Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis

A CCA1-like MYB subfamily member CsMYB128 participates in chilling sensitivity and cold tolerance in tea plants (Camellia sinensis)

While flavonoid accumulation, light radiation, and cold stress are intrinsically connected in tea plants, yet the underlying mechanisms remain elusive. The circadian protein CCA1 and CCA1-like MYB transcription factors (TFs) play important roles in coordinating light and temperature signals in plant-environment interactions, their homologs in tea plants have not been addressed. Here we analyzed CsCCA1-like MYB subfamily in tea genome and found one member, a circadian gene CsMYB128 responding to cold stress. Antisense knockdown of CsMYB128 in tea buds rendered cold tolerance in cold tolerance tests. Metabolite profiling, yeast hybrid and promoter trans-activation assays further demonstrated that CsMYB128 negatively regulated flavonol biosynthesis by repressing CsFLS1 in flavonol biosynthesis and CsCBF1 in cold tolerance. Given CsCBF1 also activated CsMYB128 transcription, the negative feedback regulation loop indicates a balance between tea plant growth promoted by CsMYB128 and cold tolerance meanwhile growth inhibition by CsCBF1. Moreover, CsICE1 interacted with and inhibited CsMYB128 repressor activity to promote cold tolerance. CsMYB128 is thus characterized as an early cold-responsive gene negatively regulating tea plant cold response and balancing tea plant growth and cold tolerance. This study provides insights into the roles of CCA1-like subfamily MYB TFs in regulating tea plant growth and interactions with environments.

Circadian gating: concepts, processes, and opportunities

Circadian clocks provide a biological measure of time that coordinates metabolism, physiology and behaviour with 24 h cycles in the environment. Circadian systems have a variety of characteristic properties, such as entrainment to environmental cues, a self-sustaining rhythm of about 24 h and temperature compensation of the circadian rhythm. In this perspective, we discuss the process of circadian gating, which refers to the restriction of a biological event to particular times of day by the circadian clock. We introduce principles and processes associated with circadian gating in a variety of organisms, including some associated mechanisms. We highlight socioeconomic opportunities presented by the investigation of circadian gating, using selected examples from circadian medicine and agricultural crop production to illustrate its importance.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.

The clock-associated LUX ARRHYTHMO regulates high-affinity nitrate transport in Arabidopsis roots

The circadian clock organizes physiological processes in plants to occur at specific times of the day, optimizing efficient use of resources. Nitrate is a crucial inorganic nitrogen source for agricultural systems to sustain crop productivity. However, because nitrate fertilization has a negative impact on the environment, it is important to carefully manage nitrate levels. Understanding crop biological rhythms can lead to more ecologically friendly agricultural practices. Gating responses through the circadian clock could be a strategy to enhance root nitrate uptake and to limit nitrate runoff. In Arabidopsis, the NITRATE TRANSPORTER 2.1 (NRT2.1) gene encodes a key component of the high-affinity nitrate transporter system. Our study reveals that NRT2.1 exhibits a rhythmic expression pattern, with daytime increases and nighttime decreases. The NRT2.1 promoter activity remains rhythmic under constant light, indicating a circadian regulation. The clock-associated transcription factor LUX ARRHYTHMO (LUX) binds to the NRT2.1 promoter in vivo. Loss-of-function of LUX leads to increased NRT2.1 transcript levels and root nitrate uptake at dusk. This supports LUX acting as a transcriptional repressor and modulating NRT2.1 expression in a time-dependent manner. Furthermore, applying nitrate at different times of the day results in varying magnitudes of the transcriptional response in nitrate-regulated genes. We also demonstrate that a defect in the high-affinity nitrate transport system feeds back to the central oscillator by modifying the LUX promoter activity. In conclusion, this study uncovers a molecular pathway connecting the root nitrate uptake and circadian clock, with potential agro-chronobiological applications.

The circadian clock participates in seasonal growth in Norway spruce (Picea abies)

The boreal forest ecosystems of the northern hemisphere are dominated by conifers, of which Norway spruce (Picea abies [L.] H. Karst.) is one of the most common species. Due to its economic interest to the agroforestry industry, as well as its ecological significance, it is important to understand seasonal growth and biomass production in Norway spruce. Solid evidence that the circadian clock regulates growth in conifers has proved elusive, however, resulting in significant gaps in our knowledge of clock function in these trees. Here, we reassess the impact of the circadian clock on growth in Norway spruce. Using a combination of approaches monitoring the physiology of vegetative growth, transcriptomics and bioinformatics, we determined that the clock could be playing a decisive role in enabling growth, acting in specific developmental processes influenced by season and geographical location to guide bud burst and growth. Thus, the evidence indicates that there is time for spruce.

Regulatory Networks Underlying Plant Responses and Adaptation to Cold Stress

Cold is an important environmental factor limiting plant growth and development. Recent studies have revealed the complex regulatory networks associated with plant responses to cold and identified their interconnections with signaling pathways related to light, the circadian clock, plant hormones, and pathogen defense. In this article, we review recent advances in understanding the molecular basis of cold perception and signal transduction pathways. We also summarize recent developments in the study of cold-responsive growth and flowering. Finally, we propose future directions for the study of long-term cold sensing, RNA secondary structures in response to cold, and the development of cold-tolerant and high-yield crops.

