Cell autonomous and cell-type specific circadian rhythms in Arabidopsis

AraLeTA: An Arabidopsis leaf expression atlas across diurnal and developmental scales

Mature plant leaves are a composite of distinct cell types, including epidermal, mesophyll, and vascular cells. Notably, the proportion of these cells and the relative transcript concentrations within different cell types may change over time. While gene expression data at a single-cell level can provide cell-type-specific expression values, it is often too expensive to obtain these data for high-resolution time series. Although bulk RNA-seq can be performed in a high-resolution time series, RNA-seq using whole leaves measures average gene expression values across all cell types in each sample. In this study, we combined single-cell RNA-seq data with time-series data from whole leaves to assemble an atlas of cell-type-specific changes in gene expression over time for Arabidopsis (Arabidopsis thaliana). We inferred how the relative transcript concentrations of different cell types vary across diurnal and developmental timescales. Importantly, this analysis revealed 3 subgroups of mesophyll cells with distinct temporal profiles of expression. Finally, we developed tissue-specific gene networks that form a community resource: an Arabidopsis Leaf Time-dependent Atlas (AraLeTa). This allows users to extract gene networks that are confirmed by transcription factor-binding data and specific to certain cell types at certain times of day and at certain developmental stages. AraLeTa is available at https://regulatorynet.shinyapps.io/araleta/.

Root PRR7 Improves the Accuracy of the Shoot Circadian Clock through Nutrient Transport

The circadian clock allows plants to anticipate and adapt to periodic environmental changes. Organ- and tissue-specific properties of the circadian clock and shoot-to-root circadian signaling have been reported. While this long-distance signaling is thought to coordinate physiological functions across tissues, little is known about the feedback regulation of the root clock on the shoot clock in the hierarchical circadian network. Here, we show that the plant circadian clock conveys circadian information between shoots and roots through sucrose and K+. We also demonstrate that K+ transport from roots suppresses the variance of period length in shoots and then improves the accuracy of the shoot circadian clock. Sucrose measurements and qPCR showed that root sucrose accumulation was regulated by the circadian clock. Furthermore, root circadian clock genes, including PSEUDO-RESPONSE REGULATOR7 (PRR7), were regulated by sucrose, suggesting the involvement of sucrose from the shoot in the regulation of root clock gene expression. Therefore, we performed time-series measurements of xylem sap and micrografting experiments using prr7 mutants and showed that root PRR7 regulates K+ transport and suppresses variance of period length in the shoot. Our modeling analysis supports the idea that root-to-shoot signaling contributes to the precision of the shoot circadian clock. We performed micrografting experiments that illustrated how root PRR7 plays key roles in maintaining the accuracy of shoot circadian rhythms. We thus present a novel directional signaling pathway for circadian information from roots to shoots and propose that plants modulate physiological events in a timely manner through various timekeeping mechanisms.

Limited water stress modulates expression of circadian clock genes in Brachypodium distachyon roots

Organisms have evolved a circadian clock for the precise timing of their biological processes. Studies primarily on model dicots have shown the complexity of the inner timekeeper responsible for maintaining circadian oscillation in plants and have highlighted that circadian regulation is more than relevant to a wide range of biological processes, especially organ development and timing of flowering. Contribution of the circadian clock to overall plant fitness and yield has also long been known. Nevertheless, the organ- and species-specific functions of the circadian clock and its relation to stress adaptation have only recently been identified. Here we report transcriptional changes of core clock genes of the model monocot Brachypodium distachyon under three different light regimes (18:6 light:dark, 24:0 light and 0:24 dark) in response to mild drought stress in roots and green plant parts. Comparative monitoring of core clock gene expression in roots and green plant parts has shown that both phase and amplitude of expression in the roots of Brachypodium plants differ markedly from those in the green plant parts, even under well-watered conditions. Moreover, circadian clock genes responded to water depletion differently in root and shoot. These results suggest an organ-specific form and functions of the circadian clock in Brachypodium roots.

The diurnal emission of floral scent in Oncidium hybrid orchid is controlled by CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) through the direct regulation on terpene synthase

BACKGROUND

To adapt the periodic fluctuation of environmental factors, plants are subtle to monitor the natural variation for the growth and development. The daily activities and physiological functions in coordination with the natural variation are regulated by circadian clock genes. The circadian emission of floral scents is one of the rhythmic physiological activities controlled by circadian clock genes. Here, we study the molecular mechanism of circadian emission pattern of ocimene and linalool compounds in Oncidium Sharry Baby (Onc. SB) orchid.

RESULTS

GC-Mass analysis revealed that Onc. SB periodically emitted ocimene and linalool during 6 to 14 o'clock daily. Terpene synthase, one of the key gene in the terpenoid biosynthetic pathway is expressed in coordination with scent emission. The promoter structure of terpene synthase revealed a circadian binding sequence (CBS), 5'-AGATTTTT-3' for CIRCADIAN CLOCK ASSOCIATED1 (CCA1) transcription factor. EMSA data confirms the binding affinity of CCA1. Transactivation assay further verified that TPS expression is regulated by CCA1. It suggests that the emission of floral scents is controlled by CCA1.

CONCLUSIONS

The work validates that the mechanism of circadian emission of floral scents in Onc. Sharry Baby is controlled by the oscillator gene, CCA1(CIRCADIAN CLOCK ASSOCIATED 1) under light condition. CCA1 transcription factor up-regulates terpene synthase (TPS) by binding on CBS motif, 5'-AGATTTTT-3' of promoter region to affect the circadian emission of floral scents in Onc. SB.

Spatially specific mechanisms and functions of the plant circadian clock

Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.

