Ambient temperature signal feeds into the circadian clock transcriptional circuitry through the EC night-time repressor in Arabidopsis thaliana

Decoding the plant clock: a review of mathematical models for the circadian regulatory network

Most organisms have evolved specific mechanisms to respond to changes in environmental conditions such as light and temperature over the course of day. These periodic changes in the physiology and behaviour of organisms, referred to as circadian rhythms, are a consequence of intricate molecular mechanisms in the form of transcription and translational feedback loops. The plant circadian regulatory network is a complex web of interconnected feedback loops involving various transcription factors such as CCA1, LHY, PRRs, TOC1, LUX, ELF3, ELF4, RVE8, and more. This network enables plants to adapt and thrive in diverse environmental conditions. It responds to entrainment signals, including light, temperature, and nutrient concentrations and interacts with most of the physiological functions such as flowering, growth and stress response. Mathematical modelling of these gene regulatory networks enables a deeper understanding of not only the function but also the perturbations that may affect the plant growth and function with changing climate. Over the years, numerous mathematical models have been developed to understand the diverse aspects of plant circadian regulation. In this review, we have delved into the systematic development of these models, outlining the model components and refinements over time. We have also highlighted strengths and limitations of each of the models developed so far. Finally, we conclude the review by describing the prospects for investigation and advancement of these models for better understanding of plant circadian regulation.

Circadian and environmental signal integration in a natural population of Arabidopsis

Plants sense and respond to environmental cues during 24 h fluctuations in their environment. This requires the integration of internal cues such as circadian timing with environmental cues such as light and temperature to elicit cellular responses through signal transduction. However, the integration and transduction of circadian and environmental signals by plants growing in natural environments remains poorly understood. To gain insights into 24 h dynamics of environmental signaling in nature, we performed a field study of signal transduction from the nucleus to chloroplasts in a natural population of Arabidopsis halleri. Using several modeling approaches to interpret the data, we identified that the circadian clock and temperature are key regulators of this pathway under natural conditions. We identified potential time-delay steps between pathway components, and diel fluctuations in the response of the pathway to temperature cues that are reminiscent of the process of circadian gating. We found that our modeling framework can be extended to other signaling pathways that undergo diel oscillations and respond to environmental cues. This approach of combining studies of gene expression in the field with modeling allowed us to identify the dynamic integration and transduction of environmental cues, in plant cells, under naturally fluctuating diel cycles.

The phytochrome-interacting factor genes PIF1 and PIF4 are functionally diversified due to divergence of promoters and proteins

Phytochrome-interacting factors (PIFs) are basic helix-loop-helix transcription factors that regulate light responses downstream of phytochromes. In Arabidopsis (Arabidopsis thaliana), 8 PIFs (PIF1-8) regulate light responses, either redundantly or distinctively. Distinctive roles of PIFs may be attributed to differences in mRNA expression patterns governed by promoters or variations in molecular activities of proteins. However, elements responsible for the functional diversification of PIFs have yet to be determined. Here, we investigated the role of promoters and proteins in the functional diversification of PIF1 and PIF4 by analyzing transgenic lines expressing promoter-swapped PIF1 and PIF4, as well as chimeric PIF1 and PIF4 proteins. For seed germination, PIF1 promoter played a major role, conferring dominance to PIF1 gene with a minor contribution from PIF1 protein. Conversely, for hypocotyl elongation under red light, PIF4 protein was the major element conferring dominance to PIF4 gene with the minor contribution from PIF4 promoter. In contrast, both PIF4 promoter and PIF4 protein were required for the dominant role of PIF4 in promoting hypocotyl elongation at high ambient temperatures. Together, our results support that the functional diversification of PIF1 and PIF4 genes resulted from contributions of both promoters and proteins, with their relative importance varying depending on specific light responses.

A warm temperature-released negative feedback loop fine-tunes PIF4-mediated thermomorphogenesis in Arabidopsis

Plants can sense temperature changes and adjust their growth accordingly. In Arabidopsis, high ambient temperatures stimulate stem elongation by activating a key thermoresponsive regulator, PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Here, we show that warmth promotes the nighttime transcription of GI, which is necessary for the high temperature-induced transcription of TOC1. Genetic analyses suggest that GI prevents excessive thermoresponsive growth by inhibiting PIF4, with this regulatory mechanism being partially reliant on TOC1. GI transcription is repressed by ELF3 and HY5, which concurrently inhibit PIF4 expression and activity. Temperature elevation causes the deactivation or degradation of ELF3 and HY5, leading to PIF4 activation and relief of GI transcriptional repression at high temperatures. This allows PIF4 to further activate GI transcription in response to elevated temperatures. GI, in turn, inhibits PIF4, establishing a negative feedback loop that fine-tunes PIF4 activity. In addition, we demonstrate that ELF3, HY5, and PIF4 regulate GI transcription by modulating the enrichment of histone variant H2A.Z at the GI locus. Together, our findings suggest that thermal release of a negative feedback loop finely adjusts plant thermomorphogenesis.

euAP2a, a key gene that regulates flowering time in peach (Prunus persica) by modulating thermo-responsive transcription programming

Frequent spring frost damage threatens temperate fruit production, and breeding of late-flowering cultivars is an effective strategy for preventing such damage. However, this effort is often hampered by the lack of specific genes and markers and a lack of understanding of the mechanisms. We examined a Late-Flowering Peach (LFP) germplasm and found that its floral buds require a longer chilling period to release from their dormancy and a longer warming period to bloom than the control cultivar, two key characteristics associated with flowering time. We discovered that a 983-bp deletion in euAP2a, an APETALA2 (AP2)-related gene with known roles in regulating floral organ identity and flowering time, was primarily responsible for late flowering in LFP. This deletion disrupts an miR172 binding site, resulting in a gain-of-function mutation in euAP2a. Transcriptomic analyses revealed that at different stages of floral development, two chilling-responsive modules and four warm-responsive modules, comprising approximately 600 genes, were sequentially activated, forming a unique transcription programming. Furthermore, we found that euAP2a was transiently downregulated during the activation of these thermal-responsive modules at various stages. However, the loss of such transient, stage-specific downregulation of euAP2a caused by the deletion of miR172 binding sites resulted in the deactivation or delay of these modules in the LFP flower buds, suggesting that euAP2a acts as a transcription repressor to control floral developmental pace in peaches by modulating the thermo-responsive transcription programming. The findings shed light on the mechanisms behind late flowering in deciduous fruit trees, which is instrumental for breeding frost-tolerant cultivars.

