Phase response of the Arabidopsis thaliana circadian clock to light pulses of different wavelengths

Application of time lags between light and temperature cycles for growth control based on the circadian clock of Lactuca sativa L. seedlings

The circadian clock plays an important role in agriculture, especially in highly controlled environments, such as plant factories. However, multiple environmental factors have an extremely high degree of freedom, and it is difficult to experimentally search for the optimal design conditions. A recent study demonstrated that the effect of time lags between light and temperature cycles on plant growth could be predicted by the entrainment properties of the circadian clock in Arabidopsis thaliana. Based on this prediction, it was possible to control plant growth by adjusting the time lag. However, for application in plant factories, it is necessary to verify the effectiveness of this method using commercial vegetables, such as leaf lettuce. In this study, we investigated the entrainment properties of the circadian clock and the effect of the time lag between light and temperature cycles on circadian rhythms and plant growth in Lactuca sativa L. seedlings. For evaluation of circadian rhythms, we used transgenic L. sativa L. with a luciferase reporter in the experiment and a phase oscillator model in the simulation. We found that the entrainment properties for the light and temperature stimuli and the effects of time lags on circadian rhythm and growth were similar to those of A. thaliana. Moreover, we demonstrated that changes in growth under different time lags could be predicted by simulation based on the entrainment properties of the circadian clock. These results showed the importance of designing a cultivation environment that considers the circadian clock and demonstrated a series of methods to achieve this.

Variations in Circadian Clock Organization & Function: A Journey from Ancient to Recent

Circadian clock components exhibit structural variations in different plant systems, and functional variations during various abiotic stresses. These variations bear relevance for plant fitness and could be important evolutionarily. All organisms on earth have the innate ability to measure time as diurnal rhythms that occur due to the earth's rotations in a 24-h cycle. Circadian oscillations arising from the circadian clock abide by its fundamental properties of periodicity, entrainment, temperature compensation, and oscillator mechanism, which is central to its function. Despite the fact that a myriad of research in Arabidopsis thaliana illuminated many detailed aspects of the circadian clock, many more variations in clock components' organizations and functions remain to get deciphered. These variations are crucial for sustainability and adaptation in different plant systems in the varied environmental conditions in which they grow. Together with these variations, circadian clock functions differ drastically even during various abiotic and biotic stress conditions. The present review discusses variations in the organization of clock components and their role in different plant systems and abiotic stresses. We briefly introduce the clock components, entrainment, and rhythmicity, followed by the variants of the circadian clock in different plant types, starting from lower non-flowering plants, marine plants, dicots to the monocot crop plants. Furthermore, we discuss the interaction of the circadian clock with components of various abiotic stress pathways, such as temperature, light, water stress, salinity, and nutrient deficiency with implications for the reprogramming during these stresses. We also update on recent advances in clock regulations due to post-transcriptional, post-translation, non-coding, and micro-RNAs. Finally, we end this review by summarizing the points of applicability, a remark on the future perspectives, and the experiments that could clear major enigmas in this area of research.

Modelling of plant circadian clock for characterizing hypocotyl growth under different light quality conditions

To meet the ever-increasing global food demand, the food production rate needs to be increased significantly in the near future. Speed breeding is considered as a promising agricultural technology solution to achieve the zero-hunger vision as specified in the United Nations Sustainable Development Goal 2. In speed breeding, the photoperiod of the artificial light has been manipulated to enhance crop productivity. In particular, regulating the photoperiod of different light qualities rather than solely white light can further improve speed breading. However, identifying the optimal light quality and the associated photoperiod simultaneously remains a challenging open problem due to complex interactions between multiple photoreceptors and proteins controlling plant growth. To tackle this, we develop a first comprehensive model describing the profound effect of multiple light qualities with different photoperiods on plant growth (i.e. hypocotyl growth). The model predicts that hypocotyls elongated more under red light compared to both red and blue light. Drawing similar findings from previous related studies, we propose that this might result from the competitive binding of red and blue light receptors, primarily Phytochrome B (phyB) and Cryptochrome 1 (cry1) for the core photomorphogenic regulator, CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). This prediction is validated through an experimental study on Arabidopsis thaliana. Our work proposes a potential molecular mechanism underlying plant growth under different light qualities and ultimately suggests an optimal breeding protocol that takes into account light quality.

