although all circadian rhythms retain normal period length. This is the first such mutant to be characterized in Arabidopsis. oop1 also displays a strong photoperception defect in red light characteristic of phytochrome B (phyB) mutants. The oop1 mutation is a nonsense mutation of PHYB that results in a truncated protein of 904 amino acids. The defect in circadian phasing is seen in seedlings entrained by a light-dark cycle but not in seedlings entrained by a temperature cycle. Thus, PHYB contributes light information critical for proper determination of circadian phase.