The interplay between the circadian clock and abiotic stress responses mediated by ABF3 and CCA1/LHY

Climate change is a global concern for all life on our planet, including humans and plants. Plants' growth and development are significantly affected by abiotic stresses, including adverse temperature, inadequate or excess water availability, nutrient deficiency, and salinity. The circadian clock is a master regulator of numerous developmental and metabolic processes in plants. In an effort to identify new clock-related genes and outputs through bioinformatic analysis, we have revealed that CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) play a crucial role in regulating a wide range of abiotic stress responses and target ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING FACTOR3 (ABF3), a key transcription factor in the plant hormone Abscisic acid (ABA)-signaling pathway. Specifically, we found that CCA1 and LHY regulate the expression of ABF3 under diel conditions, as well as seed germination under salinity. Conversely, ABF3 controls the expression of core clock genes and orchestrates the circadian period in a stress-responsive manner. ABF3 delivers the stress signal to the central oscillator by binding to the promoter of CCA1 and LHY. Overall, our study uncovers the reciprocal regulation between ABF3 and CCA1/LHY and molecular mechanisms underlying the interaction between the circadian clock and abiotic stress. This finding may aid in developing molecular and genetic solutions for plants to survive and thrive in the face of climate change.

early maturity 7 promotes early flowering by controlling the light input into the circadian clock in barley

Breeding for variation in photoperiod response is crucial to adapt crop plants to various environments. Plants measure changes in day length by the circadian clock, an endogenous timekeeper that allows plants to anticipate changes in diurnal and seasonal light-dark cycles. Here, we describe the early maturity 7 (eam7) locus in barley (Hordeum vulgare), which interacts with PHOTOPERIOD 1 (Ppd-H1) to cause early flowering under non-inductive short days. We identify LIGHT-REGULATED WD 1 (LWD1) as a putative candidate to underlie the eam7 locus in barley as supported by genetic mapping and CRISPR-Cas9-generated lwd1 mutants. Mutations in eam7 cause a significant phase advance and a misregulation of core clock and clock output genes under diurnal conditions. Early flowering was linked to an upregulation of Ppd-H1 during the night and consequent induction of the florigen FLOWERING LOCUS T1 under short days. We propose that EAM7 controls photoperiodic flowering in barley by controlling the light input into the clock and diurnal expression patterns of the major photoperiod response gene Ppd-H1.

GIGANTEA Unveiled: Exploring Its Diverse Roles and Mechanisms

GIGANTEA (GI) is a conserved nuclear protein crucial for orchestrating the clock-associated feedback loop in the circadian system by integrating light input, modulating gating mechanisms, and regulating circadian clock resetting. It serves as a core component which transmits blue light signals for circadian rhythm resetting and overseeing floral initiation. Beyond circadian functions, GI influences various aspects of plant development (chlorophyll accumulation, hypocotyl elongation, stomatal opening, and anthocyanin metabolism). GI has also been implicated to play a pivotal role in response to stresses such as freezing, thermomorphogenic stresses, salinity, drought, and osmotic stresses. Positioned at the hub of complex genetic networks, GI interacts with hormonal signaling pathways like abscisic acid (ABA), gibberellin (GA), salicylic acid (SA), and brassinosteroids (BRs) at multiple regulatory levels. This intricate interplay enables GI to balance stress responses, promoting growth and flowering, and optimize plant productivity. This review delves into the multifaceted roles of GI, supported by genetic and molecular evidence, and recent insights into the dynamic interplay between flowering and stress responses, which enhance plants' adaptability to environmental challenges.

Environmental F actors coordinate circadian clock function and rhythm to regulate plant development

Changes in the external environment necessitate plant growth plasticity, with environmental signals such as light, temperature, and humidity regulating growth and development. The plant circadian clock is a biological time keeper that can be "reset" to adjust internal time to changes in the external environment. Exploring the regulatory mechanisms behind plant acclimation to environmental factors is important for understanding how plant growth and development are shaped and for boosting agricultural production. In this review, we summarize recent insights into the coordinated regulation of plant growth and development by environmental signals and the circadian clock, further discussing the potential of this knowledge.

A Small-Molecule Modulator Affecting the Clock-Associated PSEUDO-RESPONSE REGULATOR 7 Amount

Circadian clocks are biological timekeeping systems that coordinate genetic, metabolic and physiological behaviors with the external day-night cycle. The clock in plants relies on the transcriptional-translational feedback loops transcription-translation feedback loop (TTFL), consisting of transcription factors including PSUEDO-RESPONSE REGULATOR (PRR) proteins, plant lineage-specific transcriptional repressors. Here, we report that a novel synthetic small-molecule modulator, 5-(3,4-dichlorophenyl)-1-phenyl-1,7-dihydro-4H-pyrazolo[3,4-d] pyrimidine-4,6(5H)-dione (TU-892), affects the PRR7 protein amount. A clock reporter line of Arabidopsis was screened against the 10,000 small molecules in the Maybridge Hitfinder 10K chemical library. This screening identified TU-892 as a period-lengthening molecule. Gene expression analyses showed that TU-892 treatment upregulates CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) mRNA expression. TU-892 treatment reduced the amount of PRR7 protein, a transcriptional repressor of CCA1. Other PRR proteins including TIMING OF CAB EXPRESSION 1 were altered less by TU-892 treatment. TU-892-dependent CCA1 upregulation was attenuated in mutants impaired in PRR7. Collectively, TU-892 is a novel type of clock modulator that reduces the levels of PRR7 protein.

Clarifying the Temporal Dynamics of the Circadian Clock and Flowering Gene Network Using Overexpression and Targeted Mutagenesis of Soybean EARLY FLOWERING 3-1 ( GmELF3-1 )

With progressing climate fluctuations, an understanding of the molecular mechanisms of crop plants that regulate their flowering responses to environments is crucial. To achieve this goal, we aimed at clarifying the gene regulatory networks among the circadian clock and flowering genes in soybean ( Glycine max ). Based on our network inference approach , we hypothesize that GmELF3-1 , one of the Evening Complex (EC) gene homologs in soybean's circadian clock, may have an integrative role in transcriptional regulation of the circadian clock and flowering gene network. In this study, we verify GmELF3-1 ' s regulatory roles in its potential downstream genes by modulating the activity of GmELF3-1 using overexpression and CRISPR-Cas9 in soybean protoplasts. Our results indicate that GmELF3-1 may control the expression of the PRR genes in the circadian clock and the flowering gene GmCOL1a .

