Circadian Control of cab Gene Transcription and mRNA Accumulation in Arabidopsis

Inhibition of RNA degradation integrates the metabolic signals induced by osmotic stress into the Arabidopsis circadian system

The circadian clock system acts as an endogenous timing reference that coordinates many metabolic and physiological processes in plants. Previous studies have shown that the application of osmotic stress delays circadian rhythms via 3'-phospho-adenosine 5'-phosphate (PAP), a retrograde signalling metabolite that is produced in response to redox stress within organelles. PAP accumulation leads to the inhibition of exoribonucleases (XRNs), which are responsible for RNA degradation. Interestingly, we are now able to demonstrate that post-transcriptional processing is crucial for the circadian response to osmotic stress. Our data show that osmotic stress increases the stability of specific circadian RNAs, suggesting that RNA metabolism plays a vital role in circadian clock coordination during drought. Inactivation of XRN4 is sufficient to extend circadian rhythms as part of this response, with PRR7 and LWD1 identified as transcripts that are post-transcriptionally regulated to delay circadian progression.

Physiological and biochemical responses of Limonium tetragonum to NaCl concentrations in hydroponic solution

Introduction

Limonium (L.) tetragonum (Thunb.) A. A. Bullock, a halophyte that grows all over the southwest coast of Korea, is a medicinal plant with various pharmacological effects. The salt defense mechanism stimulates the biosynthesis of various secondary metabolites and improves functional substances. In this study, we investigated the optimal NaCl concentration for the growth and enhancement of secondary metabolites in hydroponically grown L. tetragonum.

Methods

The seedlings grown for 3 weeks in a hydroponic cultivation system were treated with 0-, 25-, 50-, 75-, and 100-mM NaCl in Hoagland's nutrient solution for 8 weeks. No significant effect on the growth and chlorophyll fluorescence was observed for the NaCl concentrations below 100-mM.

Results and discussions

The increase in the NaCl concentration resulted in the decrease in the water potential of the L. tetragonum leaves. The Na⁺ content accumulated in the aerial part increased rapidly and the content of K⁺, which acts as an antagonist, decreased with the increase in NaCl concentrations in hydroponics. The total amino acid content of L. tetragonum decreased compared to the 0-mM NaCl, and most of the amino acid content decreased as the NaCl concentration increased. In contrast, the content of urea, proline (Pro), β-alanine, ornithine, and arginine was increased with an increase in NaCl concentration. The Pro content at 100-mM NaCl accounted for 60% of the total amino acids and was found to be a major osmoregulator as an important component of the salt defense mechanisms. The top five compounds identified in the L. tetragonum were classified as flavonoids while the flavanone compound was detected only in the NaCl treatments. A total of four myricetin glycosides were increased in comparison to the 0-mM NaCl. Among the differentially expressed genes, a significantly large change in Gene ontology was seen in the circadian rhythm. NaCl treatment enhanced the flavonoid-based substances of L. tetragonum. The optimum NaCl concentration for the enhancement of secondary metabolites of the L. tetragonum in the vertical farm-hydroponic cultivation system was 75-mM NaCl.

Circadian regulation of the transcriptome in a complex polyploid crop

The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.

Comprehensive Effects of Flowering Locus T-Mediated Stem Growth in Tobacco

In flowering plants, Flowering locus T (FT) encodes a major florigen. It is a key flowering hormone in controlling flowering time and has a wide range of effects on plant development. Although the mechanism by which FT promotes flowering is currently clearly understood, comprehensive effects of the FT gene on plant growth have not been evaluated. Therefore, the effects of FT on vegetative growth need to be explored for a complete understanding of the molecular functions of the FT gene. In this study, the Jatropha curcas L. FT gene was overexpressed in tobacco (JcFT^OE) in order to discover multiple aspects and related mechanisms of how the FT gene affects plant development. In JcFT^OE plants, root, stem, and leaf development was strongly affected. Stem tissues were selected for further transcriptome analysis. In JcFT^OE plants, stem growth was affected because of changes in the nucleus, cytoplasm, and cell wall. In the nucleus of JcFT^OE plants, the primary effect was to weaken all aspects of DNA replication, which ultimately affected the cell cycle and cell division. The number of stem cells decreased significantly in JcFT^OE plants, which decreased the thickness and height of tobacco stems. In the cell wall of JcFT^OE plants, hemicellulose and cellulose contents increased, with the increase in hemicellulose associated with up-regulation of xylan synthase-related genes expression. In the cytoplasm of JcFT^OE plants, the primary effects were on biogenesis of ribonucleoprotein complexes, photosynthesis, carbohydrate biosynthesis, and the cytoskeleton. In addition, in the cytoplasm of JcFT^OE plants, there were changes in certain factors of the core oscillator, expression of many light-harvesting chlorophyll a/b binding proteins was down-regulated, and expression of fructose 1,6-bisphosphatase genes was up-regulated to increase starch content in tobacco stems. Changes in the xylem and phloem of JcFT^OE plants were also identified, and in particular, xylem development was affected by significant increases in expression of irregular xylem genes.

Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

BACKGROUND

Rose is one of most popular ornamental plants worldwide and is of high economic value and great cultural importance. However, cold damage restricts its planting application in cold areas. To elucidate the metabolic response of rose under low temperature stress, we conducted transcriptome and de novo analysis of Rosa xanthina f. spontanea.

RESULTS

A total of 124,106 unigenes from 9 libraries were generated by de novo assembly, with N50 length was 1470 bp, under 4 °C and - 20 °C stress (23 °C was used as a control). Functional annotation and prediction analyses identified 55,084 unigenes, and 67.72% of these unigenes had significant similarity (BLAST, E ≤ 10^- 5) to those in the public databases. A total of 3031 genes were upregulated and 3891 were downregulated at 4 °C compared with 23 °C, and 867 genes were upregulated and 1763 were downregulated at - 20 °C compared with 23 °C. A total of 468 common DEGs were detected under cold stress, and the matched DEGs were involved in three functional categories: biological process (58.45%), cellular component (11.27%) and molecular function (30.28%). Based on KEGG functional annotations, four pathways were significantly enriched: metabolic pathway, response to plant pathogen interaction (32 genes); starch and sucrose metabolism (21 genes); circadian rhythm plant (8 genes); and photosynthesis antenna proteins (7 genes).

CONCLUSIONS

Our study is the first to report the response to cold stress at the transcriptome level in R. xanthina f. spontanea. The results can help to elucidate the molecular mechanism of cold resistance in rose and provide new insights and candidate genes for genetically enhancing cold stress tolerance.

Genome-wide circadian regulation: A unique system for computational biology

Circadian rhythms are 24-hour oscillations affecting an organism at multiple levels from gene expression all the way to tissues and organs. They have been observed in organisms across the kingdom of life, spanning from cyanobacteria to humans. In mammals, the master circadian pacemaker is located in the hypothalamic suprachiasmatic nuclei (SCN) in the brain where it synchronizes the peripheral oscillators that exist in other tissues. This system regulates the circadian activity of a large part of the transcriptome and recent findings indicate that almost every cell in the body has this clock at the molecular level. In this review, we briefly summarize the different factors that can influence the circadian transcriptome, including light, temperature, and food intake. We then summarize recently identified general principles governing genome-scale circadian regulation, as well as future lines of research. Genome-scale circadian activity represents a fascinating study model for computational biology. For this purpose, systems biology methods are promising exploratory tools to decode the global regulatory principles of circadian regulation.

Modulation of Circadian Gene Expression and Metabolic Compensation by the RCO-1 Corepressor of Neurospora crassa

Neurospora crassa is a model organism for the study of circadian clocks, molecular machineries that confer ∼24-hr rhythms to different processes at the cellular and organismal levels. The FREQUENCY (FRQ) protein is a central component of the Neurospora core clock, a transcription/translation negative feedback loop that controls genome-wide rhythmic gene expression. A genetic screen aimed at determining new components involved in the latter process identified regulation of conidiation 1 (rco-1), the ortholog of the Saccharomyces cerevisiae Tup1 corepressor, as affecting period length. By employing bioluminescent transcriptional and translational fusion reporters, we evaluated frq and FRQ expression levels in the rco-1 mutant background observing that, in contrast to prior reports, frq and FRQ expression are robustly rhythmic in the absence of RCO-1, although both amplitude and period length of the core clock are affected. Moreover, we detected a defect in metabolic compensation, such that high-glucose concentrations in the medium result in a significant decrease in period when RCO-1 is absent. Proteins physically interacting with RCO-1 were identified through co-immunoprecipitation and mass spectrometry; these include several components involved in chromatin remodeling and transcription, some of which, when absent, lead to a slight change in period. In the aggregate, these results indicate a dual role for RCO-1: although it is not essential for core-clock function, it regulates proper period and amplitude of core-clock dynamics and is also required for the rhythmic regulation of several clock-controlled genes.