Circadian autonomy and rhythmic precision of the Arabidopsis female reproductive organ

The plant circadian clock regulates essential biological processes including flowering time or petal movement. However, little is known about how the clock functions in flowers. Here, we identified the circadian components and transcriptional networks contributing to the generation of rhythms in pistils, the female reproductive organ. When detached from the rest of the flower, pistils sustain highly precise rhythms, indicating organ-specific circadian autonomy. Analyses of clock mutants and chromatin immunoprecipitation assays showed distinct expression patterns and specific regulatory functions for clock activators and repressors in pistils. Genetic interaction studies also suggested a hierarchy of the repressing activities that provide robustness and precision to the pistil clock. Globally, the circadian function in pistils primarily governs responses to environmental stimuli and photosynthesis and controls pistil growth and seed weight and production. Understanding the circadian intricacies in reproductive organs may prove useful for optimizing plant reproduction and productivity.

Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes

Background

Cell and circadian cycles control a large fraction of cell and organismal physiology by regulating large periodic transcriptional programs that encompass anywhere from 15 to 80% of the genome despite performing distinct functions. In each case, these large periodic transcriptional programs are controlled by gene regulatory networks (GRNs), and it has been shown through genetics and chromosome mapping approaches in model systems that at the core of these GRNs are small sets of genes that drive the transcript dynamics of the GRNs. However, it is unlikely that we have identified all of these core genes, even in model organisms. Moreover, large periodic transcriptional programs controlling a variety of processes certainly exist in important non-model organisms where genetic approaches to identifying networks are expensive, time-consuming, or intractable. Ideally, the core network components could be identified using data-driven approaches on the transcriptome dynamics data already available.

Results

This study shows that a unified set of quantified dynamic features of high-throughput time series gene expression data are more prominent in the core transcriptional regulators of cell and circadian cycles than in their outputs, in multiple organism, even in the presence of external periodic stimuli. Additionally, we observe that the power to discriminate between core and non-core genes is largely insensitive to the particular choice of quantification of these features.

Conclusions

There are practical applications of the approach presented in this study for network inference, since the result is a ranking of genes that is enriched for core regulatory elements driving a periodic phenotype. In this way, the method provides a prioritization of follow-up genetic experiments. Furthermore, these findings reveal something unexpected—that there are shared dynamic features of the transcript abundance of core components of unrelated GRNs that control disparate periodic phenotypes.

Adaptive Diversification in the Cellular Circadian Behavior of Arabidopsis Leaf- and Root-Derived Cells

The plant circadian system is based on self-sustained cellular oscillations and is utilized to adapt to daily and seasonal environmental changes. The cellular circadian clocks in the above- and belowground plant organs are subjected to diverse local environments. Individual cellular clocks are affected by other cells/tissues in plants, and the intrinsic circadian properties of individual cells remain to be elucidated. In this study, we monitored bioluminescence circadian rhythms of individual protoplast-derived cells from leaves and roots of a CCA1::LUC Arabidopsis transgenic plant. We analyzed the circadian properties of the leaf- and root-derived cells and demonstrated that the cells with no physical contact with other cells harbor a genuine circadian clock with ∼24-h periodicity, entrainability and temperature compensation of the period. The stability of rhythm was dependent on the cell density. High cell density resulted in an improved circadian rhythm of leaf-derived cells while this effect was observed irrespective of the phase relation between cellular rhythms. Quantitative and statistical analyses for individual cellular bioluminescence rhythms revealed a difference in amplitude and precision of light/dark entrainment between the leaf- and root-derived cells. Circadian systems in the leaves and roots are diversified to adapt to their local environments at the cellular level.

A spatial model of the plant circadian clock reveals design principles for coordinated timing

Individual plant cells possess a genetic network, the circadian clock, that times internal processes to the day-night cycle. Mathematical models of the clock are typically either "whole-plant" that ignore tissue or cell type-specific clock behavior, or "phase-only" that do not include molecular components. To address the complex spatial coordination observed in experiments, here we implemented a clock network model on a template of a seedling. In our model, the sensitivity to light varies across the plant, and cells communicate their timing via local or long-distance sharing of clock components, causing their rhythms to couple. We found that both varied light sensitivity and long-distance coupling could generate period differences between organs, while local coupling was required to generate the spatial waves of clock gene expression observed experimentally. We then examined our model under noisy light-dark cycles and found that local coupling minimized timing errors caused by the noise while allowing each plant region to maintain a different clock phase. Thus, local sensitivity to environmental inputs combined with local coupling enables flexible yet robust circadian timing.

The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues

As sessile organisms, plants are finely tuned to respond dynamically to developmental, circadian and environmental cues. Genome-wide studies investigating these types of cues have uncovered the intrinsically different ways they can impact gene expression over time. Recent advances in single-cell sequencing and time-based bioinformatic algorithms are now beginning to reveal the dynamics of these time-based responses within individual cells and plant tissues. Here, we review what these techniques have revealed about the spatiotemporal nature of gene regulation, paying particular attention to the three distinct ways in which plant tissues are time sensitive. (i) First, we discuss how studying plant cell identity can reveal developmental trajectories hidden in pseudotime. (ii) Next, we present evidence that indicates that plant cell types keep their own local time through tissue-specific regulation of the circadian clock. (iii) Finally, we review what determines the speed of environmental signaling responses, and how they can be contingent on developmental and circadian time. By these means, this review sheds light on how these different scales of time-based responses can act with tissue and cell-type specificity to elicit changes in whole plant systems.