LUX ARRHYTHMO links CBF pathway and jasmonic acid metabolism to regulate cold tolerance of tea plants

Cold stress declines the quality and yield of tea, yet the molecular basis underlying cold tolerance of tea plants (Camellia sinensis) remains largely unknown. Here, we identified a circadian rhythm component LUX ARRHYTHMO (LUX) that potentially regulates cold tolerance of tea plants through a genome-wide association study and transcriptomic analysis. The expression of CsLUX phased with sunrise and sunset and was strongly induced by cold stress. Genetic assays indicated that CsLUX is a positive regulator of freezing tolerance in tea plants. CsLUX was directly activated by CsCBF1 and repressed the expression level of CsLOX2, which regulates the cold tolerance of tea plants through dynamically modulating jasmonic acid content. Furthermore, we showed that the CsLUX-CsJAZ1 complex attenuated the physical interaction of CsJAZ1 with CsICE1, liberating CsICE1 with transcriptional activities to withstand cold stress. Notably, a single-nucleotide variation of C-to-A in the coding region of CsLUX was functionally validated as the potential elite haplotype for cold response, which provided valuable molecular markers for future cold resistance breeding in tea plants.

The circadian clock and thermal regulation in plants: novel insights into the role of positive circadian clock regulators in temperature responses

The impact of rising global temperatures on crop yields is a serious concern, and the development of heat-resistant crop varieties is crucial for mitigating the effects of climate change on agriculture. To achieve this, a better understanding of the molecular basis of the thermal responses of plants is necessary. The circadian clock plays a central role in modulating plant biology in synchrony with environmental changes, including temperature fluctuations. Recent studies have uncovered the role of transcriptional activators of the core circadian network in plant temperature responses. This expert view highlights key novel findings regarding the role of the RVE and LNK gene families in controlling gene expression patterns and plant growth under different temperature conditions, ranging from regular diurnal oscillations to extreme stress temperatures. These findings reinforce the essential role of the circadian clock in plant adaptation to changing temperatures and provide a basis for future studies on crop improvement.

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.

The Roles of Circadian Clock Genes in Plant Temperature Stress Responses

Plants monitor day length and memorize changes in temperature signals throughout the day, creating circadian rhythms that support the timely control of physiological and metabolic processes. The DEHYDRATION-RESPONSE ELEMENT-BINDING PROTEIN 1/C-REPEAT BINDING FACTOR (DREB1/CBF) transcription factors are known as master regulators for the acquisition of cold stress tolerance, whereas PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is involved in plant adaptation to heat stress through thermomorphogenesis. Recent studies have shown that circadian clock genes control plant responses to temperature. Temperature-responsive transcriptomes show a diurnal cycle and peak expression levels at specific times of throughout the day. Circadian clock genes play essential roles in allowing plants to maintain homeostasis by accommodating temperature changes within the normal temperature range or by altering protein properties and morphogenesis at the cellular level for plant survival and growth under temperature stress conditions. Recent studies revealed that the central oscillator genes CIRCADIAN CLOCK ASSOCIATED 1/LATE ELONGATED HYPOCOTYL (CCA1/LHY) and PSEUDO-RESPONSE REGULATOR5/7/9 (PRR5/7/9), as well as the EVENING COMPLEX (EC) genes REVEILLE4/REVEILLE8 (REV4/REV8), were involved in the DREB1 pathway of the cold signaling transcription factor and regulated the thermomorphogenesis gene PIF4. Further studies showed that another central oscillator, TIMING OF CAB EXPRESSION 1 (TOC1), and the regulatory protein ZEITLUPE (ZTL) are also involved. These studies led to attempts to utilize circadian clock genes for the acquisition of temperature-stress resistance in crops. In this review, we highlight circadian rhythm regulation and the clock genes involved in plant responses to temperature changes, as well as strategies for plant survival in a rapidly changing global climate.

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.

The Circadian Clock Coordinates the Tradeoff between Adaptation to Abiotic Stresses and Yield in Crops

Plants have evolved a circadian clock to adapt to ever-changing diel and seasonal environmental conditions. The circadian clock is generally considered an internal system that has evolved to adapt to cyclic environmental cues, especially diel light and temperature changes, which is essential for higher plants as they are sessile organisms. This system receives environmental signals as input pathways which are integrated by circadian core oscillators to synchronize numerous output pathways, such as photosynthesis, the abiotic stress response, metabolism, and development. Extreme temperatures, salinity, and drought stresses cause huge crop losses worldwide, imposing severe pressure on areas of agricultural land. In crop production, the circadian system plays a significant role in determining flowering time and responding to external abiotic stresses. Extensive studies over the last two decades have revealed that the circadian clock can help balance the tradeoff between crop yield-related agronomic traits and adaptation to stress. Herein, we focus on summarizing how the circadian clock coordinates abiotic stress responses and crop yield. We also propose that there might be an urgent need to better utilize circadian biology in the future design of crop breeding to achieve high yields under stress conditions.