Circadian regulation of chloroplasts

Circadian rhythms produce a biological measure of time that increases plant performance. The mechanisms that underlie this increase in productivity require investigation to provide information that will underpin future crop improvement. There is a growing body of evidence that a sophisticated signalling network interconnects the circadian oscillator and chloroplasts. We consider this in the context of circadian signalling to chloroplasts and the relationship between retrograde signalling and circadian regulation. We place circadian signalling to chloroplasts by sigma factors within an evolutionary context. We describe selected recent developments in the integration of light and circadian signals that control chloroplast gene expression.

Effects of light and circadian clock on growth and chlorophyll accumulation of Nannochloropsis gaditana

Circadian clocks synchronize various physiological, metabolic and developmental processes of organisms with specific phases of recurring changes in their environment (e.g. day and night or seasons). Here, we investigated whether the circadian clock plays a role in regulation of growth and chlorophyll (Chl) accumulation in Nannochloropsis gaditana, an oleaginous marine microalga which is considered as a potential feedstock for biofuels and for which a draft genome sequence has been published. Optical density (OD) of N. gaditana culture was monitored at 680 and 735 nm under 12:12 h or 18:6 h light-dark (LD) cycles and after switching to continuous illumination in photobioreactors. In parallel, Chl fluorescence was measured to assess the quantum yield of photosystem II. Furthermore, to test if red- or blue-light photoreceptors are involved in clock entrainment in N. gaditana, some of the experiments were conducted by using only red or blue light. Growth and Chl accumulation were confined to light periods in the LD cycles, increasing more strongly in the first half than in the second half of the light periods. After switching to continuous light, rhythmic oscillations continued (especially for OD680 ) at least in the first 24 h, with a 50% decrease in the capacity to grow and accumulate Chl during the first subjective night. Pronounced free-running oscillations were induced by blue light, but not by red light. In contrast, the photosystem II quantum yield was determined by light conditions. The results indicate interactions between circadian and light regulation of growth and Chl accumulation in N. gaditana.

Emerging roles for post-transcriptional regulation in circadian clocks

Circadian clocks temporally organize behavior and physiology across the 24-h day. Great progress has been made in understanding the molecular basis of timekeeping, with a focus on transcriptional feedback networks that are post-translationally modulated. Yet emerging evidence indicates an important role for post-transcriptional regulation, from splicing, polyadenylation and mRNA stability to translation and non-coding functions exemplified by microRNAs. This level of regulation affects virtually all aspects of circadian systems, from the core timing mechanism and input pathways that synchronize clocks to the environment and output pathways that control overt rhythmicity. We hypothesize that post-transcriptional control confers on circadian clocks enhanced robustness as well as the ability to adapt to different environments. As much of what is known derives from nonneural cells or tissues, future work will be required to investigate the role of post-transcriptional regulation in neural clocks.

Os-GIGANTEA confers robust diurnal rhythms on the global transcriptome of rice in the field

The circadian clock controls physiological traits such as flowering time, photosynthesis, and growth in plants under laboratory conditions. Under natural field conditions, however, little is known about the significance of the circadian clock in plants. By time-course transcriptome analyses of rice (Oryza sativa) leaves, using a newly isolated rice circadian clock-related mutant carrying a null mutation in Os-GIGANTEA (Os-GI), we show here that Os-GI controlled 75% (false discovery rate = 0.05) of genes among 27,201 genes tested and was required for strong amplitudes and fine-tuning of the diurnal rhythm phases of global gene expression in the field. However, transcripts involved in primary metabolism were not greatly affected by osgi. Time-course metabolome analyses of leaves revealed no trends of change in primary metabolites in osgi plants, and net photosynthetic rates and grain yields were not affected. By contrast, some transcripts and metabolites in the phenylpropanoid metabolite pathway were consistently affected. Thus, net primary assimilation of rice was still robust in the face of such osgi mutation-related circadian clock defects in the field, unlike the case with defects caused by Arabidopsis thaliana toc1 and ztl mutations in the laboratory.