Transcriptional and post-translational regulation of plant autophagy

In response to changing environmental conditions, plants activate cellular responses to enable them to adapt. One such response is autophagy, in which cellular components, for example proteins and organelles, are delivered to the vacuole for degradation. Autophagy is activated by a wide range of conditions, and the regulatory pathways controlling this activation are now being elucidated. However, key aspects of how these factors may function together to properly modulate autophagy in response to specific internal or external signals are yet to be discovered. In this review we discuss mechanisms for regulation of autophagy in response to environmental stress and disruptions in cell homeostasis. These pathways include post-translational modification of proteins required for autophagy activation and progression, control of protein stability of the autophagy machinery, and transcriptional regulation, resulting in changes in transcription of genes involved in autophagy. In particular, we highlight potential connections between the roles of key regulators and explore gaps in research, the filling of which can further our understanding of the autophagy regulatory network in plants.

Light and temperature perceptions go through a phase separation

Light and temperature are two distinct but closely linked environmental factors that profoundly affect plant growth and development. Biomolecular condensates are membraneless micron-scale compartments formed through liquid-liquid phase separation, which have been shown to be involved in a wide range of biological processes. In the last few years, biomolecular condensates are emerged to serve as phase separation-based sensors for plant sensing and/or responding to external environmental cues. This review summarizes the recently reported plant biomolecular condensates in sensing light and temperature signals. The current understanding of the biophysical properties and the action modes of phase separation-based environmental sensors are highlighted. Unresolved questions and possible challenges for future studies of phase-separation sensors are also discussed.

Reciprocal regulation of flower induction by ELF3α and ELF3β generated via alternative promoter usage

Flowering is critical for sexual reproduction and fruit production. Several pear (Pyrus sp.) varieties produce few flower buds, but the underlying mechanisms are unknown. The circadian clock regulator EARLY FLOWERING3 (ELF3) serves as a scaffold protein in the evening complex that controls flowering. Here, we report that the absence of a 58-bp sequence in the 2nd intron of PbELF3 is genetically associated with the production of fewer flower buds in pear. From rapid amplification of cDNA ends sequencing results, we identified a short, previously unknown transcript from the PbELF3 locus, which we termed PbELF3β, whose transcript level was significantly lower in pear cultivars that lacked the 58-bp region. The heterologous expression of PbELF3β in Arabidopsis (Arabidopsis thaliana) accelerated flowering, whereas the heterologous expression of the full-length transcript PbELF3α caused late flowering. Notably, ELF3β was functionally conserved in other plants. Deletion of the 2nd intron reduced AtELF3β expression and caused delayed flowering time in Arabidopsis. AtELF3β physically interacted with AtELF3α, disrupting the formation of the evening complex and consequently releasing its repression of flower induction genes such as GIGANTEA (GI). AtELF3β had no effect in the absence of AtELF3α, supporting the idea that AtELF3β promotes flower induction by blocking AtELF3α function. Our findings show that alternative promoter usage at the ELF3 locus allows plants to fine-tune flower induction.

The Regulatory Networks of the Circadian Clock Involved in Plant Adaptation and Crop Yield

Global climatic change increasingly threatens plant adaptation and crop yields. By synchronizing internal biological processes, including photosynthesis, metabolism, and responses to biotic and abiotic stress, with external environmental cures, such as light and temperature, the circadian clock benefits plant adaptation and crop yield. In this review, we focus on the multiple levels of interaction between the plant circadian clock and environmental factors, and we summarize recent progresses on how the circadian clock affects yield. In addition, we propose potential strategies for better utilizing the current knowledge of circadian biology in crop production in the future.

EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time

The photoperiodic response is critical for plants to adjust their reproductive phase to the most favorable season. Wheat heads earlier under long days (LD) than under short days (SD) and this difference is mainly regulated by the PHOTOPERIOD1 (PPD1) gene. Tetraploid wheat plants carrying the Ppd-A1a allele with a large deletion in the promoter head earlier under SD than plants carrying the wildtype Ppd-A1b allele with an intact promoter. Phytochromes PHYB and PHYC are necessary for the light activation of PPD1, and mutations in either of these genes result in the downregulation of PPD1 and very late heading time. We show here that both effects are reverted when the phyB mutant is combined with loss-of-function mutations in EARLY FLOWERING 3 (ELF3), a component of the Evening Complex (EC) in the circadian clock. We also show that the wheat ELF3 protein interacts with PHYB and PHYC, is rapidly modified by light, and binds to the PPD1 promoter in planta (likely as part of the EC). Deletion of the ELF3 binding region in the Ppd-A1a promoter results in PPD1 upregulation at dawn, similar to PPD1 alleles with intact promoters in the elf3 mutant background. The upregulation of PPD1 is correlated with the upregulation of the florigen gene FLOWERING LOCUS T1 (FT1) and early heading time. Loss-of-function mutations in PPD1 result in the downregulation of FT1 and delayed heading, even when combined with the elf3 mutation. Taken together, these results indicate that ELF3 operates downstream of PHYB as a direct transcriptional repressor of PPD1, and that this repression is relaxed both by light and by the deletion of the ELF3 binding region in the Ppd-A1a promoter. In summary, the regulation of the light mediated activation of PPD1 by ELF3 is critical for the photoperiodic regulation of wheat heading time.

HOS15 represses flowering by promoting GIGANTEA degradation in response to low temperature in Arabidopsis

Flowering is the primary stage of the plant developmental transition and is tightly regulated by environmental factors such as light and temperature. However, the mechanisms by which temperature signals are integrated into the photoperiodic flowering pathway are still poorly understood. Here, we demonstrate that HOS15, which is known as a GI transcriptional repressor in the photoperiodic flowering pathway, controls flowering time in response to low ambient temperature. At 16°C, the hos15 mutant exhibits an early flowering phenotype, and HOS15 acts upstream of photoperiodic flowering genes (GI, CO, and FT). GI protein abundance is increased in the hos15 mutant and is insensitive to the proteasome inhibitor MG132. Furthermore, the hos15 mutant has a defect in low ambient temperature-mediated GI degradation, and HOS15 interacts with COP1, an E3 ubiquitin ligase for GI degradation. Phenotypic analyses of the hos15 cop1 double mutant revealed that repression of flowering by HOS15 is dependent on COP1 at 16°C. However, the HOS15-COP1 interaction was attenuated at 16°C, and GI protein abundance was additively increased in the hos15 cop1 double mutant, indicating that HOS15 acts independently of COP1 in GI turnover at low ambient temperature. This study proposes that HOS15 controls GI abundance through multiple modes as an E3 ubiquitin ligase and transcriptional repressor to coordinate appropriate flowering time in response to ambient environmental conditions such as temperature and day length.

