Independent action of ELF3 and phyB to control hypocotyl elongation and flowering time

A nanopore-based cucumber genome assembly reveals structural variations at two QTLs controlling hypocotyl elongation

The Xishuangbanna (XIS) cucumber (Cucumis sativus var. xishuangbannanesis) is a semiwild variety that has many distinct agronomic traits. Here, long reads generated by Nanopore sequencing technology helped assembling a high-quality genome (contig N50 = 8.7 Mb) of landrace XIS49. A total of 10,036 structural/sequence variations (SVs) were identified when comparing with Chinese Long (CL), and known SVs controlling spines, tubercles, and carpel number were confirmed in XIS49 genome. Two QTLs of hypocotyl elongation under low light, SH3.1 and SH6.1, were fine-mapped using introgression lines (donor parent, XIS49; recurrent parent, CL). SH3.1 encodes a red-light receptor Phytochrome B (PhyB, CsaV3_3G015190). A ∼4 kb region with large deletion and highly divergent regions (HDRs) were identified in the promoter of the PhyB gene in XIS49. Loss of function of this PhyB caused a super-long hypocotyl phenotype. SH6.1 encodes a CCCH-type zinc finger protein FRIGIDA-ESSENTIAL LIKE (FEL, CsaV3_6G050300). FEL negatively regulated hypocotyl elongation but it was transcriptionally suppressed by long terminal repeats retrotransposon insertion in CL cucumber. Mechanistically, FEL physically binds to the promoter of CONSTITUTIVE PHOTOMORPHOGENIC 1a (COP1a), regulating the expression of COP1a and the downstream hypocotyl elongation. These above results demonstrate the genetic mechanism of cucumber hypocotyl elongation under low light.

The evening complex promotes maize flowering and adaptation to temperate regions

Maize (Zea mays) originated in southern Mexico and has spread over a wide latitudinal range. Maize expansion from tropical to temperate regions has necessitated a reduction of its photoperiod sensitivity. In this study, we cloned a quantitative trait locus (QTL) regulating flowering time in maize and show that the maize ortholog of Arabidopsis thaliana EARLY FLOWERING3, ZmELF3.1, is the causal locus. We demonstrate that ZmELF3.1 and ZmELF3.2 proteins can physically interact with ZmELF4.1/4.2 and ZmLUX1/2, to form evening complex(es; ECs) in the maize circadian clock. Loss-of-function mutants for ZmELF3.1/3.2 and ZmLUX1/2 exhibited delayed flowering under long-day and short-day conditions. We show that EC directly represses the expression of several flowering suppressor genes, such as the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) genes ZmCCT9 and ZmCCT10, ZmCONSTANS-LIKE 3, and the PSEUDORESPONSE REGULATOR (PRR) genes ZmPRR37a and ZmPRR73, thus alleviating their inhibition, allowing florigen gene expression and promoting flowering. Further, we identify two closely linked retrotransposons located in the ZmELF3.1 promoter that regulate the expression levels of ZmELF3.1 and may have been positively selected during postdomestication spread of maize from tropical to temperate regions during the pre-Columbian era. These findings provide insights into circadian clock-mediated regulation of photoperiodic flowering in maize and new targets of genetic improvement for breeding.

Flower Development in Arabidopsis

Like in other angiosperms, the development of flowers in Arabidopsis starts right after the floral transition, when the shoot apical meristem (SAM) stops producing leaves and makes flowers instead. On the flanks of the SAM emerge the flower meristems (FM) that will soon differentiate into the four main floral organs, sepals, petals, stamens, and pistil, stereotypically arranged in concentric whorls. Each phase of flower development-floral transition, floral bud initiation, and floral organ development-is under the control of specific gene networks. In this chapter, we describe these different phases and the gene regulatory networks involved, from the floral transition to the floral termination.