Chilling stress drives organ-specific transcriptional cascades and dampens diurnal oscillation in tomato

Improving chilling tolerance in cold-sensitive crops, e.g. tomato, requires knowledge of the early molecular response to low temperature in these under-studied species. To elucidate early responding processes and regulators, we captured the transcriptional response at 30 minutes and 3 hours in the shoots and at 3 hours in the roots of tomato post-chilling from 24°C to 4°C. We used a pre-treatment control and a concurrent ambient temperature control to reveal that majority of the differential expression between cold and ambient conditions is due to severely compressed oscillation of a large set of diurnally regulated genes in both the shoots and roots. This compression happens within 30 minutes of chilling, lasts for the duration of cold treatment, and is relieved within 3 hours of return to ambient temperatures. Our study also shows that the canonical ICE1/CAMTA-to-CBF cold response pathway is active in the shoots, but not in the roots. Chilling stress induces synthesis of known cryoprotectants (trehalose and polyamines), in a CBF-independent manner, and induction of multiple genes encoding proteins of photosystems I and II. This study provides nuanced insights into the organ-specific response in a chilling sensitive plant, as well as the genes influenced by an interaction of chilling response and the circadian clock.

OsLUX Confers Rice Cold Tolerance as a Positive Regulatory Factor

During the early seedling stage, rice (Oryza sativa L.) must overcome low-temperature stress. While a few cold-tolerance genes have been characterized, further excavation of cold-resistance genes is still needed. In this study, we identified a cold-induced transcription factor—LUX ARRHYTHMO (LUX)—in rice. OsLUX was found to be specifically expressed in leaf blades and upregulated by both cold stress and circadian rhythm. The full-length OsLUX showed autoactivation activity, and the OsLUX protein localized throughout the entire onion cell. Overexpressing OsLUX resulted in increased cold tolerance and reduced ion leakage under cold-stress conditions during the seedling stage. In contrast, the knockout of OsLUX decreased seedling cold tolerance and showed higher ion leakage compared to the wild type. Furthermore, overexpressing OsLUX upregulated the expression levels of oxidative stress-responsive genes, which improved reactive oxygen species (ROS) scavenging ability and enhanced tolerance to chilling stress. Promoter analysis showed that the OsLUX promoter contains two dehydration-responsive element binding (DREB) motifs at positions −510/−505 (GTCGGa) and −162/−170 (cCACCGccc), which indicated that OsDREB1s and OsDREB2s probably regulate OsLUX expression by binding to the motif to respond to cold stress. Thus, OsLUX may act as a downstream gene of the DREB pathway. These results demonstrate that OsLUX serves as a positive regulatory factor of cold stress and that overexpressing OsLUX could be used in rice breeding programs to enhance abiotic stress tolerance.

Recent progress and perspectives on physiological and molecular mechanisms underlying cold tolerance of tea plants

Tea is one of the most consumed and widely planted beverage plant worldwide, which contains many important economic, healthy, and cultural values. Low temperature inflicts serious damage to tea yields and quality. To cope with cold stress, tea plants have evolved a cascade of physiological and molecular mechanisms to rescue the metabolic disorders in plant cells caused by the cold stress; this includes physiological, biochemical changes and molecular regulation of genes and associated pathways. Understanding the physiological and molecular mechanisms underlying how tea plants perceive and respond to cold stress is of great significance to breed new varieties with improved quality and stress resistance. In this review, we summarized the putative cold signal sensors and molecular regulation of the CBF cascade pathway in cold acclimation. We also broadly reviewed the functions and potential regulation networks of 128 cold-responsive gene families of tea plants reported in the literature, including those particularly regulated by light, phytohormone, and glycometabolism. We discussed exogenous treatments, including ABA, MeJA, melatonin, GABA, spermidine and airborne nerolidol that have been reported as effective ways to improve cold resistance in tea plants. We also present perspectives and possible challenges for functional genomic studies on cold tolerance of tea plants in the future.

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.

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 direct targets of CBFs: In cold stress response and beyond

Cold acclimation in Arabidopsis thaliana triggers a significant transcriptional reprogramming altering the expression patterns of thousands of cold-responsive (COR) genes. Essential to this process is the C-repeat binding factor (CBF)-dependent pathway, involving the activity of AP2/ERF (APETALA2/ethylene-responsive factor)-type CBF transcription factors required for plant cold acclimation. In this study, we performed chromatin immunoprecipitation assays followed by deep sequencing (ChIP-seq) to determine the genome-wide binding sites of the CBF transcription factors. Cold-induced CBF proteins specifically bind to the conserved C-repeat (CRT)/dehydration-responsive elements (CRT/DRE; G/ACCGAC) of their target genes. A Gene Ontology enrichment analysis showed that 1,012 genes are targeted by all three CBFs. Combined with a transcriptional analysis of the cbf1,2,3 triple mutant, we define 146 CBF regulons as direct CBF targets. In addition, the CBF-target genes are significantly enriched in functions associated with hormone, light, and circadian rhythm signaling, suggesting that the CBFs act as key integrators of endogenous and external environmental cues. Our findings not only define the genome-wide binding patterns of the CBFs during the early cold response, but also provide insights into the role of the CBFs in regulating multiple biological processes of plants.

Growing in time: exploring the molecular mechanisms of tree growth

Trees cover vast areas of the Earth's landmasses. They mitigate erosion, capture carbon dioxide, produce oxygen and support biodiversity, and also are a source of food, raw materials and energy for human populations. Understanding the growth cycles of trees is fundamental for many areas of research. Trees, like most other organisms, have evolved a circadian clock to synchronize their growth and development with the daily and seasonal cycles of the environment. These regular changes in light, daylength and temperature are perceived via a range of dedicated receptors and cause resetting of the circadian clock to local time. This allows anticipation of daily and seasonal fluctuations and enables trees to co-ordinate their metabolism and physiology to ensure vital processes occur at the optimal times. In this review, we explore the current state of knowledge concerning the regulation of growth and seasonal dormancy in trees, using information drawn from model systems such as Populus spp.