Abscisic Acid Machinery Is under Circadian Clock Regulation at Multiple Levels

Abscisic acid (ABA) is recognized as the key hormonal regulator of plant stress physiology. This phytohormone is also involved in plant growth and development under normal conditions. Over the last 50 years the components of ABA machinery have been well characterized, from synthesis to molecular perception and signaling; knowledge about the fine regulation of these ABA machinery components is starting to increase. In this article, we review a particular regulation of the ABA machinery that comes from the plant circadian system and extends to multiple levels. The circadian clock is a self-sustained molecular oscillator that perceives external changes and prepares plants to respond to them in advance. The circadian system constitutes the most important predictive homeostasis mechanism in living beings. Moreover, the circadian clock has several output pathways that control molecular, cellular and physiological downstream processes, such as hormonal response and transcriptional activity. One of these outputs involves the ABA machinery. The circadian oscillator components regulate expression and post-translational modification of ABA machinery elements, from synthesis to perception and signaling response. The circadian clock establishes a gating in the ABA response during the day, which fine tunes stomatal closure and plant growth response.

High Spatial Resolution Luciferase Imaging of the Arabidopsis thaliana Circadian Clock

The A. thaliana circadian clock is an example of a gene network that generates rich temporal and spatial dynamics. Bioluminescent imaging has proven a powerful method to help dissect the genetic mechanisms that generate oscillations of gene expression over the course of the day. However, its use for the study of spatial regulation is often limited by resolution. Here, we describe a modified luciferase imaging method for the study of the Arabidopsis circadian clock across the plant at sub-tissue-level resolution.

The circadian clock gene circuit controls protein and phosphoprotein rhythms in Arabidopsis thaliana

Twenty-four-hour, circadian rhythms control many eukaryotic mRNA levels, whereas the levels of their more stable proteins are not expected to reflect the RNA rhythms, emphasizing the need to test the circadian regulation of protein abundance and modification. Here we present circadian proteomic and phosphoproteomic time series from Arabidopsis thaliana plants under constant light conditions, estimating that just 0.4% of quantified proteins but a much larger proportion of quantified phospho-sites were rhythmic. Approximately half of the rhythmic phospho-sites were most phosphorylated at subjective dawn, a pattern we term the “phospho-dawn.” Members of the SnRK/CDPK family of protein kinases are candidate regulators. A CCA1-overexpressing line that disables the clock gene circuit lacked most circadian protein phosphorylation. However, the few phospho-sites that fluctuated despite CCA1-overexpression still tended to peak in abundance close to subjective dawn, suggesting that the canonical clock mechanism is necessary for most but perhaps not all protein phosphorylation rhythms. To test the potential functional relevance of our datasets, we conducted phosphomimetic experiments using the bifunctional enzyme fructose-6-phosphate-2-kinase/phosphatase (F2KP), as an example. The rhythmic phosphorylation of diverse protein targets is controlled by the clock gene circuit, implicating posttranslational mechanisms in the transmission of circadian timing information in plants.

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Circadian (phospho)proteomics time courses of plants with or without functional clock.

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Most protein abundance/phosphorylation rhythms require a transcriptional oscillator.

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The majority of rhythmic phosphosites peak around subjective dawn (“phospho-dawn”).

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A phosphorylated serine of the metabolic enzyme F2KP has functional relevance.

Cut the noise or couple up: Coordinating circadian and synthetic clocks

Circadian clocks are important to much of life on Earth and are of inherent interest to humanity, implicated in fields ranging from agriculture and ecology to developmental biology and medicine. New techniques show that it is not simply the presence of clocks, but coordination between them that is critical for complex physiological processes across the kingdoms of life. Recent years have also seen impressive advances in synthetic biology to the point where parallels can be drawn between synthetic biological and circadian oscillators. This review will emphasize theoretical and experimental studies that have revealed a fascinating dichotomy of coupling and heterogeneity among circadian clocks. We will also consolidate the fields of chronobiology and synthetic biology, discussing key design principles of their respective oscillators.

Time Will Tell: Intercellular Communication in the Plant Clock

Multicellular organisms have evolved local and long-distance signaling mechanisms to synchronize development and response to stimuli among a complex network of cells, tissues, and organs. Biological timekeeping is one such activity that is suggested to be coordinated within an organism to anticipate and respond to daily and seasonal patterns in the environment. New research into the plant clock suggests circadian rhythms are communicated between cells and across long distances. However, further clarity is required on the nature of the signaling molecules and the mechanisms underlying signal translocation. Here we summarize the roles and properties of tissue-specific circadian rhythms, discuss the evidence for local and long-distance clock communication, and evaluate the potential signaling molecules and transport mechanisms involved in this system.

Stochastic simulation of a model for circadian rhythms in plants

Circadian clocks allow living organisms to anticipate and adapt to the daily variations of the environment. The interlocked feedback loops of the transcription factors network in the plant clock generate oscillations with expression peaks at specific times of the day. In this work, we explore the effect of molecular noise on the behavior of the plant circadian clock through numerical simulations. The influence of system size, photoperiod, and mutations of clock genes on the robustness of the oscillations are discussed. Our simulations show that the oscillations remain robust when the mRNA and protein levels are in the range of a few hundreds molecules. Entrainment by light-dark cycles enhances the robustness compared to constant conditions. Multiple light inputs and inter-cellular coupling also contribute to the robustness of the oscillations. The comparison between deterministic and stochastic simulations of single and double mutants shows that stochasticity does not qualitatively affect the behaviour of mutants but that they do not have the same robustness to noise. Finally, the model shows that noise can induce transitions between two limit cycles in a birhythmic clock mutant.