A competition-attenuation mechanism modulates thermoresponsive growth at warm temperatures in plants

Global warming has profound impact on growth and development, and plants constantly adjust their internal circadian clock to cope with external environment. However, how clock-associated genes fine-tune thermoresponsive growth in plants is little understood. We found that loss-of-function mutation of REVEILLE5 (RVE5) reduces the expression of circadian gene EARLY FLOWERING 4 (ELF4) in Arabidopsis, and confers accelerated hypocotyl growth under warm-temperature conditions. Both RVE5 and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) accumulate at warm temperatures and bind to the same EE cis-element presented on ELF4 promoter, but the transcriptional repression activity of RVE5 is weaker than that of CCA1. The binding of CCA1 to ELF4 promoter is enhanced in the rve5-2 mutant at warm temperatures, and overexpression of ELF4 in the rve5-2 mutant background suppresses the rve5-2 mutant phenotype at warm temperatures. Therefore, the transcriptional repressor RVE5 finetunes ELF4 expression via competing at a cis-element with the stronger transcriptional repressor CCA1 at warm temperatures. Such a competition-attenuation mechanism provides a balancing system for modulating the level of ELF4 and thermoresponsive hypocotyl growth under warm-temperature conditions.

The plant circadian clock regulates autophagy rhythm through transcription factor LUX ARRHYTHMO

Autophagy is an evolutionarily conserved degradation pathway in eukaryotes; it plays a critical role in nutritional stress tolerance. The circadian clock is an endogenous timekeeping system that generates biological rhythms to adapt to daily changes in the environment. Accumulating evidence indicates that the circadian clock and autophagy are intimately interwoven in animals. However, the role of the circadian clock in regulating autophagy has been poorly elucidated in plants. Here, we show that autophagy exhibits a robust circadian rhythm in both light/dark cycle (LD) and in constant light (LL) in Arabidopsis. However, autophagy rhythm showed a different pattern with a phase-advance shift and a lower amplitude in LL compared to LD. Moreover, mutation of the transcription factor LUX ARRHYTHMO (LUX) removed autophagy rhythm in LL and led to an enhanced amplitude in LD. LUX represses expression of the core autophagy genes ATG2, ATG8a, and ATG11 by directly binding to their promoters. Phenotypic analysis revealed that LUX is responsible for improved resistance of plants to carbon starvation, which is dependent on moderate autophagy activity. Comprehensive transcriptomic analysis revealed that the autophagy rhythm is ubiquitous in plants. Taken together, our findings demonstrate that the LUX-mediated circadian clock regulates plant autophagy rhythms.

Plant clock modifications for adapting flowering time to local environments

During and after the domestication of crops from ancestral wild plants, humans selected cultivars that could change their flowering time in response to seasonal daylength. Continuous selection of this trait eventually allowed the introduction of crops into higher or lower latitudes and different climates from the original regions where domestication initiated. In the past two decades, numerous studies have found the causal genes or alleles that change flowering time and have assisted in adapting crop species such as barley (Hordeum vulgare), wheat (Triticum aestivum L.), rice (Oryza sativa L.), pea (Pisum sativum L.), maize (Zea mays spp. mays), and soybean (Glycine max (L.) Merr.) to new environments. This updated review summarizes the genes or alleles that contributed to crop adaptation in different climatic areas. Many of these genes are putative orthologs of Arabidopsis (Arabidopsis thaliana) core clock genes. We also discuss how knowledge of the clock's molecular functioning can facilitate molecular breeding in the future.

Circadian entrainment in Arabidopsis

Circadian clocks coordinate physiology and development as an adaption to the oscillating day/night cycle caused by the rotation of Earth on its axis and the changing length of day and night away from the equator caused by orbiting the sun. Circadian clocks confer advantages by entraining to rhythmic environmental cycles to ensure that internal events within the plant occur at the correct time with respect to the cyclic external environment. Advances in determining the structure of circadian oscillators and the pathways that allow them to respond to light, temperature, and metabolic signals have begun to provide a mechanistic insight to the process of entrainment in Arabidopsis (Arabidopsis thaliana). We describe the concepts of entrainment and how it occurs. It is likely that a thorough mechanistic understanding of the genetic and physiological basis of circadian entrainment will provide opportunities for crop improvement.

The adaptive nature of the plant circadian clock in natural environments

The plant circadian clock coordinates developmental, physiological, and metabolic processes with diel changes in light and temperature throughout the year. The balance between the persistence and plasticity of the clock in response to predictable and unpredictable environmental changes may be key to the clock's adaptive nature across temporal and spatial scales. Studies under controlled conditions have uncovered critical signaling pathways involved in light and temperature perception by the clock; however, they don't account for the natural lag of temperature behind photoperiod. Studies in natural environments provide key insights into the clock's adaptive advantage under more complex natural settings. Here, we discuss the role of the circadian clock in light and temperature perception and signaling, how the clock integrates these signals for a coordinated and adaptive response, and the adaptive advantage conferred by the clock across time and space in natural environments.

Molecular Cloning and Expression Responses of Jarid2b to High-Temperature Treatment in Nile Tilapia (Oreochromis niloticus)

Nile tilapia is a GSD + TE (Genetic Sex Determination + Temperature Effect) fish, and high-temperature treatment during critical thermosensitive periods (TSP) can induce the sex reversal of Nile tilapia genetic females, and brain transcriptomes have revealed the upregulation of Jarid2 (Jumonji and AT-rich domain containing 2) expression after 36 °C high-temperature treatment for 12 days during TSP. It was shown that JARID2 forms a complex with polycomb repressive complex 2 (PRC2) that catalyzed H3K27me3, which was strongly associated with transcriptional repression. In this study, Jarid2b was cloned and characterized in Nile tilapia, which was highly conserved among the analyzed fish species. The expression of Jarid2b was upregulated in the gonad of 21 dpf XX genetic females after 12-day high-temperature treatment and reached a similar level to that of males. Similar responses to high-temperature treatment also appeared in the brain, heart, liver, muscle, eye, and skin tissues. Interestingly, Jarid2b expression was only in response to high-temperature treatment, and not to 17α-methyltestosterone (MT) or letrozole treatments; although, these treatments can also induce the sex reversal of genetic Nile tilapia females. Further studies revealed that Jarid2b responded rapidly at the 8th hour after high-temperature treatment. Considering that JARID2 can recruit PRC2 and establish H3K27me3, we speculated that it might be an upstream gene participating in the regulation of Nile tilapia GSD + TE through regulating the H3K27 methylation level at the locus of many sex differentiation-related genes.