Spatial Organization and Coordination of the Plant Circadian System

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

It's a matter of time: the role of transcriptional regulation in the circadian clock-pathogen crosstalk in plants

Most living organisms possess an internal timekeeping mechanism known as the circadian clock, which enhances fitness by synchronizing the internal timing of biological processes with diurnal and seasonal environmental changes. In plants, the pace of these biological rhythms relies on oscillations in the expression level of hundreds of genes tightly controlled by a group of core clock regulators and co-regulators that engage in transcriptional and translational feedback loops. In the last decade, the role of several core clock genes in the control of defense responses has been addressed, and a growing amount of evidence demonstrates that circadian regulation is relevant for plant immunity. A reciprocal connection between these pathways was also established following the observation that in Arabidopsis thaliana, as well as in crop species like tomato, plant-pathogen interactions trigger a reconfiguration of the circadian transcriptional network. In this review, we summarize the current knowledge regarding the interaction between the circadian clock and biotic stress responses at the transcriptional level, and discuss the relevance of this crosstalk in the plant-pathogen evolutionary arms race. A better understanding of these processes could aid in the development of genetic tools that improve traditional breeding practices, enhancing tolerance to plant diseases that threaten crop yield and food security all around the world.

Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

Plants are continuously exposed to diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24 h period, enabling the anticipation of these events. We used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions. Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion than reported in most other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon, we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore, we identified sequence motifs enriched in the promoters of similarly phased genes, some potentially associated with transcription factors. When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles was the prevailing cue that controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species.

Coordination of light, circadian clock with temperature: The potential mechanisms regulating chilling tolerance in rice

Rice (Oryza sativa L.) is a major staple food crop for over half of the world's population. As a crop species originated from the subtropics, rice production is hampered by chilling stress. The genetic mechanisms of rice responses to chilling stress have attracted much attention, focusing on chilling-related gene mining and functional analyses. Plants have evolved sophisticated regulatory systems to respond to chilling stress in coordination with light signaling pathway and internal circadian clock. However, in rice, information about light-signaling pathways and circadian clock regulation and their roles in chilling tolerance remains elusive. Further investigation into the regulatory network of chilling tolerance in rice is needed, as knowledge of the interaction between temperature, light, and circadian clock dynamics is limited. Here, based on phenotypic analysis of transgenic and mutant rice lines, we delineate the relevant genes with important regulatory roles in chilling tolerance. In addition, we discuss the potential coordination mechanism among temperature, light, and circadian clock in regulating chilling response and tolerance of rice, and provide perspectives for the ongoing chilling signaling network research in rice.

Molecular Regulation of Plant Responses to Environmental Temperatures

Temperature is a key factor governing the growth and development, distribution, and seasonal behavior of plants. The entire plant life cycle is affected by environmental temperatures. Plants grow rapidly and exhibit specific changes in morphology under mild average temperature conditions, a response termed thermomorphogenesis. When exposed to chilling or moist chilling low temperatures, flowering or seed germination is accelerated in some plant species; these processes are known as vernalization and cold stratification, respectively. Interestingly, once many temperate plants are exposed to chilling temperatures for some time, they can acquire the ability to resist freezing stress, a process termed cold acclimation. In the face of global climate change, heat stress has emerged as a frequent challenge, which adversely affects plant growth and development. In this review, we summarize and discuss recent progress in dissecting the molecular mechanisms regulating plant thermomorphogenesis, vernalization, and responses to extreme temperatures. We also discuss the remaining issues that are crucial for understanding the interactions between plants and temperature.

Light Perception: A Matter of Time

Optimizing the perception of external cues and regulating physiology accordingly help plants to cope with the constantly changing environmental conditions to which they are exposed. An array of photoreceptors and intricate signaling pathways allow plants to convey the surrounding light information and synchronize an endogenous timekeeping system known as the circadian clock. This biological clock integrates multiple cues to modulate a myriad of downstream responses, timing them to occur at the best moment of the day and the year. Notably, the mechanism underlying entrainment of the light-mediated clock is not clear. This review addresses known interactions between the light-signaling and circadian-clock networks, focusing on the role of light in clock entrainment and known molecular players in this process.

Interaction between the Circadian Clock and Regulators of Heat Stress Responses in Plants

The circadian clock is found ubiquitously in nature, and helps organisms coordinate internal biological processes with environmental cues that inform the time of the day or year. Both temperature stress and the clock affect many important biological processes in plants. Specifically, clock-controlled gene regulation and growth are impacted by a compromised clock or heat stress. The interactions linking these two regulatory pathways include several rhythmic transcription factors that are important for coordinating the appropriate response to temperature stress. Here we review the current understanding of clock control of the regulators involved in heat stress responses in plants.