Layers of crosstalk between circadian regulation and environmental signalling in plants

Circadian regulation has a pervasive influence upon plant development, physiology and metabolism, impacting upon components of fitness and traits of agricultural importance. Circadian regulation is inextricably connected to the responses of plants to their abiotic environments, from the cellular to whole plant scales. Here, we review the crosstalk that occurs between circadian regulation and responses to the abiotic environment from the intracellular scale through to naturally fluctuating environments. We examine the spatial crosstalk that forms part of plant circadian regulation, at the subcellular, tissue, organ and whole-plant scales. This includes a focus on chloroplast and mitochondrial signalling, alternative splicing, long-distance circadian signalling and circadian regulation within natural environments. We also consider mathematical models for plant circadian regulation, to suggest future areas for advancing understanding of roles for circadian regulation in plant responses to environmental cues.

Spatial Organization and Coordination of the Plant Circadian System

The plant circadian clock has a pervasive influence on many aspects of plant biology and is proposed to function as a developmental manager. To do so, the circadian oscillator needs to be able to integrate a multiplicity of environmental signals and coordinate an extensive and diverse repertoire of endogenous rhythms accordingly. Recent studies on tissue-specific characteristics and spatial structure of the plant circadian clock suggest that such plasticity may be achieved through the function of distinct oscillators, which sense the environment locally and are then coordinated across the plant through both intercellular coupling and long-distance communication. This review summarizes the current knowledge on tissue-specific features of the clock in plants and their spatial organization and synchronization at the organismal level.

Chromatin Dynamics and Transcriptional Control of Circadian Rhythms in Arabidopsis

Circadian rhythms pervade nearly all aspects of plant growth, physiology, and development. Generation of the rhythms relies on an endogenous timing system or circadian clock that generates 24-hour oscillations in multiple rhythmic outputs. At its bases, the plant circadian function relies on dynamic interactive networks of clock components that regulate each other to generate rhythms at specific phases during the day and night. From the initial discovery more than 13 years ago of a parallelism between the oscillations in chromatin status and the transcriptional rhythms of an Arabidopsis clock gene, a number of studies have later expanded considerably our view on the circadian epigenome and transcriptome landscapes. Here, we describe the most recent identification of chromatin-related factors that are able to directly interact with Arabidopsis clock proteins to shape the transcriptional waveforms of circadian gene expression and clock outputs. We discuss how changes in chromatin marks associate with transcript initiation, elongation, and the rhythms of nascent RNAs, and speculate on future interesting research directions in the field.

Circadian Regulation Does Not Optimize Stomatal Behaviour

The circadian clock is a molecular timer of metabolism that affects the diurnal pattern of stomatal conductance (gs), amongst other processes, in a broad array of plant species. The function of circadian gs regulation remains unknown and here, we test whether circadian regulation helps to optimize diurnal variations in stomatal conductance. We subjected bean (Phaseolus vulgaris) and cotton (Gossypium hirsutum) canopies to fixed, continuous environmental conditions of photosynthetically active radiation, temperature, and vapour pressure deficit (free-running conditions) over 48 h. We modelled gs variations in free-running conditions to test for two possible optimizations of stomatal behaviour under circadian regulation: (i) that stomata operate to maintain constant marginal water use efficiency; or (ii) that stomata maximize C net gain minus the costs or risks of hydraulic damage. We observed that both optimization models predicted gs poorly under free-running conditions, indicating that circadian regulation does not directly lead to stomatal optimization. We also demonstrate that failure to account for circadian variation in gs could potentially lead to biased parameter estimates during calibrations of stomatal models. More broadly, our results add to the emerging field of plant circadian ecology, where circadian controls may partially explain leaf-level patterns observed in the field.

Heritable gene expression variability and stochasticity govern clonal heterogeneity in circadian period

A ubiquitous feature of the circadian clock across life forms is its organization as a network of cellular oscillators, with individual cellular oscillators within the network often exhibiting considerable heterogeneity in their intrinsic periods. The interaction of coupling and heterogeneity in circadian clock networks is hypothesized to influence clock’s entrainability, but our knowledge of mechanisms governing period heterogeneity within circadian clock networks remains largely elusive. In this study, we aimed to explore the principles that underlie intercellular period variation in circadian clock networks (clonal period heterogeneity). To this end, we employed a laboratory selection approach and derived a panel of 25 clonal cell populations exhibiting circadian periods ranging from 22 to 28 h. We report that a single parent clone can produce progeny clones with a wide distribution of circadian periods, and this heterogeneity, in addition to being stochastically driven, has a heritable component. By quantifying the expression of 20 circadian clock and clock-associated genes across our clone panel, we found that inheritance of expression patterns in at least three clock genes might govern clonal period heterogeneity in circadian clock networks. Furthermore, we provide evidence suggesting that heritable epigenetic variation in gene expression regulation might underlie period heterogeneity.

How do genetically identical cells exhibit a different circadian phenotype? This study reveals that a single parent clone can produce progeny with a wide distribution of circadian periods and that this heterogeneity, in addition to being stochastically driven, has a heritable component, likely via heritable epigenetic variation in gene expression regulation.

A mobile ELF4 delivers circadian temperature information from shoots to roots

The circadian clock is synchronized by environmental cues, mostly by light and temperature. Explaining how the plant circadian clock responds to temperature oscillations is crucial to understanding plant responsiveness to the environment. Here, we found a prevalent temperature-dependent function of the Arabidopsis clock component EARLY FLOWERING 4 (ELF4) in the root clock. Although the clocks in roots are able to run in the absence of shoots, micrografting assays and mathematical analyses show that ELF4 moves from shoots to regulate rhythms in roots. ELF4 movement does not convey photoperiodic information, but trafficking is essential for controlling the period of the root clock in a temperature-dependent manner. Low temperatures favour ELF4 mobility, resulting in a slow-paced root clock, whereas high temperatures decrease movement, leading to a faster clock. Hence, the mobile ELF4 delivers temperature information and establishes a shoot-to-root dialogue that sets the pace of the clock in roots.

