Photosynthetic Entrainment of the Circadian Clock Facilitates Plant Growth under Environmental Fluctuations: Perspectives from an Integrated Model of Phase Oscillator and Phloem Transportation

Assessing the impacts of genetic defects on starch metabolism in Arabidopsis plants using the carbon homeostasis model

Starch serves as an important carbon storage mechanism for many plant species, facilitating their adaptation to the cyclic variations in the light environment, including day-night cycles as well as seasonal changes in photoperiod. By dynamically adjusting starch accumulation and degradation rates, plants maintain carbon homeostasis, enabling continuous growth under fluctuating environmental conditions. To understand dynamic nature of starch metabolism at the molecular level, it is necessary to integrate empirical knowledge from genetic defects in specific regulatory pathways into the dynamical system of starch metabolism. To achieve this, we evaluated the impact of genetic defects in the circadian clock, sugar sensing and starch degradation pathways using the carbon homeostasis model that encompasses the interplay between these pathways. Through the collection of starch metabolism data from 10 Arabidopsis mutants, we effectively fitted the experimental data to the model. The system-level assessment revealed that genetic defects in both circadian clock components and sugar sensing pathway hindered the appropriate adjustment of the starch degradation rate, particularly under long-day conditions. These findings not only confirmed the previous empirical findings but also provide the novel insights into the role of each gene within the gene regulatory network on the emergence of carbon homeostasis.

Arabidopsis cryptochrome 2 forms photobodies with TCP22 under blue light and regulates the circadian clock

Cryptochromes are blue light receptors that regulate plant growth and development. They also act as the core components of the central clock oscillator in animals. Although plant cryptochromes have been reported to regulate the circadian clock in blue light, how they do so is unclear. Here we show that Arabidopsis cryptochrome 2 (CRY2) forms photobodies with the TCP22 transcription factor in response to blue light in plant cells. We provide evidence that PPK kinases influence the characteristics of these photobodies and that together these components, along with LWD transcriptional regulators, can positively regulate the expression of CCA1 encoding a central component of the circadian oscillator.

Cryptochrome signaling has been reported to regulate circadian oscillations in plants. Here the authors show that CRY2 and the TCP22 transcription factors can form photobodies in a blue light dependent manner and induce expression of CCA1, a core component of the circadian oscillator.

Daily Regulation of Key Metabolic Pathways in Two Seagrasses Under Natural Light Conditions

The circadian clock is an endogenous time-keeping mechanism that enables organisms to adapt to external environmental cycles. It produces rhythms of plant metabolism and physiology, and interacts with signaling pathways controlling daily and seasonal environmental responses through gene expression regulation. Downstream metabolic outputs, such as photosynthesis and sugar metabolism, besides being affected by the clock, can also contribute to the circadian timing itself. In marine plants, studies of circadian rhythms are still way behind in respect to terrestrial species, which strongly limits the understanding of how they coordinate their physiology and energetic metabolism with environmental signals at sea. Here, we provided a first description of daily timing of key core clock components and clock output pathways in two seagrass species, Cymodocea nodosa and Zostera marina (order Alismatales), co-occurring at the same geographic location, thus exposed to identical natural variations in photoperiod. Large differences were observed between species in the daily timing of accumulation of transcripts related to key metabolic pathways, such as photosynthesis and sucrose synthesis/transport, highlighting the importance of intrinsic biological, and likely ecological attributes of the species in determining the periodicity of functions. The two species exhibited a differential sensitivity to light-to-dark and dark-to-light transition times and could adopt different growth timing based on a differential strategy of resource allocation and mobilization throughout the day, possibly coordinated by the circadian clock. This behavior could potentially derive from divergent evolutionary adaptations of the species to their bio-geographical range of distributions.