Genetic and transcriptome analyses reveal the candidate genes and pathways involved in the inactive shade-avoidance response enabling high-density planting of soybean

High-density planting is a major way to improve crop yields. However, shade-avoidance syndrome (SAS) is a major factor limiting increased planting density. First Green Revolution addressed grass lodging problem by using dwarf/semi-dwarf genes. However, it is not suitable for soybean, which bear seeds on stalk and whose seed yield depends on plant height. Hence, mining shade-tolerant germplasms and elucidating the underlying mechanism could provide meaningful resources and information for high-yield breeding. Here, we report a high-plant density-tolerant soybean cultivar, JiDou 17, which exhibited an inactive SAS (iSAS) phenotype under high-plant density or low-light conditions at the seedling stage. A quantitative trait locus (QTL) mapping analysis using a recombinant inbred line (RIL) population showed that this iSAS phenotype is related to a major QTL, named shade-avoidance response 1 (qSAR1), which was detected. The mapping region was narrowed by a haplotype analysis into a 554 kb interval harboring 44 genes, including 4 known to be key regulators of the SAS network and 4 with a variance response to low-light conditions between near isogenic line (NIL) stems. Via RNA-seq, we identified iSAS-specific genes based on one pair of near isogenic lines (NILs) and their parents. The iSAS-specific genes expressed in the stems were significantly enriched in the "proteasomal protein catabolic" process and the proteasome pathway, which were recently suggested to promote the shade-avoidance response by enhancing PIF7 stability. Most iSAS-specific proteasome-related genes were downregulated under low-light conditions. The expression of genes related to ABA, CK, and GA significantly varied between the low- and normal-light conditions. This finding is meaningful for the cloning of genes that harbor beneficial variation(s) conferring the iSAS phenotype fixed in domestication and breeding practice.

Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

BACKGROUND

In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear.

RESULTS

We used two geographically, phenotypically and genetically distinct cultivars, conventional juvenile Zhonghuang 24 (with functional J/GmELF3a, a homolog of the circadian clock indispensable component EARLY FLOWERING 3) and long juvenile Huaxia 3 (with dysfunctional j/Gmelf3a) to dissect the soybean circadian clock with time-series transcriptomal RNA-Seq analysis of unifoliate leaves on a day scale. The results showed that several known circadian clock components, including RVE1, GI, LUX and TOC1, phase differently in soybean than in Arabidopsis, demonstrating that the soybean circadian clock is obviously different from the canonical model in Arabidopsis. In contrast to the observation that ELF3 dysfunction results in clock arrhythmia in Arabidopsis, the circadian clock is conserved in soybean regardless of the functional status of J/GmELF3a. Soybean exhibits a circadian rhythmicity in both gene expression and alternative splicing. Genes can be grouped into six clusters, C1-C6, with different expression profiles. Many more genes are grouped into the night clusters (C4-C6) than in the day cluster (C2), showing that night is essential for gene expression and regulation. Moreover, soybean chromosomes are activated with a circadian rhythmicity, indicating that high-order chromosome structure might impact circadian rhythmicity. Interestingly, night time points were clustered in one group, while day time points were separated into two groups, morning and afternoon, demonstrating that morning and afternoon are representative of different environments for soybean growth and development. However, no genes were consistently differentially expressed over different time-points, indicating that it is necessary to perform a circadian rhythmicity analysis to more thoroughly dissect the function of a gene. Moreover, the analysis of the circadian rhythmicity of the GmFT family showed that GmELF3a might phase- and amplitude-modulate the GmFT family to regulate the juvenility and maturity traits of soybean.

CONCLUSIONS

These results and the resultant RNA-seq data should be helpful in understanding the soybean circadian clock and elucidating the connection between the circadian clock and soybean maturity.

The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype

Morphotypes of Brassica oleracea are the result of a dynamic interaction between genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales, ornate leaves, extended vegetative phase, and nutritional quality are some of the characters potentially selected by humans during domestication. We used a combination of developmental studies and transcriptomics to understand the vegetative domestication syndrome of kale. To identify candidate genes that are responsible for the evolution of domestic kale, we searched for transcriptome-wide differences among three vegetative B. oleracea morphotypes. RNA-seq experiments were used to understand the global pattern of expressed genes during a mixture of stages at one time in kale, cabbage, and the rapid cycling kale line TO1000. We identified gene expression patterns that differ among morphotypes and estimate the contribution of morphotype-specific gene expression that sets kale apart (3958 differentially expressed genes). Differentially expressed genes that regulate the vegetative to reproductive transition were abundant in all morphotypes. Genes involved in leaf morphology, plant architecture, defense, and nutrition were differentially expressed in kale. This allowed us to identify a set of candidate genes we suggest may be important in the kale domestication syndrome. Understanding candidate genes responsible for kale domestication is of importance to ultimately improve Cole crop production.