The circadian clock coordinates plant development through specificity at the tissue and cellular level

The circadian clock is a genetic circuit that allows organisms to anticipate daily events caused by the rotation of the Earth. The plant clock regulates physiology at multiple scales, from cell division to ecosystem-scale interactions. It is becoming clear that rather than being a single perfectly synchronised timer throughout the plant, the clock can be sensitive to different cues, run at different speeds, and drive distinct processes in different cell types and tissues. This flexibility may help the plant clock to regulate such a range of developmental and physiological processes. In this review, using examples from the literature, we describe how the clock regulates development at multiple scales and discuss how the clock might allow local flexibility in regulation whilst remaining coordinated across the plant.

Element content and expression of genes of interest in guard cells are connected to spatiotemporal variations in stomatal conductance

Element content and expression of genes of interest on single cell types, such as stomata, provide valuable insights into their specific physiology, improving our understanding of leaf gas exchange regulation. We investigated how far differences in stomatal conductance (g_s ) can be ascribed to changes in guard cells functioning in amphistomateous leaves. g_s was measured during the day on both leaf sides, on well-watered and drought-stressed trees (two Populus euramericana Moench and two Populus nigra L. genotypes). In parallel, guard cells were dissected for element content and gene expressions analyses. Both were strongly arranged according to genotype, and drought had the lowest impact overall. Normalizing the data by genotype highlighted a structure on the basis of leaf sides and time of day both for element content and gene expression. Guard cells magnesium, phosphorus, and chlorine were the most abundant on the abaxial side in the morning, where g_s was at the highest. In contrast, genes encoding H⁺ -ATPase and aquaporins were usually more abundant in the afternoon, whereas genes encoding Ca²⁺ -vacuolar antiporters, K⁺ channels, and ABA-related genes were in general more abundant on the adaxial side. Our work highlights the unique physiology of each leaf side and their analogous rhythmicity through the day.

Thermal plasticity of the circadian clock is under nuclear and cytoplasmic control in wild barley

Temperature compensation, expressed as the ability to maintain clock characteristics (mainly period) in face of temperature changes, that is, robustness, is considered a key feature of circadian clock systems. In this study, we explore the genetic basis for lack of robustness, that is, plasticity, of circadian clock as reflected by photosynthesis rhythmicity. The clock rhythmicity of a new wild barley reciprocal doubled haploid population was analysed with a high temporal resolution of pulsed amplitude modulation of chlorophyll fluorescence under optimal (22°C) and high (32°C) temperature. This comparison between two environments pointed to the prevalence of clock acceleration under heat. Genotyping by sequencing of doubled haploid lines indicated a rich recombination landscape with minor fixation (less than 8%) for one of the parental alleles. Quantitative genetic analysis included genotype by environment interactions and binary-threshold models. Variation in the circadian rhythm plasticity phenotypes, expressed as change (delta) of period and amplitude under two temperatures, was associated with maternal organelle genome (the plasmotype), as well as with several nuclear loci. This first reported rhythmicity driven by nuclear loci and plasmotype with few identified variants, paves the way for studying impact of cytonuclear variations on clock robustness and on plant adaptation to changing environments.

Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana

Individual plant cells have a genetic circuit, the circadian clock, that times key processes to the day-night cycle. These clocks are aligned to the day-night cycle by multiple environmental signals that vary across the plant. How does the plant integrate clock rhythms, both within and between organs, to ensure coordinated timing? To address this question, we examined the clock at the sub-tissue level across Arabidopsis thaliana seedlings under multiple environmental conditions and genetic backgrounds. Our results show that the clock runs at different speeds (periods) in each organ, which causes the clock to peak at different times across the plant in both constant environmental conditions and light-dark (LD) cycles. Closer examination reveals that spatial waves of clock gene expression propagate both within and between organs. Using a combination of modeling and experiment, we reveal that these spatial waves are the result of the period differences between organs and local coupling, rather than long-distance signaling. With further experiments we show that the endogenous period differences, and thus the spatial waves, can be generated by the organ specificity of inputs into the clock. We demonstrate this by modulating periods using light and metabolic signals, as well as with genetic perturbations. Our results reveal that plant clocks can be set locally by organ-specific inputs but coordinated globally via spatial waves of clock gene expression.

Interactive roles of chromatin regulation and circadian clock function in plants

Circadian rhythms in transcription ultimately result in oscillations of key biological processes. Understanding how transcriptional rhythms are generated in plants provides an opportunity for fine-tuning growth, development, and responses to the environment. Here, we present a succinct description of the plant circadian clock, briefly reviewing a number of recent studies but mostly emphasizing the components and mechanisms connecting chromatin remodeling with transcriptional regulation by the clock. The possibility that intergenomic interactions govern hybrid vigor through epigenetic changes at clock loci and the function of epialleles controlling clock output traits during crop domestication are also discussed.

Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida

Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.

On the move through time - a historical review of plant clock research

The circadian clock is an important regulator of growth and development that has evolved to help organisms to anticipate the predictably occurring events on the planet, such as light-dark transitions, and adapt growth and development to these. This review looks back in history on how knowledge about the endogenous biological clock has been acquired over the centuries, with a focus on discoveries in plants. Key findings at the physiological, genetic and molecular level are described and the role of the circadian clock in important molecular processes is reviewed.