COP1 dynamics integrate conflicting seasonal light and thermal cues in the control of Arabidopsis elongation

As the summer approaches, plants experience enhanced light inputs and warm temperatures, two environmental cues with an opposite morphogenic impact. Key components of this response are PHYTOCHROME B (phyB), EARLY FLOWERING 3 (ELF3), and CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). Here, we used single and double mutant/overexpression lines to fit a mathematical model incorporating known interactions of these regulators. The fitted model recapitulates thermal growth of all lines used and correctly predicts thermal behavior of others not used in the fit. While thermal COP1 function is accepted to be independent of diurnal timing, our model shows that it acts at temperature signaling only during daytime. Defective response of cop1-4 mutants is epistatic to phyB-9 and elf3-8, indicating that COP1 activity is essential to transduce phyB and ELF3 thermosensory function. Our thermal model provides a unique toolbox to identify best allelic combinations enhancing climate change resilience of crops adapted to different latitudes.

The intersection between circadian and heat-responsive regulatory networks controls plant responses to increasing temperatures

Increasing temperatures impact plant biochemistry, but the effects can be highly variable. Both external and internal factors modulate how plants respond to rising temperatures. One such factor is the time of day or season the temperature increase occurs. This timing significantly affects plant responses to higher temperatures altering the signaling networks and affecting tolerance levels. Increasing overlaps between circadian signaling and high temperature responses have been identified that could explain this sensitivity to the timing of heat stress. ELF3, a circadian clock component, functions as a thermosensor. ELF3 regulates thermoresponsive hypocotyl elongation in part through its cellular localization. The temperature sensitivity of ELF3 depends on the length of a polyglutamine region, explaining how plant temperature responses vary between species. However, the intersection between the circadian system and increased temperature stress responses is pervasive and extends beyond this overlap in thermosensing. Here, we review the network responses to increased temperatures, heat stress, and the impacts on the mechanisms of gene expression from transcription to translation, highlighting the intersections between the elevated temperature and heat stress response pathways and circadian signaling, focusing on the role of ELF3 as a thermosensor.

In Vivo Bioluminescence Analyses of Circadian Rhythms in Arabidopsis thaliana Using a Microplate Luminometer

Our understanding of the circadian clock function in plants has been markedly assisted by studies with the model species Arabidopsis thaliana. Molecular and genetics approaches have delivered a comprehensive view of the transcriptional regulatory networks underlying the Arabidopsis circadian system. The use of the luciferase as a reporter allowed the precise in vivo determination of circadian periods, phases, and amplitudes of clock promoter activities with unprecedented temporal resolution. An increasing repertoire of fine-tuned luciferases together with additional applications such as translational fusions or bioluminescence molecular complementation assays have considerably expanded our view of circadian protein expression and activity, far beyond transcriptional regulation. Further applications have focused on the in vivo simultaneous examination of rhythms in different parts of the plant. The use of intact versus excised plant organs has also provided a glimpse on both the organ-specific and autonomy of the clocks and the importance of long distance communication for circadian function. This chapter provides a basic protocol for in vivo high-throughput monitoring of circadian rhythms in Arabidopsis seedlings using bioluminescent reporters and a microplate luminometer.

Circadian clock in plants: Linking timing to fitness

Endogenous circadian clock integrates cyclic signals of environment and daily and seasonal behaviors of organisms to achieve spatiotemporal synchronization, which greatly improves genetic diversity and fitness of species. This review addresses recent studies on the plant circadian system in the field of chronobiology, covering topics on molecular mechanisms, internal and external Zeitgebers, and hierarchical regulation of physiological outputs. The architecture of the circadian clock involves the autoregulatory transcriptional feedback loops, post-translational modifications of core oscillators, and epigenetic modifications of DNA and histones. Here, light, temperature, humidity, and internal elemental nutrients are summarized to illustrate the sensitivity of the circadian clock to timing cues. In addition, the circadian clock runs cell-autonomously, driving independent circadian rhythms in various tissues. The core oscillators responds to each other with biochemical factors including calcium ions, mineral nutrients, photosynthetic products, and hormones. We describe clock components sequentially expressed during a 24-h day that regulate rhythmic growth, aging, immune response, and resistance to biotic and abiotic stresses. Notably, more data have suggested the circadian clock links chrono-culture to key agronomic traits in crops.

Low Fluence Ultraviolet-B Promotes Ultraviolet Resistance 8-Modulated Flowering in Arabidopsis

Ultraviolet-B (UV-B) irradiation (280-320 nm) is an integral part of sunlight and a pivotal environmental cue that triggers various plant responses, from photoprotection to photomorphogenesis and metabolic processes. UV-B is perceived by ULTRAVIOLET RESISTANCE 8 (UVR8), which orchestrates UV-B signal transduction and transcriptional control of UV-B-responsive genes. However, there is limited information on the molecular mechanism underlying the UV-B- and UVR8-dependent regulation of flowering time in plants. Here, we investigate the role of UV-B and UVR8 in photoperiodic flowering in Arabidopsis thaliana. Our findings suggest that UV-B controls photoperiodic flowering in an ecotype-specific manner and that UVR8 acts as a negative regulator of UV-B-induced flowering. Overall, our research shows that UV-B modulates flowering initiation through the action of UVR8 at the transcriptional level.

The Conserved and Specific Roles of the LUX ARRHYTHMO in Circadian Clock and Nodulation

LUX ARRHYTHMO (LUX) plays a key role in circadian rhythms and flowering. Here, we identified the MtLUX gene which is the putative ortholog of LUX in Medicago truncatula. The roles of MtLUX, in both the nodulation belowground and leaf movement aboveground, were investigated by characterizing a loss-of-function mtlux mutant. MtLUX was required for the control of flowering time under both long-day and short-day conditions. Further investigations showed that the early flowering in the mtlux mutant was correlated with the elevated expression level of the MtFTa1 gene but in a CO-like independent manner. MtLUX played a conserved role in the regulatory interactions with MtLHY, MtTOC1, and MtPRR genes, which is similar to those in other species. Meanwhile, the unexpected functions of MtLUX were revealed in nodule formation and nyctinastic leaf movement, probably through the indirect regulation in MtLHY. Its participation in nodulation is of interest in the context of functional conservation and the neo-functionalization of the products of LUX orthologs.