Physiological and Expressional Regulation on Photosynthesis, Starch and Sucrose Metabolism Response to Waterlogging Stress in Peanut

Waterlogging has negative effects on crop yield. Physiological and transcriptome data of two peanut cultivars [Zhongkaihua 1 (ZKH 1) and Huayu 39 (HY 39)] were studied under normal water supply and waterlogging stress for 5 or 10 days at the flowering stage. The results showed that the main stem height, the number of lateral branches, lateral branch length, and the stem diameter increased under waterlogging stress, followed by an increase in dry matter accumulation, which was correlated with the increase in the soil and plant analysis development (SPAD) and net photosynthetic rate (Pn) and the upregulation of genes related to porphyrin and chlorophyll metabolism and photosynthesis. However, the imbalance of the source-sink relationship under waterlogging was the main cause of yield loss, and waterlogging caused an increase in the sucrose and soluble sugar contents and a decrease in the starch content; it also decreased the activities of sucrose synthetase (SS) and sucrose phosphate synthetase (SPS), which may be due to the changes in the expression of genes related to starch and sucrose metabolism. However, the imbalance of the source-sink relationship led to the accumulation of photosynthate in the stems and leaves, which resulted in the decrease of the ratio of pod dry weight to total dry weight (PDW/TDW) and yield. Compared with ZKH 1, the PDW of HY 39 decreased more probably because more photosynthate accumulated in the stem and leaves of HY 39 and could not be effectively transported to the pod.

Arabidopsis FAR-RED ELONGATED HYPOCOTYL3 negatively regulates carbon starvation responses

Light is one of the most important environmental factors that affects various cellular processes in plant growth and development; it is also crucial for the metabolism of carbohydrates as it provides the energy source for photosynthesis. Under extended darkness conditions, carbon starvation responses are triggered by depletion of stored energy. Although light rapidly inhibits starvation responses, the molecular mechanisms by which light signalling affects this process remain largely unknown. In this study, we showed that the Arabidopsis thaliana light signalling protein FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1) are essential for plant survival after extended darkness treatment at both seedling and adult stages. Transmission electron microscopy analyses revealed that disruption of both FHY3 and FAR1 resulted in destruction of chloroplast envelopes and thylakoid membranes under extended darkness conditions. Furthermore, treatment with sucrose, but not glucose, completely rescued carbon starvation-induced cell death in the rosette leaves and arrested early seedling establishment in the fhy3 far1 plants. We thus concluded that the light signalling proteins FHY3 and FAR1 negatively regulate carbon starvation responses in Arabidopsis.

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.

Photoperiod-dependent transcriptional modifications in key metabolic pathways in Coffea arabica

Photoperiod length induces in temperate plants major changes in growth rates, morphology and metabolism with, for example, modifications in the partitioning of photosynthates to avoid starvation at the end of long nights. However, this has never been studied for a tropical perennial species adapted to grow in a natural photoperiod close to 12 h/12 h all year long. We grew Coffea arabica L., an understorey perennial evergreen tropical species in its natural 12 h/12 h and in a short 8 h/16 h photoperiod, and we investigated its responses at the physiological, metabolic and transcriptomic levels. The expression pattern of rhythmic genes, including core clock genes, was affected by changes in photoperiod. Overall, we identified 2859 rhythmic genes, of which 89% were also rhythmic in Arabidopsis thaliana L. Under short-days, plant growth was reduced, and leaves were thinner with lower chlorophyll content. In addition, secondary metabolism was also affected with chlorogenic acid and epicatechin levels decreasing, and in agreement, the genes involved in lignin synthesis were overexpressed and those involved in the flavanol pathway were underexpressed. Our results show that the 8 h/16 h photoperiod induces drastic changes in morphology, metabolites and gene expression, and the responses for gene expression are similar to those observed in the temperate annual A. thaliana species. Short photoperiod induces drastic changes in gene expression, metabolites and leaf structure, some of these responses being similar to those observed in A. thaliana.