Long-term monitoring of bioluminescence circadian rhythms of cells in a transgenic Arabidopsis mesophyll protoplast culture

The circadian system of plants is based on the cell-autonomously oscillating circadian clock. In the plant body, these cellular clocks are associated with each other, but their basic and intrinsic properties are still largely unknown. Here we report a method that enables long-term monitoring of bioluminescence circadian rhythms of a protoplast culture in a complete synthetic medium. From the leaves of Arabidopsis transgenic plants carrying the luciferase gene under a clock-gene promoter, mesophyll protoplasts were isolated and their bioluminescence was automatically measured every 20 min for more than one week. Decreasing luminescence intensities were observed in protoplasts when they were cultured in a Murashige and Skoog-based medium and also in W5 solution. This decrease was dramatically improved by adding the phytohormones auxin and cytokinin to the MS-based medium; robust circadian rhythms were successfully monitored. Interestingly, the period lengths of bioluminescence circadian rhythms of protoplasts under constant conditions were larger than those of detached leaves, suggesting that the period lengths of mesophyll cells in leaves were modulated from their intrinsic properties by the influence of other tissues/cells. The entrainability of protoplasts to light/dark signals was clearly demonstrated by using this monitoring system. By analyzing the circadian behavior of isolated protoplasts, the basic circadian system of plant cells may be better understood.

Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression

The Arabidopsis circadian clock orchestrates gene regulation across the day/night cycle. Although a multiple feedback loop circuit has been shown to generate the 24-hr rhythm, it remains unclear how robust the clock is in individual cells, or how clock timing is coordinated across the plant. Here we examine clock activity at the single cell level across Arabidopsis seedlings over several days under constant environmental conditions. Our data reveal robust single cell oscillations, albeit desynchronised. In particular, we observe two waves of clock activity; one going down, and one up the root. We also find evidence of cell-to-cell coupling of the clock, especially in the root tip. A simple model shows that cell-to-cell coupling and our measured period differences between cells can generate the observed waves. Our results reveal the spatial structure of the plant clock and suggest that unlike the centralised mammalian clock, the Arabidopsis clock has multiple coordination points.

Preparation and applications of guard cell protoplasts from the leaf epidermis of Solanum lycopersicum

BACKGROUND

Guard cell protoplasts (GCPs) isolated from various plants have proven to be especially useful for studies of signal transduction pathways and plant development. But it is not easy to isolate highly purified preparations of large numbers of GCPs from plants. In this research, our focus is on a method to isolate large numbers of guard cells from tomato leaves. The protocols described yield millions of highly purified, viable GCPs, which are also suitable for studies on guard cell physiology.

RESULTS

We developed an efficient method for isolating GCPs from epidermal fragments of tomato leaves. The protocol requires a two-step digestion to isolate high-quality tomato GCPs. In this procedure, cellulysin (in method L) was replaced by cellulose "Onozuka" RS (in method S) in the first digestion step, which indicated that cellulase RS was more effective than cellulysin. Method S dramatically shortened the time required for obtaining high yields and high-quality GCPs. Moreover, according to the GCP yields, hydroponic plants were more effective than substrate-cultured plants.

CONCLUSIONS

In this paper, protocols for large-scale preparation of GCPs and mesophyll cell protoplasts were described, followed by some success examples of their use in biochemical and molecular approaches such as reverse-transcription polymerase chain reaction, real-time polymerase chain reaction and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The method was proved to be a more efficient GCP-isolating method, capable of providing high yields with better quality in less time.

Monitoring circadian rhythms of individual cells in plants

The circadian clock is an endogenous timing system based on the self-sustained oscillation in individual cells. These cellular circadian clocks compose a multicellular circadian system working at respective levels of tissue, organ, plant body. However, how numerous cellular clocks are coordinated within a plant has been unclear. There was little information about behavior of circadian clocks at a single-cell level due to the difficulties in monitoring circadian rhythms of individual cells in an intact plant. We developed a single-cell bioluminescence imaging system using duckweed as the plant material and succeeded in observing behavior of cellular clocks in intact plants for over a week. This imaging technique quantitatively revealed heterogeneous and independent manners of cellular clock behaviors. Furthermore, these quantitative analyses uncovered the local synchronization of cellular circadian rhythms that implied phase-attractive interactions between cellular clocks. The cell-to-cell interaction looked to be too weak to coordinate cellular clocks against their heterogeneity under constant conditions. On the other hand, under light-dark conditions, the heterogeneity of cellular clocks seemed to be corrected by cell-to-cell interactions so that cellular clocks showed a clear spatial pattern of phases at a whole plant level. Thus, it was suggested that the interactions between cellular clocks was an adaptive trait working under day-night cycles to coordinate cellular clocks in a plant body. These findings provide a novel perspective for understanding spatio-temporal architectures in the plant circadian system.

Sumoylation of the Plant Clock Transcription Factor CCA1 Suppresses DNA Binding

In plants, the circadian clock regulates the expression of one-third of all transcripts and is crucial to virtually every aspect of metabolism and growth. We now establish sumoylation, a posttranslational protein modification, as a novel regulator of the key clock protein CCA1 in the model plant Arabidopsis. Dynamic sumoylation of CCA1 is observed in planta and confirmed in a heterologous expression system. To characterize how sumoylation might affect the activity of CCA1, we investigated the properties of CCA1 in a wild-type plant background in comparison with ots1 ots2, a mutant background showing increased overall levels of sumoylation. Neither the localization nor the stability of CCA1 was significantly affected. However, binding of CCA1 to a target promoter was significantly reduced in chromatin-immunoprecipitation experiments. In vitro experiments using recombinant protein revealed that reduced affinity to the cognate promoter element is a direct consequence of sumoylation of CCA1 that does not require any other factors. Combined, these results suggest sumoylation as a mechanism that tunes the DNA binding activity of the central plant clock transcription factor CCA1.