LUX ARRHYTHMO Interacts With ELF3a and ELF4a to Coordinate Vegetative Growth and Photoperiodic Flowering in Rice

The evening complex (EC) plays a critical role in photoperiod flowering in Arabidopsis. Nevertheless, the underlying functions of individual components and coordinate regulation mechanism of EC genes in rice flowering remain to be elucidated. Here, we characterized the critical role of LUX ARRHYTHMO (LUX) in photoperiod perception and coordinating vegetative growth and flowering in rice. Non-functional alleles of OsLUX extremely extended vegetative phase, leading to photoperiod-insensitive late flowering and great increase of grain yield. OsLUX displayed an obvious diurnal rhythm expression with the peak at dusk and promoted rice flowering via coordinating the expression of genes associated with the circadian clock and the output integrators of photoperiodic flowering. OsLUX combined with OsELF4a and OsELF3a or OsELF3b to form two ECs, of which the OsLUX-OsELF3a-OsELF4a was likely the dominant promoter for photoperiodic flowering. In addition, OsELF4a was also essential for promoting rice flowering. Unlike OsLUX, loss OsELF4a displayed a marginal influence under short-day (SD) condition, but markedly delayed flowering time under long-day (LD) condition. These results suggest that rice EC genes share the function of promoting flowering. This is agreement with the orthologs of SD plant, but opposite to the counterparts of LD species. Taken together, rice EC genes display similar but not identical function in photoperiodic flowering, probably through regulating gene expression cooperative and independent. These findings facilitate our understanding of photoperiodic flowering in plants, especially the SD crops.

Arabidopsis EARLY FLOWERING 3 controls temperature responsiveness of the circadian clock independently of the evening complex

Daily changes in light and temperature are major entrainment cues that enable the circadian clock to generate internal biological rhythms that are synchronized with the external environment. With the average global temperature predicted to keep increasing, the intricate light-temperature coordination that is necessary for clock functionality is expected to be seriously affected. Hence, understanding how temperature signals are perceived by the circadian clock has become an important issue. In Arabidopsis, the clock component EARLY FLOWERING 3 (ELF3) not only serves as a light Zeitnehmer, but also functions as a thermosensor participating in thermomorphogenesis. However, the role of ELF3 in temperature entrainment of the circadian clock is not fully understood. Here, we report that ELF3 is essential for delivering temperature input to the clock. We demonstrate that in the absence of ELF3, the oscillator is unable to respond to temperature changes, resulting in an impaired gating of thermoresponses. Consequently, clock-controlled physiological processes such as rhythmic growth and cotyledon movement were disturbed. Genetic analyses suggest that the evening complex is not required for ELF3-controlled thermoresponsiveness. Together, our results reveal that ELF3 is an essential Zeitnehmer for temperature sensing of the oscillator, and thereby for coordinating the rhythmic control of thermoresponsive physiological outputs.

Timing to grow: roles of clock in thermomorphogenesis

Plants coordinate their growth and developmental programs with changes in temperature. This process is termed thermomorphogenesis. The underlying molecular mechanisms have begun to emerge in these nonstressful responses to adjustments in prevailing temperature. The circadian clock is an internal timekeeper that ensures growth, development, and fitness across a wide range of environmental conditions and it responds to thermal changes. Here, we highlight how the circadian clock gates thermoresponsive hypocotyl growth in plants, with an emphasis on different action mode of evening complex (EC) in thermomorphogenesis. We also discuss the biochemical and molecular mechanisms of EC in transducing temperature signals to the key integrator PIF4. This provides future perspectives on unanswered questions on EC-associated thermomorphogenesis.

Phase separation in plants: New insights into cellular compartmentalization

A fundamental challenge for cells is how to coordinate various biochemical reactions in space and time. To achieve spatiotemporal control, cells have developed organelles that are surrounded by lipid bilayer membranes. Further, membraneless compartmentalization, a process induced by dynamic physical association of biomolecules through phase transition offers another efficient mechanism for intracellular organization. While our understanding of phase separation was predominantly dependent on yeast and animal models, recent findings have provided compelling evidence for emerging roles of phase separation in plants. In this review, we first provide an overview of the current knowledge of phase separation, including its definition, biophysical principles, molecular features and regulatory mechanisms. Then we summarize plant-specific phase separation phenomena and describe their functions in plant biological processes in great detail. Moreover, we propose that phase separation is an evolutionarily conserved and efficient mechanism for cellular compartmentalization which allows for distinct metabolic processes and signaling pathways, and is especially beneficial for the sessile lifestyle of plants to quickly and efficiently respond to the changing environment.

Plant growth: the What, the How, and the Why

Growth is a widely used term in plant science and ecology, but it can have different meanings depending on the context and the spatiotemporal scale of analysis. At the meristem level, growth is associated with the production of cells and initiation of new organs. At the organ or plant scale and over short time periods, growth is often used synonymously with tissue expansion, while over longer time periods the increase in biomass is a common metric. At even larger temporal and spatial scales, growth is mostly described as net primary production. Here, we first address the question 'what is growth?'. We propose a general framework to distinguish between the different facets of growth, and the corresponding physiological processes, environmental drivers and mathematical formalisms. Based on these different definitions, we then review how plant growth can be measured and analysed at different organisational, spatial and temporal scales. We conclude by discussing why gaining a better understanding of the different facets of plant growth is essential to disentangle genetic and environmental effects on the phenotype, and to uncover the causalities around source or sink limitations of plant growth.

A clock regulatory module is required for salt tolerance and control of heading date in rice

The circadian clock plays multiple roles in plant stress responses and developmental transition phases. Nevertheless, the underlying molecular mechanisms and individual clock components that coordinately regulate important agronomic traits of rice such as salt tolerance and heading date remain to be elucidated. Here, we identify a rice ternary repressive protein complex composed of OsELF4a, OsELF3-1 and OsLUX, which was designated as OsEC1 in analogy to a similar complex in Arabidopsis. OsELF4a physically interacts with OsELF3-1 and OsELF3-2 in nucleus, whilst OsELF3-1 rather than OsELF3-2 strongly interacts with OsLUX, a Myb-domain containing transcriptional factor. Phenotypic analyses show a role for this complex in heading and salt tolerance. The loss-of-function mutants of OsEC1 exhibit lower survival rate under salt stress and late heading date. Transcriptomic profiling together with biochemical assays identified the GIGANTEA homologue OsGI as a direct transcriptional target of OsEC1. Notably, the osgi-101 mutant, generated by CRISPR/Cas9, is salt tolerant and exhibits early heading date in long day conditions. Together, our findings characterized a transcriptional module in rice composed by the OsEC1 repressing OsGI, which links the circadian clock with salt tolerance and control of heading date.