Circadian Rhythms in Plants

The circadian oscillator is a complex network of interconnected feedback loops that regulates a wide range of physiological processes. Indeed, variation in clock genes has been implicated in an array of plant environmental adaptations, including growth regulation, photoperiodic control of flowering, and responses to abiotic and biotic stress. Although the clock is buffered against the environment, maintaining roughly 24-h rhythms across a wide range of conditions, it can also be reset by environmental cues such as acute changes in light or temperature. These competing demands may help explain the complexity of the links between the circadian clock network and environmental response pathways. Here, we discuss our current understanding of the clock and its interactions with light and temperature-signaling pathways. We also describe different clock gene alleles that have been implicated in the domestication of important staple crops.

LUX ARRHYTHMO mediates crosstalk between the circadian clock and defense in Arabidopsis

The circadian clock is known to regulate plant innate immunity but the underlying mechanism of this regulation remains largely unclear. We show here that mutations in the core clock component LUX ARRHYTHMO (LUX) disrupt circadian regulation of stomata under free running and Pseudomonas syringae challenge conditions as well as defense signaling mediated by SA and JA, leading to compromised disease resistance. RNA-seq analysis reveals that both clock- and defense-related genes are regulated by LUX. LUX binds to clock gene promoters that have not been shown before, expanding the clock gene networks that require LUX function. LUX also binds to the promoters of EDS1 and JAZ5, likely acting through these genes to affect SA- and JA-signaling. We further show that JA signaling reciprocally affects clock activity. Thus, our data support crosstalk between the circadian clock and plant innate immunity and imply an important role of LUX in this process.

LUX ARRHYTHMO mediates crosstalk between the circadian clock and defense in Arabidopsis

The circadian clock is known to regulate plant innate immunity but the underlying mechanism of this regulation remains largely unclear. We show here that mutations in the core clock component LUX ARRHYTHMO (LUX) disrupt circadian regulation of stomata under free running and Pseudomonassyringae challenge conditions as well as defense signaling mediated by SA and JA, leading to compromised disease resistance. RNA-seq analysis reveals that both clock- and defense-related genes are regulated by LUX. LUX binds to clock gene promoters that have not been shown before, expanding the clock gene networks that require LUX function. LUX also binds to the promoters of EDS1 and JAZ5, likely acting through these genes to affect SA- and JA-signaling. We further show that JA signaling reciprocally affects clock activity. Thus, our data support crosstalk between the circadian clock and plant innate immunity and imply an important role of LUX in this process.

Circadian control of plant defence likely reflects plants’ ability to coordinate development and defense. Here, Zhang et al. show that LUX regulates stomatal defense  and SA/JA signaling, leading to broad-spectrum disease resistance, and that JA signaling can, in turn, regulate clock activity.

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.

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

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

Arabidopsis JMJD5/JMJ30 Acts Independently of LUX ARRHYTHMO Within the Plant Circadian Clock to Enable Temperature Compensation

The circadian system ensures that plants respond appropriately to environmental change by predicting regular transitions that occur during diel cycles. In order to be most useful, the circadian system needs to be compensated against daily and seasonal changes in temperature that would otherwise alter the pace of this biological oscillator. We demonstrate that an evening-phased protein, the putative histone demethylase JMJD5, contributes to temperature compensation. JMJD5 is co-expressed with components of the Evening Complex, an agglomeration of proteins including EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHYMO (LUX), which also integrates temperature changes into the molecular clockwork. One role of the Evening Complex is to regulate expression of PSEUDORESPONSE REGULATOR9 (PRR9) and PRR7, important components of the temperature compensation mechanism. Surprisingly we find that LUX, but not other Evening Complex components, is dispensable for clock function at low temperatures. Further genetic analysis suggests JMJD5 acts in a parallel pathway to LUX within the circadian system. Although an intact JMJD5 catalytic domain is required for its function within the clock, our findings suggest JMJD5 does not directly regulate H3K36 methylation at circadian loci. Such data refine our understanding of how JMDJ5 acts within the Arabidopsis circadian system.

Conservation and Diversification of Circadian Rhythmicity Between a Model Crassulacean Acid Metabolism Plant Kalanchoë fedtschenkoi and a Model C3 Photosynthesis Plant Arabidopsis thaliana

Crassulacean acid metabolism (CAM) improves photosynthetic efficiency under limited water availability relative to C3 photosynthesis. It is widely accepted that CAM plants have evolved from C3 plants and it is hypothesized that CAM is under the control of the internal circadian clock. However, the role that the circadian clock plays in the evolution of CAM is not well understood. To identify the molecular basis of circadian control over CAM evolution, rhythmic gene sets were identified in a CAM model plant species (Kalanchoë fedtschenkoi) and a C3 model plant species (Arabidopsis thaliana) through analysis of diel time-course gene expression data using multiple periodicity detection algorithms. Based on protein sequences, ortholog groups were constructed containing genes from each of these two species. The ortholog groups were categorized into five gene sets based on conservation and diversification of rhythmic gene expression. Interestingly, minimal functional overlap was observed when comparing the rhythmic gene sets of each species. Specifcally, metabolic processes were enriched in the gene set under circadian control in K. fedtschenkoi and numerous genes were found to have retained or gained rhythmic expression in K. fedtsechenkoi. Additonally, several rhythmic orthologs, including CAM-related orthologs, displayed phase shifts between species. Results of this analysis point to several mechanisms by which the circadian clock plays a role in the evolution of CAM. These genes provide a set of testable hypotheses for future experiments.

Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome-wide analysis of LHY binding targets

The LATE ELONGATED HYPOCOTYL (LHY) transcription factor functions as part of the oscillatory mechanism of the Arabidopsis circadian clock. This paper reports the genome-wide analysis of its binding targets and reveals a role in the control of abscisic acid (ABA) biosynthesis and downstream responses. LHY directly repressed expression of 9-cis-epoxycarotenoid dioxygenase enzymes, which catalyse the rate-limiting step of ABA biosynthesis. This suggested a mechanism for the circadian control of ABA accumulation in wild-type plants. Consistent with this hypothesis, ABA accumulated rhythmically in wild-type plants, peaking in the evening. LHY-overexpressing plants had reduced levels of ABA under drought stress, whereas loss-of-function mutants exhibited an altered rhythm of ABA accumulation. LHY also bound the promoter of multiple components of ABA signalling pathways, suggesting that it may also act to regulate responses downstream of the hormone. LHY promoted expression of ABA-responsive genes responsible for increased tolerance to drought and osmotic stress but alleviated the inhibitory effect of ABA on seed germination and plant growth. This study reveals a complex interaction between the circadian clock and ABA pathways, which is likely to make an important contribution to plant performance under drought and osmotic stress conditions.

Mechanism of Overwintering in Trees

Boreal trees possess very high freezing resistance, which is induced by short-day length and low temperatures, in order to survive severe subzero temperatures in winter. During autumn, cooperation of photoreceptors and circadian clock system perceiving photoperiod shortening results in growth cessation, dormancy development, and first induction of freezing resistance. The freezing resistance is further enhanced by subsequent low temperature during seasonal cold acclimation with concomitant changes in various morphological and physiological features including accumulation of sugars and late embryogenesis abundant proteins. The mechanism of adaptation to freezing temperatures differs depending on the type of tissue in boreal trees. For example, bark, cambium, and leaf cells tolerate freezing-induced dehydration by extracellular freezing, whereas xylem parenchyma cells avoid intracellular freezing by deep supercooling. In addition, dormant buds in some trees respond by extraorgan freezing. Boreal trees have evolved overwintering mechanisms such as dormancy and high freezing resistance in order to survive freezing temperatures in winter.

Response of Arabidopsis primary metabolism and circadian clock to low night temperature in a natural light environment

Plants are exposed to varying irradiance and temperature within a day and from day to day. We previously investigated metabolism in a temperature-controlled greenhouse at the spring equinox on both a cloudy and a sunny day [daily light integral (DLI) of 7 mol m-2 d-1 and 12 mol m-2 d-1]. Diel metabolite profiles were largely captured in sinusoidal simulations at similar DLIs in controlled-environment chambers, except that amino acids were lower in natural light regimes. We now extend the DLI12 study by investigating metabolism in a natural light regime with variable temperature including cool nights. Starch was not completely turned over, anthocyanins and proline accumulated, and protein content rose. Instead of decreasing, amino acid content rose. Connectivity in central metabolism, which decreased in variable light, was not further weakened by variable temperature. We propose that diel metabolism operates better when light and temperature are co-varying. We also compared transcript abundance of 10 circadian clock genes in this temperature-variable regime with the temperature-controlled natural and sinusoidal light regimes. Despite temperature compensation, peak timing and abundance for dawn- and day-phased genes and GIGANTEA were slightly modified in the variable temperature treatment. This may delay dawn clock activity until the temperature rises enough to support rapid metabolism and photosynthesis.

An early-flowering einkorn wheat mutant with deletions of PHYTOCLOCK 1/LUX ARRHYTHMO and VERNALIZATION 2 exhibits a high level of VERNALIZATION 1 expression induced by vernalization

Using heavy-ion beam mutagenesis of Triticum monococcum strain KU104-1, we identified a mutant that shows extra early-flowering; it was named extra early-flowering 3 (exe3). Here, we carried out expression analyses of clock-related genes, clock downstream genes and photoperiod pathway genes, and found that the clock component gene PHYTOCLOCK 1/LUX ARRHYTHMO (PCL1/LUX) was not expressed in exe3 mutant plants. A PCR analysis of DNA markers indicated that the exe3 mutant had a deletion of wheat PCL1/LUX (WPCL1), and that the WPCL1 deletion was correlated with the mutant phenotype in the segregation line. We confirmed that the original strain KU104-1 carried a mutation that produced a null allele of a flowering repressor gene VERNALIZATION 2 (VRN2). As a result, the exe3 mutant has both WPCL1 and VRN2 loss-of-function mutations. Analysis of plant development in a growth chamber showed that vernalization treatment accelerated flowering time in the exe3 mutant under short day (SD) as well as long day (LD) conditions, and the early-flowering phenotype was correlated with the earlier up-regulation of VRN1. The deletion of WPCL1 affects the SD-specific expression patterns of some clock-related genes, clock downstream genes and photoperiod pathway genes, suggesting that the exe3 mutant causes a disordered SD response. The present study indicates that VRN1 expression is associated with the biological clock and the VRN1 up-regulation is not influenced by the presence or absence of VRN2.