Effect of Light/Dark Cycle on Photosynthetic Pathway Switching and CO2 Absorption in Two Dendrobium Species

Many Dendrobium species are both ornamental and medicinal plants in China. Several wild species have been exploited to near extinction, and facility cultivation has become an important way to meet the great market demand. Most Dendrobium species have evolved into crassulacean acid metabolism (CAM) pathways in adapting to harsh epiphytic environment, leading to low daily net CO₂ absorption. Photosynthetic pathways of many facultative CAM plants are regulated by various environmental factors. Light/dark cycle plays an important role in regulating the photosynthetic pathway of several CAM species. The aims of this study were to investigate whether the photosynthetic pathway of Dendrobium species could be regulated between C3 and CAM by changing light/dark cycles and the daily net CO₂ absorption could be enhanced by shortening light/dark cycle. In this study, net CO₂ exchange rates of D. officinale and D. primulinum were monitored continuously during two different light/dark cycles conversion compared to Kalanchoe daigremontiana as an obligate CAM plant. The net CO₂ exchange pattern and stomatal behavior of D. officinale and D. primulinum were switched from CAM to C3-like by changing the light/dark cycle from 12/12 h to 4/4 h. However, this switching was not completely reversible. Compared to the original 12/12 h light/dark cycle, the dark, light, and daily net CO₂ exchange amount of D. officinale were significantly increased after the light/dark cycle was changed from 4/4 h to 12/12 h, but those in D. primulinum was opposite and those in K. daigremontiana was not affected. Daily net CO₂ exchange amount of D. officinale increased by 47% after the light/dark cycle was changed from 12/12 h to 4/4 h, due to the sharp increase of light net CO₂ exchange amount. However, the large decrease of dark net CO₂ exchange amount could not be offset by increased light net CO₂ exchange amount, leading to reduced daily net CO₂ exchange amount of D. primulinum. In conclusion, the 4/4 h light/dark cycle can induce the photosynthetic pathway of D. officinale and D. primulinum to C3-like, and improve the daily CO₂ absorption of D. officinale.

Using a Mathematical Model of Phloem Transport to Optimize Strategies for Crop Improvement

It is valuable to set an ideotype plant structure (i.e., ideal numbers and arrangement of sucrose sources, sinks, and pathways that maximize crop yield) as a goal for breeding with modern and near-future technologies. However, it is not easy to theoretically specify an ideotype because multiple factors need to be considered simultaneously. Here a method to obtain plant ideotypes using a simple mathematical model is described. The model identifies plant structures with maximal yield through a series of simulations of the dynamic changes in sucrose concentration at different positions of the plant. Originally developed for rice, this revised method can be applied to a wide range of crop plants.

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.

Acclimation to Fluctuating Light Impacts the Rapidity of Response and Diurnal Rhythm of Stomatal Conductance

Plant acclimation to growth light environment has been studied extensively; however, the majority of these studies have focused on light intensity and photo-acclimation, with few studies exploring the impact of dynamic growth light on stomatal acclimation and behavior. To assess the impact of growth light regime on stomatal acclimation, we grew Arabidopsis (Arabidopsis thaliana) plants in three different lighting regimes (with the same average daily intensity), fluctuating with a fixed pattern of light, fluctuating with a randomized pattern of light (sinusoidal), and nonfluctuating (square wave), to assess the effect of light regime dynamics on gas exchange. We demonstrated that gs (stomatal conductance to water vapor) acclimation is influenced by both intensity and light pattern, modifying the stomatal kinetics at different times of the day and resulting in differences in the rapidity and magnitude of the gs response. We also describe and quantify the response to an internal signal that uncouples variation in A and gs over the majority of the diurnal period and represents 25% of the total diurnal gs This gs response can be characterized by a Gaussian element and when incorporated into the widely used Ball-Berry model greatly improved the prediction of gs in a dynamic environment. From these findings, we conclude that acclimation of gs to growth light could be an important strategy for maintaining carbon fixation and overall plant water status and should be considered when inferring responses in the field from laboratory-based experiments.