Circadian control of carbohydrate availability for growth in Arabidopsis plants at night

Plant growth is driven by photosynthetic carbon fixation during the day. Some photosynthate is accumulated, often as starch, to support nocturnal metabolism and growth at night. The rate of starch degradation in Arabidopsis leaves at night is essentially linear, and is such that almost all of the starch is used by dawn. We have investigated the timer that matches starch utilization to the duration of the night. The rate of degradation adjusted immediately and appropriately to an unexpected early onset of night. Starch was still degraded in an appropriate manner when the preceding light period was interrupted by a period of darkness. However, when Arabidopsis was grown in abnormal day lengths (28 h or 17 h) starch was exhausted approximately 24 h after the last dawn, irrespective of the actual dawn. A mutant lacking the LHY and CCA1 clock components exhausted its starch at the dawn anticipated by its fast-running circadian clock, rather than the actual dawn. Reduced growth of wild-type plants in 28-h days and lhy/cca1 mutants in 24-h days was attributable to the inappropriate rate of starch degradation and the consequent carbon starvation at the end of night. Thus, starch degradation is under circadian control to ensure that carbohydrate availability is maintained until the next anticipated dawn, and this control is necessary for maintaining plant productivity.

Two new clock proteins, LWD1 and LWD2, regulate Arabidopsis photoperiodic flowering

The "light" signal from the environment sets the circadian clock to regulate multiple physiological processes for optimal rhythmic growth and development. One such process is the control of flowering time by photoperiod perception in plants. In Arabidopsis (Arabidopsis thaliana), the flowering time is determined by the correct interconnection of light input and signal output by the circadian clock. The identification of additional clock proteins will help to better dissect the complex nature of the circadian clock in Arabidopsis. Here, we show LIGHT-REGULATED WD1 (LWD1)/LWD2 as new clock proteins involved in photoperiod control. The lwd1lwd2 double mutant has an early-flowering phenotype, contributed by the significant phase shift of CONSTANS (CO), and, therefore, an increased expression of FLOWERING LOCUS T (FT) before dusk. Under entrainment conditions, the expression phase of oscillator (CIRCADIAN CLOCK ASSOCIATED1 [CCA1], LATE ELONGATED HYPOCOTYL [LHY], TIMING OF CAB EXPRESSION1 [TOC1], and EARLY FLOWERING4 [ELF4]) and output (GIGANTEA, FLAVIN-BINDING, KELCH REPEAT, F-BOX1, CYCLING DOF FACTOR1, CO, and FT) genes in the photoperiod pathway shifts approximately 3 h forward in the lwd1lwd2 double mutant. Both the oscillator (CCA1, LHY, TOC1, and ELF4) and output (COLD, CIRCADIAN RHYTHM, AND RNA BINDING2 and CHLOROPHYLL A/B-BINDING PROTEIN2) genes have a short period length in the lwd1lwd2 double mutant. Our data imply that LWD1/LWD2 proteins function in close proximity to or within the circadian clock for photoperiodic flowering control.

FIONA1 is essential for regulating period length in the Arabidopsis circadian clock

In plants, the circadian clock controls daily physiological cycles as well as daylength-dependent developmental processes such as photoperiodic flowering and seedling growth. Here, we report that FIONA1 (FIO1) is a genetic regulator of period length in the Arabidopsis thaliana circadian clock. FIO1 was identified by screening for a mutation in daylength-dependent flowering. The mutation designated fio1-1 also affects daylength-dependent seedling growth. fio1-1 causes lengthening of the free-running circadian period of leaf movement and the transcription of various genes, including the central oscillators CIRCADIAN CLOCK-ASSOCIATED1, LATE ELONGATED HYPOCOTYL, TIMING OF CAB EXPRESSION1, and LUX ARRHYTHMO. However, period lengthening is not dependent upon environmental light or temperature conditions, which suggests that FIO1 is not a simple input component of the circadian system. Interestingly, fio1-1 exerts a clear effect on the period length of circadian rhythm but has little effect on its amplitude and robustness. FIO1 encodes a novel nuclear protein that is highly conserved throughout the kingdoms. We propose that FIO1 regulates period length in the Arabidopsis circadian clock in a close association with the central oscillator and that the circadian period can be controlled separately from amplitude and robustness.