Plant circadian networks and responses to the environment

There are regular, and therefore predictable, environmental changes on Earth due to the rotation of the planet on its axis and its orbit around the sun. Thus organisms have adapted their metabolism, physiology and behaviour to minimise stresses caused by unfavourable conditions and maximise efficiency of growth. Additionally, most organisms are able to anticipate these changes and accordingly maximise metabolic efficiency and growth, because they have a complex biological time-keeping system commonly referred to as the circadian clock. Multiple pathways in plants are organised in a temporal manner through circadian clock-regulation of gene transcription and post-translational modifications. What is becoming more apparent is the bidirectional nature of interactions between the clock and stress response pathways. Until recently, the focus of many studies had been on the unidirectional, hierarchical control of biological processes by the circadian clock, and impacts on the clock in response to environmental stress had been largely ignored. Studies of interactions of the circadian clock with the environment have primarily been to understand mechanisms of entrainment. We review the evidence and implications of the reciprocal interactions between the clock and the environment.

Construction of Arabidopsis Transcription Factor ORFeome Collections and Identification of Protein-DNA Interactions by High-Throughput Yeast One-Hybrid Screens

Identification of transcription factor (TF)-promoter interactions is key to understanding the basic molecular underpinnings of gene regulation. The complexity of gene regulation, however, is driven by the combined function of several TFs recruited to the promoter region, which often confounds the discovery of transcriptional regulatory mechanisms. Genome sequencing enabled the construction of TF-specific ORFeome clone collections that can be used to study TF function with unprecedented coverage. Among the recently developed methods, gene-centered yeast one-hybrid (Y1H) screens performed with these ORFeome collections provide a simple and reliable strategy to identify TF-promoter interactions. Here, we describe high-throughput cloning protocols used to generate a gold standard TF ORFeome collection for the model organism Arabidopsis thaliana. Furthermore, we outline the protocol to build a daughter clone collection suitable for the Y1H assay and a high-throughput Y1H screening procedure that enables rapid assessment of thousands TF-promoter interactions using a robotic platform. These protocols can be universally adopted to build ORFeome libraries and thus expand the usage of gene-centered Y1H screens or other alternative strategies for discovery and characterization of TF functions.

Successive evolutionary steps drove Pooideae grasses from tropical to temperate regions

Angiosperm adaptations to seasonally cold climates have occurred multiple times independently. However, the observation that less than half of all angiosperm families are represented in temperate latitudes suggests internal constraints on the evolution of cold tolerance/avoidance strategies. Similar to angiosperms as a whole, grasses are primarily tropical, but one major clade, subfamily Pooideae, radiated extensively within temperate regions. It is posited that this Pooideae niche transition was facilitated by an early origin of long-term cold responsiveness around the base of the subfamily, and that a set of more ancient pathways enabled evolution of seasonal cold tolerance. To test this, we compared transcriptome-level responses of disparate Pooideae to short-/long-term cold and with those previously known in the subtropical grass rice (Ehrhartoideae). Analyses identified several highly conserved cold-responsive 'orthogroups' within our focal Pooideae species that originated successively during the diversification of land plants, predominantly via gene duplication. The majority of conserved Pooideae cold-responsive genes appear to have ancient roles in stress responses, with most of the orthogroups also being sensitive to cold in rice. However, a subgroup of genes was likely co-opted de novo early in the Pooideae. These results highlight a plausible stepwise evolutionary trajectory for cold adaptations across Pooideae.

Gene Regulation and Signal Transduction in the ICE-CBF-COR Signaling Pathway during Cold Stress in Plants

Low temperature is an abiotic stress that adversely affects the growth and production of plants. Resistance and adaptation of plants to cold stress is dependent upon the activation of molecular networks and pathways involved in signal transduction and the regulation of cold-stress related genes. Because it has numerous and complex genes, regulation factors, and pathways, research on the ICE-CBF-COR signaling pathway is the most studied and detailed, which is thought to be rather important for cold resistance of plants. In this review, we focus on the function of each member, interrelation among members, and the influence of manipulators and repressors in the ICE-CBF-COR pathway. In addition, regulation and signal transduction concerning plant hormones, circadian clock, and light are discussed. The studies presented provide a detailed picture of the ICE-CBF-COR pathway.

Shining a light on the Arabidopsis circadian clock

The circadian clock provides essential timing information to ensure optimal growth to prevailing external environmental conditions. A major time-setting mechanism (zeitgeber) in clock synchronization is light. Differing light wavelengths, intensities, and photoperiodic duration are processed for the clock-setting mechanism. Many studies on light-input pathways to the clock have focused on Arabidopsis thaliana. Photoreceptors are specific chromic proteins that detect light signals and transmit this information to the central circadian oscillator through a number of different signalling mechanisms. The most well-characterized clock-mediating photoreceptors are cryptochromes and phytochromes, detecting blue, red, and far-red wavelengths of light. Ultraviolet and shaded light are also processed signals to the oscillator. Notably, the clock reciprocally generates rhythms of photoreceptor action leading to so-called gating of light responses. Intermediate proteins, such as Phytochrome interacting factors (PIFs), constitutive photomorphogenic 1 (COP1) and EARLY FLOWERING 3 (ELF3), have been established in signalling pathways downstream of photoreceptor activation. However, the precise details for these signalling mechanisms are not fully established. This review highlights both historical and recent efforts made to understand overall light input to the oscillator, first looking at how each wavelength of light is detected, this is then related to known input mechanisms and their interactions.