Multicellularity enriches the entrainment of Arabidopsis circadian clock

The phase response curve (PRC) of the circadian clock provides one of the most significant indices for anticipating entrainment of outer cycles, despite the difficulty of making precise PRC determinations in experiments. We characterized the PRC of the Arabidopsisthaliana circadian clock on the basis of its phase-locking property to variable periodic pulse perturbations. Experiments revealed that the PRC changed remarkably from continuous to discontinuous fashion, depending on the oscillation amplitude. Our hypothesis of amplitude-dependent adaptability to outer cycles was successfully clarified by elucidation of this transition of PRC as a change in the collective response of the circadian oscillator network. These findings provide an essential criterion against which to evaluate the precision of PRC measurement and an advanced understanding of the adaptability of plant circadian systems to environmental conditions.

An Unstable Singularity Underlies Stochastic Phasing of the Circadian Clock in Individual Cyanobacterial Cells

The endogenous circadian clock synchronizes with environmental time by appropriately resetting its phase in response to external cues. Of note, some resetting stimuli induce attenuated oscillations of clock output, which has been observed at the population-level in several organisms and in studies of individual humans. To investigate what is happening in individual cellular clocks, we studied the unicellular cyanobacterium S. elongatus. By measuring its phase-resetting responses to temperature changes, we found that population-level arrhythmicity occurs when certain perturbations cause stochastic phases of oscillations in individual cells. Combining modeling with experiments, we related stochastic phasing to the dynamical structure of the cyanobacterial clock as an oscillator and explored the physiological relevance of the oscillator structure for accurately timed rhythmicity in changing environmental conditions. Our findings and approach can be applied to other biological oscillators.

Heterogeneity of cellular circadian clocks in intact plants and its correction under light-dark cycles

Recent advances in single-cell analysis have revealed the stochasticity and nongenetic heterogeneity inherent to cellular processes. However, our knowledge of the actual cellular behaviors in a living multicellular organism is still limited. By using a single-cell bioluminescence imaging technique on duckweed, Lemna gibba, we demonstrate that, under constant conditions, cells in the intact plant work as individual circadian clocks that oscillate with their own frequencies and respond independently to external stimuli. Quantitative analysis uncovered the heterogeneity and instability of cellular clocks and partial synchronization between neighboring cells. Furthermore, we found that cellular clocks in the plant body under light-dark cycles showed a centrifugal phase pattern in which the effect of cell-to-cell heterogeneity in period lengths was almost masked. The inherent heterogeneity in the properties of cellular clocks observed under constant conditions is corrected under light-dark cycles to coordinate the daily rhythms of the plant body. These findings provide a novel perspective of spatiotemporal architectures in the plant circadian system.

Tissue-specific circadian clocks in plants

Circadian clocks affect a large proportion of differentially expressed genes in many organisms. Tissue-specific hierarchies in circadian networks in mammals have been contentiously debated, whereas little attention has been devoted to the concept in plants, owing to technical difficulties. Recently, several studies have demonstrated tissue-specific circadian clocks and their coupling in plants, suggesting that plants possess a hierarchical network of circadian clocks. The following review summarizes recent studies describing the tissue-specific functions and properties of these circadian clocks and discusses the network structure and potential messengers that might share temporal information on such a network.

Preparation of Epidermal Peels and Guard Cell Protoplasts for Cellular, Electrophysiological, and -Omics Assays of Guard Cell Function

Bioassays are commonly used to study stomatal phenotypes. There are multiple options in the choice of plant materials and species used for observation of stomatal and guard cell responses in vivo. Here, detailed procedures for bioassays of stomatal responses to abscisic acid (ABA) in Arabidopsis thaliana are described, including ABA promotion of stomatal closure, ABA inhibition of stomatal opening, and ABA promotion of reaction oxygen species (ROS) production in guard cells. We also include an example of a stomatal bioassay for the guard cell CO2 response using guard cell-enriched epidermal peels from Brassica napus. Highly pure preparations of guard cell protoplasts can be produced, which are also suitable for studies on guard cell signaling, as well as for studies on guard cell ion transport. Small-scale and large-scale guard cell protoplast preparations are commonly used for electrophysiological and -omics studies, respectively. We provide a procedure for small-scale guard cell protoplasting from A. thaliana. Additionally, a general protocol for large-scale preparation of guard cell protoplasts, with specifications for three different species, A. thaliana, B. napus, and Vicia faba is also provided.

Decentralized circadian clocks process thermal and photoperiodic cues in specific tissues

The circadian clock increases organisms' fitness by regulating physiological responses(1). In mammals, the circadian clock in the suprachiasmatic nucleus (SCN) governs daily behavioural rhythms(2). Similarly, in Arabidopsis, tissue-specific circadian clock functions have emerged, and the importance of the vasculature clock for photoperiodic flowering has been demonstrated(3-5). However, it remains unclear if the vasculature clock regulates the majority of physiological responses, like the SCN in mammals, and if other environmental signals are also processed by the vasculature clock. Here, we studied the involvement of tissue-specific circadian clock regulation of flowering and cell elongation under different photoperiods and temperatures. We found that the circadian clock in vascular phloem companion cells is essential for photoperiodic flowering regulation; by contrast, the epidermis has a crucial impact on ambient temperature-dependent cell elongation. Thus, there are clear assignments of roles among circadian clocks in each tissue. Our results reveal that, unlike the more centralized circadian clock in mammals, the plant circadian clock is decentralized, where each tissue specifically processes individual environmental cues and regulates individual physiological responses. Our new conceptual framework will be a starting point for deciphering circadian clock functions in each tissue, which will lead to a better understanding of how circadian clock processing of environmental signals may be affected by ongoing climate change(6).