ZEITLUPE enhances expression of PIF4 and YUC8 in the upper aerial parts of Arabidopsis seedlings to positively regulate hypocotyl elongation

Microarray and genetic analyses reveal that ZTL induces the expression of genes related to auxin synthesis, thereby promoting hypocotyl elongation. ZTL is a blue-light receptor that possesses a light-oxygen-voltage-sensing (LOV) domain, an F-box motif, and a kelch repeat domain. ZTL promotes hypocotyl elongation under high temperature (28 °C) in Arabidopsis thaliana; however, the mechanism of this regulation is unknown. Here, we divided seedlings into hypocotyls and upper aerial parts, and performed microarray analyses. In hypocotyl, 1062 genes were down-regulated in ztl mutants (ztl-3 and ztl-105) compared with wild type; some of these genes encoded enzymes involved in cell wall modification, consistent with reduced hypocotyl elongation. In upper aerial parts, 1038 genes were down-regulated in the ztl mutants compared with wild type; these included genes involved in auxin synthesis and auxin response. Furthermore, the expression of the PHYTOCHROME INTERACTING FACTOR 4 (PIF4) gene, which encodes a transcription factor known to positively regulate YUCCA genes (YUCs), was also decreased in the ztl mutants. Genetic analysis revealed that overexpression of PIF4 and YUC8 could restore the suppressed hypocotyl length in the ztl mutants. Our results suggest that ZTL induces expression of YUC8 via PIF4 in upper aerial parts and promotes hypocotyl elongation.

Molecular and functional dissection of EARLY-FLOWERING 3 (ELF3) and ELF4 in Arabidopsis

The circadian clock is an endogenous timekeeper system that generates biological rhythms of approximately 24 h in most organisms. EARLY FLOWERING 3 (ELF3) and ELF4 were initially identified as negative regulators of flowering time in Arabidopsis thaliana. They were then found to play crucial roles in the circadian clock by integrating environmental light and ambient temperature signals and transmitting them to the central oscillator, thereby regulating various downstream cellular and physiological processes. At dusk, ELF3 acts as a scaffold, interacting with ELF4 and the transcription factor LUX ARRHYTHMO (PHYTOCLOCK1) to form an EVENING COMPLEX (EC). This complex represses the transcription of multiple circadian clock-related genes, thus inhibiting hypocotyl elongation and flowering. Subsequent studies have expanded knowledge about the regulatory roles of the EC in thermomorphogenesis and shade responses. In addition, ELF3 and ELF4 also form multiple complexes with other proteins including chromatin remodeling factors, histone deacetylase, and transcription factors, thus enabling the transcriptional repression of diverse targets. In this review, we summarize the recent advances in elucidating the regulatory mechanisms of ELF3 and ELF4 in plants and discuss directions for future research on ELF3 and ELF4.

Overexpression of BBX18 Promotes Thermomorphogenesis Through the PRR5-PIF4 Pathway

Thermomorphogenesis is the morphological response of plants to an elevation in the ambient temperature, which is mediated by the bHLH transcription factor PIF4. The evening-expressed clock component, PRR5, directly represses the expression of PIF4 mRNA. Additionally, PRR5 interacts with PIF4 protein and represses its transactivation activity, which in turn suppresses the thermoresponsive growth in the evening. Here, we found that the B-box zinc finger protein, BBX18, interacts with PRR5 through the B-Box2 domain. Deletion of the B-Box2 domain abolished the functions of BBX18, including the stimulation of PIF4 mRNA expression and hypocotyl growth. Overexpression of BBX18, and not of B-Box2-deleted BBX18, restored the expression of thermoresponsive genes in the evening. We further show that BBX18 prevents PRR5 from inhibiting PIF4-mediated high temperature responses. Taken together, our results suggest that BBX18 regulates thermoresponsive growth through the PRR5-PIF4 pathway.