How plants tell the time

Plants, like all eukaryotes and most prokaryotes, have evolved sophisticated mechanisms for anticipating predictable environmental changes that arise due to the rotation of the Earth on its axis. These mechanisms are collectively termed the circadian clock. Many aspects of plant physiology, metabolism and development are under circadian control and a large proportion of the transcriptome exhibits circadian regulation. In the present review, we describe the advances in determining the molecular nature of the circadian oscillator and propose an architecture of several interlocking negative-feedback loops. The adaptive advantages of circadian control, with particular reference to the regulation of metabolism, are also considered. We review the evidence for the presence of multiple circadian oscillator types located in within individual cells and in different tissues.

Progression and Specificity of Protein Oxidation in the Life Cycle of Arabidopsis thaliana

Protein carbonylation is an irreversible oxidative process leading to a loss of function of the modified proteins, and in a variety of model systems, including worms, flies, and mammals, carbonyl levels gradually increase with age. In contrast, we report here that in Arabidopsis thaliana an initial increase in protein oxidation during the first 20 days of the life cycle of the plant is followed by a drastic reduction in protein carbonyls prior to bolting and flower development. Protein carbonylation prior to the transition to flowering targets specific proteins such as Hsp70, ATP synthases, the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), and proteins involved in light harvesting/energy transfer and the C2 oxidative photosynthetic carbon cycle. The precipitous fall in protein carbonyl levels is due to the specific reduction in the levels of oxidized proteins rather than an overall loss of chlorophyll and Rubisco associated with the senescence syndrome. The results are discussed in light of contemporary theories of aging in animals.

Independent action of ELF3 and phyB to control hypocotyl elongation and flowering time

Light regulates various aspects of plant growth, and the photoreceptor phytochrome B (phyB) mediates many responses to red light. In a screen for Arabidopsis mutants with phenotypes similar to those of phyB mutants, we isolated two new elf3 mutants. One has weaker morphological phenotypes than previously identified elf3 alleles, but still abolishes circadian rhythms under continuous light. Like phyB mutants, elf3 mutants have elongated hypocotyls and petioles, flower early, and have defects in the red light response. However, we found that elf3 mutations have an additive interaction with a phyB null mutation, with phyA or hy4 null mutations, or with a PHYB overexpression construct, and that an elf3 mutation does not prevent nuclear localization of phyB. These results suggest that either there is substantial redundancy in phyB and elf3 function, or the two genes regulate distinct signaling pathways.

The circadian clock controls the expression pattern of the circadian input photoreceptor, phytochrome B

Developmental and physiological responses are regulated by light throughout the entire life cycle of higher plants. To sense changes in the light environment, plants have developed various photoreceptors, including the red/far-red light-absorbing phytochromes and blue light-absorbing cryptochromes. A wide variety of physiological responses, including most light responses, also are modulated by circadian rhythms that are generated by an endogenous oscillator, the circadian clock. To provide information on local time, circadian clocks are synchronized and entrained by environmental time cues, of which light is among the most important. Light-driven entrainment of the Arabidopsis circadian clock has been shown to be mediated by phytochrome A (phyA), phytochrome B (phyB), and cryptochromes 1 and 2, thus affirming the roles of these photoreceptors as input regulators to the plant circadian clock. Here we show that the expression of PHYB::LUC reporter genes containing the promoter and 5' untranslated region of the tobacco NtPHYB1 or Arabidopsis AtPHYB genes fused to the luciferase (LUC) gene exhibit robust circadian oscillations in transgenic plants. We demonstrate that the abundance of PHYB RNA retains this circadian regulation and use a PHYB::Luc fusion protein to show that the rate of PHYB synthesis is also rhythmic. The abundance of bulk PHYB protein, however, exhibits only weak circadian rhythmicity, if any. These data suggest that photoreceptor gene expression patterns may be significant in the daily regulation of plant physiology and indicate an unexpectedly intimate relationship between the components of the input pathway and the putative circadian clock mechanism in higher plants.