Time Lag Between Light and Heat Diurnal Cycles Modulates CIRCADIAN CLOCK ASSOCIATION 1 Rhythm and Growth in Arabidopsis thaliana

Plant growth responses to cues such as light, temperature, and humidity enable the entrainment of the circadian rhythms with diurnal cycles. For example, the temperature variations between day and night affect plant growth and accompany the time lag to light cycle. Despite its importance, there has been no systematic investigation into time lags, and the mechanisms behind the entrainment of the circadian rhythms with multiple cycles remain unknown. Here, we investigated systemically the effects of the time lag on the circadian rhythm and growth in Arabidopsis thaliana. To investigate the entrainment status of the circadian clock, the rhythm of the clock gene CIRCADIAN CLOCK ASSOCIATION 1 (CCA1) was measured with a luciferase reporter assay. As a result, the rhythm was significantly modulated by the time lag with +10°C heating for 4 h every day but not -10°C cooling. A model based on coupled cellular oscillators successfully described these rhythm modulations. In addition, seedling growth depended on the time lag of the heating cycle but not that of the cooling cycle. Based on the relationship between the CCA1 rhythms and growth, we established an estimation method for the effects of the time lag. Our results found that plant growth relates to the CCA1 rhythm and provides a method by which to estimate the appropriate combination of light-dark and temperature cycles.

The singularity response reveals entrainment properties of the plant circadian clock

Circadian clocks allow organisms to synchronize their physiological processes to diurnal variations. A phase response curve allows researchers to understand clock entrainment by revealing how signals adjust clock genes differently according to the phase in which they are applied. Comprehensively investigating these curves is difficult, however, because of the cost of measuring them experimentally. Here we demonstrate that fundamental properties of the curve are recoverable from the singularity response, which is easily measured by applying a single stimulus to a cellular network in a desynchronized state (i.e. singularity). We show that the singularity response of Arabidopsis to light/dark and temperature stimuli depends on the properties of the phase response curve for these stimuli. The measured singularity responses not only allow the curves to be precisely reconstructed but also reveal organ-specific properties of the plant circadian clock. The method is not only simple and accurate, but also general and applicable to other coupled oscillator systems as long as the oscillators can be desynchronized. This simplified method may allow the entrainment properties of the circadian clock of both plants and other species in nature.

Phase response curves reveal how biological clocks respond to stimuli applied during different circadian phases but can be costly to produce. Here Masuda et al. show that phase response curves for plants can be reconstructed by monitoring how a desynchronized population responds to a single stimulus.

Thermal adaptation and plasticity of the plant circadian clock

Contents Summary 1215 I. Introduction 1215 II. Molecular organization of the plant circadian clock 1216 III. Temperature compensation 1219 IV. Temperature regulation of circadian behaviors 1220 V. Thermal adaptation of the clock: evolutionary considerations 1223 VI. Light and temperature information for the clock function - synergic or individual? 1224 VII. Concluding remarks and future prospects 1225 Acknowledgements 1225 References 1225 SUMMARY: Plant growth and development is widely affected by diverse temperature conditions. Although studies have been focused mainly on the effects of stressful temperature extremes in recent decades, nonstressful ambient temperatures also influence an array of plant growth and morphogenic aspects, a process termed thermomorphogenesis. Notably, accumulating evidence indicates that both stressful and nonstressful temperatures modulate the functional process of the circadian clock, a molecular timer of biological rhythms in higher eukaryotes and photosynthetic prokaryotes. The circadian clock can sustain robust and precise timing over a range of physiological temperatures. Genes and molecular mechanisms governing the temperature compensation process have been explored in different plant species. In addition, a ZEITLUPE/HSP90-mediated protein quality control mechanism helps plants maintain the thermal stability of the clock under heat stress. The thermal adaptation capability and plasticity of the clock are of particular interest in view of the growing concern about global climate changes. Considering these circumstances in the field, we believe that it is timely to provide a provoking discussion on the current knowledge of temperature regulation of the clock function. The review also will discuss stimulating ideas on this topic along with ecosystem management and future agricultural innovation.

Describing dynamics of driven multistable oscillators with phase transfer curves

Phase response curve is an important tool in the studies of stable self-sustained oscillations; it describes a phase shift under action of an external perturbation. We consider multistable oscillators with several stable limit cycles. Under a perturbation, transitions from one oscillating mode to another one may occur. We define phase transfer curves to describe the phase shifts at such transitions. This allows for a construction of one-dimensional maps that characterize periodically kicked multistable oscillators. We show that these maps are good approximations of the full dynamics for large periods of forcing.