Novel cell surface luciferase reporter for high-throughput yeast one-hybrid screens

Gene-centered yeast one-hybrid (Y1H) screens provide a powerful and effective strategy to identify transcription factor (TF)-promoter interactions. While genome-wide TF ORFeome clone collections are increasingly available, screening protocols have limitations inherent to the properties of the enzymatic reaction used to identify interactions and to the procedure required to perform the assay in a high-throughput format. Here, we present the development and validation of a streamlined strategy for quantitative and fully automated gene-centered Y1H screens using a novel cell surface Gaussia luciferase reporter.

The evening complex coordinates environmental and endogenous signals in Arabidopsis

Plants maximize their fitness by adjusting their growth and development in response to signals such as light and temperature. The circadian clock provides a mechanism for plants to anticipate events such as sunrise and adjust their transcriptional programmes. However, the underlying mechanisms by which plants coordinate environmental signals with endogenous pathways are not fully understood. Using RNA-sequencing and chromatin immunoprecipitation sequencing experiments, we show that the evening complex (EC) of the circadian clock plays a major role in directly coordinating the expression of hundreds of key regulators of photosynthesis, the circadian clock, phytohormone signalling, growth and response to the environment. We find that the ability of the EC to bind targets genome-wide depends on temperature. In addition, co-occurrence of phytochrome B (phyB) at multiple sites where the EC is bound provides a mechanism for integrating environmental information. Hence, our results show that the EC plays a central role in coordinating endogenous and environmental signals in Arabidopsis.

Making the clock tick: the transcriptional landscape of the plant circadian clock

Circadian clocks are molecular timekeepers that synchronise internal physiological processes with the external environment by integrating light and temperature stimuli. As in other eukaryotic organisms, circadian rhythms in plants are largely generated by an array of nuclear transcriptional regulators and associated co-regulators that are arranged into a series of interconnected molecular loops. These transcriptional regulators recruit chromatin-modifying enzymes that adjust the structure of the nucleosome to promote or inhibit DNA accessibility and thus guide transcription rates. In this review, we discuss the recent advances made in understanding the architecture of the Arabidopsis oscillator and the chromatin dynamics that regulate the generation of rhythmic patterns of gene expression within the circadian clock.

COR27 and COR28 encode nighttime repressors integrating Arabidopsis circadian clock and cold response

It was noted that circadian components function in plant adaptation to diurnal temperature cycles and freezing tolerance. Our genome-wide transcriptome analysis revealed that evening-phased COR27 and COR28 mainly repress the transcription of clock-associated evening genes PRR5, ELF4 and cold-responsive genes. Chromatin immunoprecipitation indicated that CCA1 is recruited to the site containing EE elements of COR27 and COR28 promoters in a temperature-dependent way. Further genetic analysis shows COR28 is essential for the circadian function of PRR9 and PRR7. Together, our results support a role of COR27 and COR28 as nighttime repressors integrating circadian clock and plant cold stress responses.

Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors

The Aux/IAA proteins are auxin-sensitive repressors that mediate diverse physiological and developmental processes in plants [1, 2]. There are 29 Aux/IAA genes in Arabidopsis that exhibit unique but partially overlapping patterns of expression [3]. Although some studies have suggested that individual Aux/IAA genes have specialized function, genetic analyses of the family have been limited by the scarcity of loss-of-function phenotypes [4]. Furthermore, with a few exceptions, our knowledge of the factors that regulate Aux/IAA expression is limited [1, 5]. We hypothesize that transcriptional control of Aux/IAA genes plays a central role in the establishment of the auxin-signaling pathways that regulate organogenesis, growth, and environmental response. Here, we describe a screen for transcription factors (TFs) that regulate the Aux/IAA genes. We identify TFs from 38 families, including 26 members of the DREB/CBF family. Several DREB/CBF TFs directly promote transcription of the IAA5 and IAA19 genes in response to abiotic stress. Recessive mutations in these IAA genes result in decreased tolerance to stress conditions, demonstrating a role for auxin in abiotic stress. Our results demonstrate that stress pathways interact with the auxin gene regulatory network (GRN) through transcription of the Aux/IAA genes. We propose that the Aux/IAA genes function as hubs that integrate genetic and environmental information to achieve the appropriate developmental or physiological outcome.

ERF105 is a transcription factor gene of Arabidopsis thaliana required for freezing tolerance and cold acclimation

Understanding the response to cold temperature stress is relevant for both basic biology and application. Here we report on ERF105, which is a novel cold-regulated transcription factor gene of Arabidopsis that makes a significant contribution to freezing tolerance and cold acclimation. The expression of cold-responsive genes in erf105 mutants suggests that its action is linked to the CBF regulon mediating cold responses.

Molecular mechanisms at the core of the plant circadian oscillator

Circadian clocks are endogenous timekeeping networks that allow organisms to align their physiology with their changing environment and to perform biological processes at the most relevant times of the day and year. Initial feedback-loop models of the oscillator have been enriched by emerging evidence highlighting the increasing variety of factors and mechanisms that contribute to the generation of rhythms. In this Review, we consider the two major input pathways that connect the circadian clock of the model plant Arabidopsis thaliana to its environment and discuss recent advances in understanding of how transcriptional, post-translational and post-transcriptional mechanisms contribute to clock function.