Different circadian oscillators control Ca(2+) fluxes and lhcb gene expression

Circadian biological clocks control many biological events, but the pathways by which these events are controlled are largely unknown. Based on a model suggesting that cytosolic-free calcium levels control the expression of the Lhcb gene in plants, we tested whether the circadian oscillation of free calcium is responsible for driving the rhythm of Lhcb expression. We found that these rhythms free-run with different periods in tobacco seedlings in constant conditions. Moreover, robust oscillations of Lhcb promoter activity continued in undifferentiated tobacco calli in the absence of Ca(2+) oscillations. Therefore, these two circadian rhythms are not linked hierarchically. These data provide evidence for separate circadian pacemakers controlling molecular events in plants.

Endogenous fluctuations of DNA topology in the chloroplast of Chlamydomonas reinhardtii

DNA supercoiling in the chloroplast of the unicellular green alga Chlamydomonas reinhardtii was found to change with a diurnal rhythm in cells growing in alternating 12-h dark-12-h light periods. Highest and lowest DNA superhelicities occurred at the beginning and towards the end of the 12-h light periods, respectively. The fluctuations in DNA supercoiling occurred concurrently and in the same direction in two separate parts of the chloroplast genome, one containing the genes psaB, rbcL, and atpA and the other containing the atpB gene. Fluctuations were not confined to transcribed DNA regions, indicating simultaneous changes in DNA conformation all over the chloroplast genome. Because the diurnal fluctuations persisted in cells kept in continuous light, DNA supercoiling is judged to be under endogenous control. The endogenous fluctuations in chloroplast DNA topology correlated tightly with the endogenous fluctuations of overall chloroplast gene transcription and with those of the pool sizes of most chloroplast transcripts analyzed. This result suggests that DNA superhelical changes have a role in the regulation of chloroplast gene expression in Chlamydomonas.

Circadian-regulated transcription of the psbD light-responsive promoter in wheat chloroplasts

The level of mRNAs derived from the plastid-encoded psbD light-responsive promoter (LRP) is controlled by a circadian clock(s) in wheat (Triticum aestivum). The circadian oscillations in the psbD LRP mRNA level persisted for at least three cycles in continuous light and for one cycle in continuous dark, with maxima in subjective morning and minima in subjective early night. In vitro transcription in chloroplast extracts revealed that the circadian cycles in the psbD LRP mRNA level were dominantly attributed to the circadian-regulated transcription of the psbD LRP. The effects of various mutations introduced into the promoter region on the psbD LRP activity in vitro suggest the existence of two positive elements located between -54 and -36, which generally enhance the transcription activity, and an anomalous core promoter structure lacking the functional "-35" element, which plays a crucial role in the circadian fluctuation and light dependency of psbD LRP transcription activity.

Chilling delays circadian pattern of sucrose phosphate synthase and nitrate reductase activity in tomato

Overnight low-temperature exposure inhibits photosynthesis in chilling-sensitive species such as tomato (Lycopersicon esculentum) and cucumber by as much as 60%. In an earlier study we showed that one intriguing effect of low temperature on chilling-sensitive plants is to stall the endogenous rhythm controlling transcription of certain nuclear-encoded genes, causing the synthesis of the corresponding transcripts and proteins to be mistimed when the plant is rewarmed. Here we show that the circadian rhythm controlling the activity of sucrose phosphate synthase (SPS) and nitrate reductase (NR), key control points of carbon and nitrogen metabolism in plant cells, is delayed in tomato by chilling treatments. Using specific protein kinase and phosphatase inhibitors, we further demonstrate that the chilling-induced delay in the circadian control of SPS and NR activity is associated with the activity of critical protein phosphatases. The sensitivity of the pattern of SPS activity to specific inhibitors of transcription and translation indicates that there is a chilling-induced delay in SPS phosphorylation status that is caused by an effect of low temperature on the expression of a gene coding for a phosphoprotein phosphatase, perhaps the SPS phosphatase. In contrast, the chilling-induced delay in NR activity does not appear to arise from effects on NR phosphorylation status, but rather from direct effects on NR expression. It is likely that the mistiming in the regulation of SPS and NR, and perhaps other key metabolic enzymes under circadian regulation, underlies the chilling sensitivity of photosynthesis in these plant species.