Flower orientation influences floral temperature, pollinator visits and plant fitness

Effective insect pollination requires appropriate responses to internal and external environmental cues in both the plant and the pollinator. Helianthus annuus, a highly outcrossing species, is marked for its uniform eastward orientation of mature pseudanthia, or capitula. Here we investigate how this orientation affects floral microclimate and the consequent effects on plant and pollinator interactions and reproductive fitness. We artificially manipulated sunflower capitulum orientation and temperature in both field and controlled conditions and assessed flower physiology, pollinator visits, seed traits and siring success. East-facing capitula were found to have earlier style elongation, pollen presentation and pollinator visits compared with capitula manipulated to face west. East-facing capitula also sired more offspring than west-facing capitula and under some conditions produced heavier and better-filled seeds. Local ambient temperature change on the capitulum was found to be a key factor regulating the timing of style elongation, pollen emergence and pollinator visits. These results indicate that eastward capitulum orientation helps to control daily rhythms in floral temperature, with direct consequences on the timing of style elongation and pollen emergence, pollinator visitation, and plant fitness.

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.

Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi

The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in Kalanchoë fedtschenkoi. We further inferred stomata-related gene targets for known and candidate core clock genes and constructed a gene regulatory network for core clock and stomata-related genes. Our results provide new insight into the mechanism of circadian control of CAM-related genes in K. fedtschenkoi, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.

External and Internal Reshaping of Plant Thermomorphogenesis

Plants dynamically adapt to changing temperatures to ensure propagation and reproductive success, among which morphogenic responses to warm temperatures have been extensively studied in recent years. As readily inferred from the cyclic co-oscillations of environmental cues in nature, plant thermomorphogenesis is coordinately reshaped by various external conditions. Accumulating evidence supports that internal and developmental cues also contribute to harmonizing thermomorphogenic responses. The external and internal reshaping of thermomorphogenesis is facilitated by versatile temperature sensing and interorgan communication processes, circadian and photoperiodic gating of thermomorphogenic behaviors, and their metabolic coordination. Here, we discuss recent advances in plant thermal responses with focus on the diel and seasonal reshaping of thermomorphogenesis and briefly explore its application to developing climate-smart crops.

Exploring PIF4 's contribution to early flowering in plants under daily variable temperature and its tissue-specific flowering gene network

Molecular mechanisms of how constant temperatures affect flowering time have been largely characterized in the model plant Arabidopsis thaliana; however, the effect of natural daily variable temperature outside laboratories is only partly explored. Several flowering genes have been shown to play important roles in temperature responses, including PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) and FLOWERING LOCUS C (FLC), the two genes encoding for the transcription factors (TFs) that act antagonistically to regulate flowering time by activating and repressing floral integrator FLOWERING LOCUS T (FT), respectively. In this study, we have taken a multidisciplinary approach to explore the contribution of PIF4 to the early flowering observed in the daily variable temperature (VAR) and to broaden its transcriptional network using publicly available transcriptomic data. We observed early flowering in the natural accessions Col-0, C24 and their late flowering hybrid C24xCol grown under VAR, as compared with a constant temperature (CON). The loss-of-function mutation of PIF4 exhibits later flowering in VAR in both the Col-0 parent and the C24xCol hybrid, suggesting that PIF4, at least in part, contributes to acceleration of flowering in the VAR condition. To investigate the interplay between PIF4 and its flowering regulator counterparts, FLC and FT, we performed transcriptional analyses and found that VAR increased PIF4 transcription at the end of the day when temperature peaked at 32°C, when FT transcription was also elevated. On the other hand, we observed a decrease in FLC transcription in the 4-week-old plants grown in VAR, as well as in the plants with PIF4 overexpression grown in CON. These results raise a possibility that PIF4 might also regulate FT indirectly through the repression of FLC, in addition to the well-characterized direct control of PIF4 over FT. To further expand our view on the PIF4-orientated flowering gene network in response to temperature changes, we have constructed a coexpression-transcriptional regulatory network by combining publicly available transcriptomic data and gene regulatory interactions of PIF4 and its closely related flowering genes, PIF5, FLC, and ELF3. The network model reveals conserved and tissue-specific regulatory functions, which are useful for confirming as well as predicting the functions and regulatory interactions between these key flowering genes.

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.

Warm nights disrupt transcriptome rhythms in field-grown rice panicles

In rice, a small increase in nighttime temperature reduces grain yield and quality. How warm nighttime temperatures (WNT) produce these detrimental effects is not well understood, especially in field conditions where the typical day-to-night temperature fluctuation exceeds the mild increase in nighttime temperature. We observed genome-wide disruption of gene expression timing during the reproductive phase in field-grown rice panicles acclimated to 2 to 3 °C WNT. Transcripts previously identified as rhythmically expressed with a 24-h period and circadian-regulated transcripts were more sensitive to WNT than were nonrhythmic transcripts. The system-wide perturbations in transcript levels suggest that WNT disrupt the tight temporal coordination between internal molecular events and the environment, resulting in reduced productivity. We identified transcriptional regulators whose predicted targets are enriched for sensitivity to WNT. The affected transcripts and candidate regulators identified through our network analysis explain molecular mechanisms driving sensitivity to WNT and identify candidates that can be targeted to enhance tolerance to WNT.

Closing the protein gap in plant chronobiology

Our modern understanding of diel cell regulation in plants stems from foundational work in the late 1990s that analysed the dynamics of selected genes and mutants in Arabidopsis thaliana. The subsequent rise of transcriptomics technologies such as microarrays and RNA sequencing has substantially increased our understanding of anticipatory (circadian) and reactive (light- or dark-triggered) diel events in plants. However, it is also becoming clear that gene expression data fail to capture critical events in diel regulation that can only be explained by studying protein-level dynamics. Over the past decade, mass spectrometry technologies and quantitative proteomic workflows have significantly advanced, finally allowing scientists to characterise diel protein regulation at high throughput. Initial proteomic investigations suggest that the diel transcriptome and proteome generally lack synchrony and that the timing of daily regulatory events in plants is impacted by multiple levels of protein regulation (e.g., post-translational modifications [PTMs] and protein-protein interactions [PPIs]). Here, we highlight and summarise how the use of quantitative proteomics to elucidate diel plant cell regulation has advanced our understanding of these processes. We argue that this new understanding, coupled with the extraordinary developments in mass spectrometry technologies, demands greater focus on protein-level regulation of, and by, the circadian clock. This includes hitherto unexplored diel dynamics of protein turnover, PTMs, protein subcellular localisation and PPIs that can be masked by simple transcript- and protein-level changes. Finally, we propose new directions for how the latest advancements in quantitative proteomics can be utilised to answer outstanding questions in plant chronobiology.