Gene regulatory network models in response to sugars in the plant circadian system

Circadian entrainment is the process by which internal circadian oscillators staying in synchronization with the local environmental rhythms. Circadian clocks are entrained by adjusting phase and period in response to environmental and metabolic signals. In Arabidopsis thaliana, light and sugar signals differentially affect the circadian phase; the former advances the phase in the late of the subjective night and delays around dusk, while the latter advances the phase mainly in the morning, which is optimal to maintain sucrose homeostasis. We have proposed that the phase adjustment of the A. thaliana circadian oscillator by sugar signals contributes to the realization of carbon homeostasis and the increase of plant growth under fluctuating day-night cycles. However, which genes in the circadian oscillator are targets of sucrose signals and how the potential target genes should be regulated by sucrose to realize sucrose homeostasis has not been studied from the theoretical perspective. Here we investigate the effect of sugar on the phase response property of the plant circadian oscillator using clock gene-regulatory network models. We simulated phase response curves (PRCs) to sucrose pulses, which were compared with an experimental PRC. Our analyses of the gene-regulatory network model demonstrated that target genes of the sugar signal could be members of the PSEUDO-RESPONSE REGULATOR gene family and the evening complex components. We also examined the phase response property using a single feedback-loop model and elucidated how phase advance is induced in the subjective morning under certain conditions of a target clock gene of sucrose and its regulatory property.

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.

Learning by Association in Plants

In complex and ever-changing environments, resources such as food are often scarce and unevenly distributed in space and time. Therefore, utilizing external cues to locate and remember high-quality sources allows more efficient foraging, thus increasing chances for survival. Associations between environmental cues and food are readily formed because of the tangible benefits they confer. While examples of the key role they play in shaping foraging behaviours are widespread in the animal world, the possibility that plants are also able to acquire learned associations to guide their foraging behaviour has never been demonstrated. Here we show that this type of learning occurs in the garden pea, Pisum sativum. By using a Y-maze task, we show that the position of a neutral cue, predicting the location of a light source, affected the direction of plant growth. This learned behaviour prevailed over innate phototropism. Notably, learning was successful only when it occurred during the subjective day, suggesting that behavioural performance is regulated by metabolic demands. Our results show that associative learning is an essential component of plant behaviour. We conclude that associative learning represents a universal adaptive mechanism shared by both animals and plants.

High-Throughput Growth Prediction for Lactuca sativa L. Seedlings Using Chlorophyll Fluorescence in a Plant Factory with Artificial Lighting

Poorly grown plants that result from differences in individuals lead to large profit losses for plant factories that use large electric power sources for cultivation. Thus, identifying and culling the low-grade plants at an early stage, using so-called seedlings diagnosis technology, plays an important role in avoiding large losses in plant factories. In this study, we developed a high-throughput diagnosis system using the measurement of chlorophyll fluorescence (CF) in a commercial large-scale plant factory, which produces about 5000 lettuce plants every day. At an early stage (6 days after sowing), a CF image of 7200 seedlings was captured every 4 h on the final greening day by a high-sensitivity CCD camera and an automatic transferring machine, and biological indices were extracted. Using machine learning, plant growth can be predicted with a high degree of accuracy based on biological indices including leaf size, amount of CF, and circadian rhythms in CF. Growth prediction was improved by addition of temporal information on CF. The present data also provide new insights into the relationships between growth and temporal information regulated by the inherent biological clock.

An extended mathematical model for reproducing the phase response of Arabidopsis thaliana under various light conditions

Experimental studies showed that light qualities such as color and strength influence the phase response properties of plant circadian systems. These effects, however, have yet to be properly addressed in theoretical models of plant circadian systems. To fill this gap, the present paper develops a mathematical model of a plant circadian clock that takes into account the intensity and wavelength of the input light. Based on experimental knowledge, we model three photoreceptors, Phytochrome A, Phytochrome B, and Cryptochrome 1, which respond to red and/or blue light, in Arabidopsis thaliana. The three photoreceptors are incorporated into a standard mathematical model of the plant system, in which activator and repressor genes form a single feedback loop. The model capability is examined by a phase response curve (PRC), which plots the phase shifts elicited by the light perturbation as a function of the perturbation phase. Numerical experiments demonstrate that the extended model reproduces the essential features of the PRCs measured experimentally under various light conditions. Particularly, unlike conventional models, the model generates the inherent shape of the PRC under dark pulse stimuli. The outcome of our modeling approach may motivate future theoretical and experimental studies of plant circadian rhythms.