Circadian expression of the maize catalase Cat3 gene is highly conserved among diverse maize genotypes with structurally different promoters

The Cat3 gene of maize exhibits a transcriptionally regulated circadian rhythm. In the present study we examined the following: (1) the extent of the circadian Cat3 expression between maize genotypes of diverse origin; (2) the functional significance of a Tourist transposable element located in the Cat3 promoter of the inbred line W64A, which harbors putative regulatory elements (GATA repeat, CCAAT boxes) shown to be involved in the light induction and circadian regulation of the Arabidopsis CAB2, as well as other plant genes; and (3) aspects of the physiological role of CAT-3 in maize metabolism. Results confirm that the circadian Cat3 expression is a general phenomenon in maize. Regulation of Cat3 gene expression is not dependent on the presence of the Tourist element in the promoter of the gene nor on the presence of motifs similar to those found significant in the circadian expression of the Arabidopsis CAB2 gene. Structural diversity was revealed in the Cat3 promoters of maize genotypes of diverse origins. However, highly conserved regions with putative regulatory motifs were identified. Relevance of the conserved regions to the circadian regulation of the gene is discussed. Possible physiological roles of CAT-3 are suggested.

PNZIP is a novel mesophyll-specific cDNA that is regulated by phytochrome and the circadian rhythm and encodes a protein with a leucine zipper motif

We isolated and characterized a novel light-regulated cDNA from the short-day plant Pharbitis nil that encodes a protein with a leucine (Leu) zipper motif, designated PNZIP (Pharbitis nil Leu zipper). The PNZIP cDNA is not similar to any other gene with a known function in the database, but it shares high sequence homology with an Arabidopsis expressed sequence tag and to two other sequences of unknown function from the cyanobacterium Synechocystis spp. and the red alga Porphyra purpurea, which together define a new family of evolutionarily conserved Leu zipper proteins. PNZIP is a single-copy gene that is expressed specifically in leaf photosynthetically active mesophyll cells but not in other nonphotosynthetic tissues such as the epidermis, trichomes, and vascular tissues. When plants were exposed to continuous darkness, PNZIP exhibited a rhythmic pattern of mRNA accumulation with a circadian periodicity of approximately 24 h, suggesting that its expression is under the control of an endogenous clock. However, the expression of PNZIP was unusual in that darkness rather than light promoted its mRNA accumulation. Accumulation of PNZIP mRNA during the dark is also regulated by phytochrome, since a brief exposure to red light in the middle of the night reduced its mRNA levels. Moreover, a far-red-light treatment at the end of day also reduced PNZIP mRNA accumulation during the dark, and that effect could be inhibited by a subsequent exposure to red light, showing the photoreversible response attributable to control through the phytochrome system.

Conserved circadian elements in phylogenetically diverse algae

Circadian expression of the luciferin-binding protein (LBP) from the dinoflagellate Gonyaulax polyedra is regulated at the translational level. A small interval in the lbp 3'-untranslated region, which contains seven UG-repeats, serves as a cis-acting element to which a trans-acting factor (CCTR) binds in a circadian manner. Its binding activity correlates negatively with the circadian expression of LBP. Here I report the identification of a protein in the green alga Chlamydomonas reinhardtii that represents a CCTR analog. It binds both specifically and under control of the circadian clock to the UG-repeat region. The data show for the first time that circadian cis-elements implicated in translational regulation have been conserved during evolution.