Genetic architecture underlying light and temperature mediated flowering in Arabidopsis, rice, and temperate cereals

Timely flowering is essential for optimum crop reproduction and yield. To determine the best flowering-time genes (FTGs) relevant to local adaptation and breeding, it is essential to compare the interspecific genetic architecture of flowering in response to light and temperature, the two most important environmental cues in crop breeding. However, the conservation and variations of FTGs across species lack systematic dissection. This review summarizes current knowledge on the genetic architectures underlying light and temperature-mediated flowering initiation in Arabidopsis, rice, and temperate cereals. Extensive comparative analyses show that most FTGs are conserved, whereas functional variations in FTGs may be species specific and confer local adaptation in different species. To explore evolutionary dynamics underpinning the conservation and variations in FTGs, domestication and selection of some key FTGs are further dissected. Based on our analyses of genetic control of flowering time, a number of key issues are highlighted. Strategies for modulation of flowering behavior in crop breeding are also discussed. The resultant resources provide a wealth of reference information to uncover molecular mechanisms of flowering in plants and achieve genetic improvement in crops.

Coordinative regulation of plants growth and development by light and circadian clock

The circadian clock, known as an endogenous timekeeping system, can integrate various cues to regulate plant physiological functions for adapting to the changing environment and thus ensure optimal plant growth. The synchronization of internal clock with external environmental information needs a process termed entrainment, and light is one of the predominant entraining signals for the plant circadian clock. Photoreceptors can detect and transmit light information to the clock core oscillator through transcriptional or post-transcriptional interactions with core-clock components to sustain circadian rhythms and regulate a myriad of downstream responses, including photomorphogenesis and photoperiodic flowering which are key links in the process of growth and development. Here we summarize the current understanding of the molecular network of the circadian clock and how light information is integrated into the circadian system, especially focus on how the circadian clock and light signals coordinately regulate the common downstream outputs. We discuss the functions of the clock and light signals in regulating photoperiodic flowering among various crop species.

Get closer and make hotspots: liquid-liquid phase separation in plants

Liquid-liquid phase separation (LLPS) facilitates the formation of membraneless compartments in a cell and allows the spatiotemporal organization of biochemical reactions by concentrating macromolecules locally. In plants, LLPS defines cellular reaction hotspots, and stimulus-responsive LLPS is tightly linked to a variety of cellular and biological functions triggered by exposure to various internal and external stimuli, such as stress responses, hormone signaling, and temperature sensing. Here, we provide an overview of the current understanding of physicochemical forces and molecular factors that drive LLPS in plant cells. We illustrate how the biochemical features of cellular condensates contribute to their biological functions. Additionally, we highlight major challenges for the comprehensive understanding of biological LLPS, especially in view of the dynamic and robust organization of biochemical reactions underlying plastic responses to environmental fluctuations in plants.

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.

Identification and expression profiling of genes involved in circadian clock regulation in red dragon fruit (Hylocereus polyrhizus) by full-length transcriptome sequencing

Crassulacean acid metabolism (CAM) plants fix CO2 at night, exhibiting a reversed regulatory pattern of metabolomic pathways compared with most model plants, which have C3 and C4 pathways. In this study, we used a valuable tropic fruit, red dragon fruit (Hylocereus polyrhizus), as model plant to identify and analyze the circadian regulation genes. Due to the absence of red dragon fruit's whole-genome dataset, we established a full-length transcriptome dataset using single-molecule real-time (SMRT) sequencing method. A 7.66-Gb dataset with 4,552,474 subreads was generated, with an average length of 1,683 bp and an N50 of 2,446 bp. Using this dataset, we identified center oscillator genes: CCA1 (CIRCADIAN CLOCK ASSOCIATED1), ELF3 (EARLY FLOWERING 3), GI (GIGANTEA), LHY (LATE ELONGATED HYPOCOTYL), LNK1 (NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED 1), and TOC1 (TIMING OF CAB EXPRESSION 1); a gene for the input pathway: CRY1 (CRYPTOCHROME); a gene for the output pathway: CO (CONSTANS); and genes related to the CAM pathway: MDH (MALATE DEHYDROGENASE), ME (MALIC ENZYMES), and PPDK (PYRUVATE PHOSPHATE DIKINASE). We further established the 24-h rhythmic expression pattern of these genes and classified these into three groups: HpCCA1, HpELF3, HpLHY, HpLNK1, and HpGI have expression peaks during the day; HpTOC1, HpCO, and HpCRY1 have highest expression levels at night; The genes involved in the CAM pathways, namely, HpMDH, HpME1, and HpPPDK, have double expression peaks in the day and night. Comparison of these expression patterns between red dragon fruit and model plants could provide clues in understanding the circadian clock regulation and the activity of the CAM pathways in cactus plants.

The Arabidopsis JMJ29 Protein Controls Circadian Oscillation through Diurnal Histone Demethylation at the CCA1 and PRR9 Loci

The circadian clock matches various biological processes to diurnal environmental cycles, such as light and temperature. Accumulating evidence shows that chromatin modification is crucial for robust circadian oscillation in plants, although chromatin modifiers involved in regulating core clock gene expression have been limitedly investigated. Here, we report that the Jumonji C domain-containing histone demethylase JMJ29, which belongs to the JHDM2/KDM3 group, shapes rhythmic changes in H3K4me3 histone marks at core clock loci in Arabidopsis. The evening-expressed JMJ29 protein interacts with the Evening Complex (EC) component EARLY FLOWERING 3 (ELF3). The EC recruits JMJ29 to the CCA1 and PRR9 promoters to catalyze the H3K4me3 demethylation at the cognate loci, maintaining a low-level expression during the evening time. Together, our findings demonstrate that interaction of circadian components with chromatin-related proteins underlies diurnal fluctuation of chromatin structures to maintain circadian waveforms in plants.