Dawn and Dusk Set States of the Circadian Oscillator in Sprouting Barley (Hordeum vulgare) Seedlings

The plant circadian clock is an internal timekeeper that coordinates biological processes with daily changes in the external environment. The transcript levels of clock genes, which oscillate to control circadian outputs, were examined during early seedling development in barley (Hordeum vulgare), a model for temperate cereal crops. Oscillations of clock gene transcript levels do not occur in barley seedlings grown in darkness or constant light but were observed with day-night cycles. A dark-to-light transition influenced transcript levels of some clock genes but triggered only weak oscillations of gene expression, whereas a light-to-dark transition triggered robust oscillations. Single light pulses of 6, 12 or 18 hours induced robust oscillations. The light-to-dark transition was the primary determinant of the timing of subsequent peaks of clock gene expression. After the light-to-dark transition the timing of peak transcript levels of clock gene also varied depending on the length of the preceding light pulse. Thus, a single photoperiod can trigger initiation of photoperiod-dependent circadian rhythms in barley seedlings. Photoperiod-specific rhythms of clock gene expression were observed in two week old barley plants. Changing the timing of dusk altered clock gene expression patterns within a single day, showing that alteration of circadian oscillator behaviour is amongst the most rapid molecular responses to changing photoperiod in barley. A barley EARLY FLOWERING3 mutant, which exhibits rapid photoperiod-insensitive flowering behaviour, does not establish clock rhythms in response to a single photoperiod. The data presented show that dawn and dusk cues are important signals for setting the state of the circadian oscillator during early development of barley and that the circadian oscillator of barley exhibits photoperiod-dependent oscillation states.

A comparison of high-throughput techniques for assaying circadian rhythms in plants

Over the last two decades, the development of high-throughput techniques has enabled us to probe the plant circadian clock, a key coordinator of vital biological processes, in ways previously impossible. With the circadian clock increasingly implicated in key fitness and signalling pathways, this has opened up new avenues for understanding plant development and signalling. Our tool-kit has been constantly improving through continual development and novel techniques that increase throughput, reduce costs and allow higher resolution on the cellular and subcellular levels. With circadian assays becoming more accessible and relevant than ever to researchers, in this paper we offer a review of the techniques currently available before considering the horizons in circadian investigation at ever higher throughputs and resolutions.

Characterisation of circadian rhythms of various duckweeds

The plant circadian clock controls various physiological phenomena that are important for adaptation to natural day-night cycles. Many components of the circadian clock have been identified in Arabidopsis thaliana, the model plant for molecular genetic studies. Recent studies revealed evolutionary conservation of clock components in green plants. Homologues of clock-related genes have been isolated from Lemna gibba and Lemna aequinoctialis, and it has been demonstrated that these homologues function in the clock system in a manner similar to their functioning in Arabidopsis. While clock components are widely conserved, circadian phenomena display diversity even within the Lemna genus. In order to survey the full extent of diversity in circadian rhythms among duckweed plants, we characterised the circadian rhythms of duckweed by employing a semi-transient bioluminescent reporter system. Using a particle bombardment method, circadian bioluminescent reporters were introduced into nine strains representing five duckweed species: Spirodela polyrhiza, Landoltia punctata, Lemna gibba, L. aequinoctialis and Wolffia columbiana. We then monitored luciferase (luc+) reporter activities driven by AtCCA1, ZmUBQ1 or CaMV35S promoters under entrainment and free-running conditions. Under entrainment, AtCCA1::luc+ showed similar diurnal rhythms in all strains. This suggests that the mechanism of biological timing under day-night cycles is conserved throughout the evolution of duckweeds. Under free-running conditions, we observed circadian rhythms of AtCCA1::luc+, ZmUBQ1::luc+ and CaMV35S::luc+. These circadian rhythms showed diversity in period length and sustainability, suggesting that circadian clock mechanisms are somewhat diversified among duckweeds.

Cell-type specific light-mediated transcript regulation in the multicellular alga Volvox carteri

BACKGROUND

The multicellular green alga Volvox carteri makes use of none less than 13 photoreceptors, which are mostly expressed in a cell-type specific manner. This gives reason to believe that trasncriptome pattern of each cell type could change differentially in response to environmental light. Here, the cell-type specific changes of various transcripts from different pathways in response to blue, red and far-red light were analyzed.

RESULTS

In response to different light qualities, distinct changes in transcript accumulation of genes encoding proteins involved in chlorophyll and carotenoid biosynthesis, light-harvesting complexes, circadian clock and cell cycle control were observed. Namely, blue light tends to be effective to accumulate transcripts in the somatic cells; while red light leads to accumulate transcripts predominantly in the reproductive cells. Blue light also induced marked accumulation of two components of circadian rhythms only in the somatic cells, indicating that these clock-relevant components are affected by blue light in a cell-type specific manner. Further, we show that photosynthetic associated genes are regulated distinctly among cell types by different light qualities.

CONCLUSION

Our results suggest that Volvox uses different sophisticated cell-type specific light signaling pathways to modulate expression of genes involved in various cellular and metabolic pathways including circadian rhythms and photosynthesis in response to environmental light.

Wheels within wheels: the plant circadian system

Circadian clocks integrate environmental signals with internal cues to coordinate diverse physiological outputs so that they occur at the most appropriate season or time of day. Recent studies using systems approaches, primarily in Arabidopsis, have expanded our understanding of the molecular regulation of the central circadian oscillator and its connections to input and output pathways. Similar approaches have also begun to reveal the importance of the clock for key agricultural traits in crop species. In this review, we discuss recent developments in the field, including a new understanding of the molecular architecture underlying the plant clock; mechanistic links between clock components and input and output pathways; and our growing understanding of the importance of clock genes for agronomically important traits.