Mutagenesis and behavioral screening for altered circadian activity identifies the mouse mutant, Wheels

The molecular processes underlying the generation of circadian behavior in mammals are virtually unknown. To identify genes that regulate or alter circadian activity rhythms, a mouse mutagenesis program was initiated in conjunction with behavioral screening for alterations in circadian period (tau), a fundamental property of the biological clock. Male mice of the inbred BALB/c strain, treated with the potent mutagen N-ethyl-N-nitrosourea were mated with wild-type hybrids. Wheel-running activity of approximately 300 male progeny was monitored for 6-10 weeks under constant dark (DD) conditions. The tau DD of a single mouse (#187) was longer than the population mean by more than three standard deviations (24.20 vs. 23.32 +/- 0.02 h; mean +/- S.E.M.; n = 277). In addition, mouse #187 exhibited other abnormal phenotypes, including hyperactive bi-directional circling/spinning activity and an abnormal response to light. Heterozygous progeny of the founder mouse, generated from outcrossings with wild-type C57BL/6J mice, displayed lengthened tau DD although approximately 20% of the animals showed no wheel-running activity despite being quite active. Under light:dark conditions, all animals displaying circling behavior that ran in the activity wheels exhibited robust wheel-running activity at lights-ON and these animals also showed enhanced wheel-running activity in constant light conditions. The genetic dissection of the complex behavior associated with this mutation was facilitated by the previously described genetic mapping of the mutant locus causing circling behavior, designated Wheels (Whl), to the subcentromeric portion of mouse chromosome 4. In this report, the same locus is shown to be responsible for the abnormal responses to light and presumably for the altered circadian behavior. Characterization of the gene altered in the novel Whl mutation will contribute to understanding the molecular elements involved in mammalian circadian regulation.

The steady-state mRNA levels for thylakoid proteins exhibit coordinate diurnal regulation

Steady-state mRNA levels for thylakoid proteins were analysed in spinach cotyledons under diurnally changing light conditions. Most fluctuate considerably throughout the day, while the levels of others show only low amplitude or no oscillation. Levels of mRNAs coding for proteins that belong to the same multiprotein complex generally oscillate in parallel and exhibit maxima that are specific for that complex: mRNAs for photosystem I proteins appear prior to those for photosystem II polypeptides and these again prior to mRNAs for the three polypeptides constituting the oxygen-evolving complex. For the mRNAs that change with high amplitudes (e.g. those for LHCP or the 20 kDa apoprotein of the CP24 complex) oscillations have also been found under constant conditions, indicating that a circadian oscillator is involved. Transgenic tobacco seedlings harbouring chimeric GUS gene fusions with 5'-flanking sequences from the spinach genes Lhcb, PsaF and AtpD (encoding a light-harvesting chlorophyll a/b apoprotein of photosystem II, subunit 3 of photosystem I and subunit delta of the plastid ATP synthase, respectively) confirm that the differences in the amplitudes as well as the timepoints of maximum mRNA accumulation are perceived via cis-regulatory elements upstream of the respective ATG codons.

Negative feedback defining a circadian clock: autoregulation of the clock gene frequency

The frequency (frq) locus of Neurospora crassa was originally identified in searches for loci encoding components of the circadian clock. The frq gene is now shown to encode a central component in a molecular feedback loop in which the product of frq negatively regulated its own transcript, which resulted in a daily oscillation in the amount of frq transcript. Rhythmic messenger RNA expression was essential for overt rhythmicity in the organism and no amount of constitutive expression rescued normal rhythmicity in frq loss-of-function mutants. Step reductions in the amount of FRQ-encoding transcript set the clock to a specific and predicted phase. These results establish frq as encoding a central component in a circadian oscillator.

Concerted circadian oscillations in transcript levels of nineteen Lha/b (cab) genes in Lycopersicon esculentum (tomato)

Steady-state mRNA levels of nineteen members of the Lha/b (cab) gene family of Lycopersicon esculentum, encoding nine different types of light-harvesting complex (LHC) polypeptides, were determined by primer extension analysis. Each Lha/b gene is expressed and individual mRNAs accumulate to distinct levels. The relative contribution of each Lha/b mRNA to the total Lha/b mRNA levels is very similar in different green organs (leaves, stems, fruits, sepals) and after light treatment of etiolated seedlings. Detailed analysis of Lha/b mRNA accumulation in leaves under light/dark conditions, continuous darkness and continuous light revealed diurnal and circadian oscillations of Lha/b mRNAs for all genes. Only minor instances of divergence from a general expression pattern are apparent. Together these results indicate a concerted expression of all genes, suggesting that similar or identical molecular mechanisms and signal transduction chain control the expression of all Lha/b genes.