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.

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.

Photoperiod sensing of the circadian clock is controlled by EARLY FLOWERING 3 and GIGANTEA

ELF3 and GI are two important components of the Arabidopsis circadian clock. They are not only essential for the oscillator function but are also pivotal in mediating light inputs to the oscillator. Lack of either results in a defective oscillator causing severely compromised output pathways, such as photoperiodic flowering and hypocotyl elongation. Although single loss of function mutants of ELF3 and GI have been well studied, their genetic interaction remains unclear. We generated an elf3 gi double mutant to study their genetic relationship in clock-controlled growth and phase transition phenotypes. We found that ELF3 and GI repress growth differentially during the night and the day, respectively. Circadian clock assays revealed that ELF3 and GI are essential that enable the oscillator to synchronize the endogenous cellular mechanisms to external environmental signals. In their absence, the circadian oscillator fails to synchronize to the light-dark cycles even under diurnal conditions. Consequently, clock-mediated photoperiod-responsive growth and development are completely lost in plants lacking both genes, suggesting that ELF3 and GI together convey photoperiod sensing to the central oscillator. Since ELF3 and GI are conserved across flowering plants and represent important breeding and domestication targets, our data highlight the possibility of developing photoperiod-insensitive crops by adjusting the allelic combination of these two key genes.

Photoperiod sensing of the circadian clock is controlled by EARLY FLOWERING 3 and GIGANTEA

ELF3 and GI are two important components of the Arabidopsis circadian clock. They are not only essential for the oscillator function but are also pivotal in mediating light inputs to the oscillator. Lack of either results in a defective oscillator causing severely compromised output pathways, such as photoperiodic flowering and hypocotyl elongation. Although single loss of function mutants of ELF3 and GI have been well studied, their genetic interaction remains unclear. We generated an elf3 gi double mutant to study their genetic relationship in clock-controlled growth and phase transition phenotypes. We found that ELF3 and GI repress growth differentially during the night and the day, respectively. Circadian clock assays revealed that ELF3 and GI are essential that enable the oscillator to synchronize the endogenous cellular mechanisms to external environmental signals. In their absence, the circadian oscillator fails to synchronize to the light-dark cycles even under diurnal conditions. Consequently, clock-mediated photoperiod-responsive growth and development are completely lost in plants lacking both genes, suggesting that ELF3 and GI together convey photoperiod sensing to the central oscillator. Since ELF3 and GI are conserved across flowering plants and represent important breeding and domestication targets, our data highlight the possibility of developing photoperiod-insensitive crops by adjusting the allelic combination of these two key genes.

The ELF3-PIF7 Interaction Mediates the Circadian Gating of the Shade Response in Arabidopsis

Light filtered through dense planting initiates the shade avoidance syndrome (SAS) in plants, which helps them compete against their neighbors. Quantitative trait loci (QTL)-based analysis identified the nighttime-expressed clock component ELF3 as a new player in the SAS, but its detailed mechanism is unclear. Here, we show that the circadian clock gates shade-induced gene expression and hypocotyl elongation at night. ELF3 is involved in nighttime suppression via interaction with and inactivation of PHYTOCHROME-INTERACTING FACTOR 7 (PIF7). Loss of function of ELF3 restores the shade induction, which is largely reduced in the absence of PIF7, indicating that ELF3 acts upstream of PIF7. Finally, we found that the repressive activity of ELF3 on the shade response is stronger under short days than under long days. Our results reveal that the interaction between ELF3 and PIF7 mediates the circadian gating of the SAS, which coordinates the daily control of physiological outputs.

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ELF3 is involved in the inhibition of the shade response at night

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ELF3 interacts with PIF7 and prevents PIF7 from binding DNA

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ELF3 acts upstream of PIF7 in shade-induced growth

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Repressive activity of ELF3 is stronger under SDs than under LDs

Luciferase-Based Screen for Post-translational Control Factors in the Regulation of the Pseudo-Response Regulator PRR7

Control of protein turnover is a key post-translational control point in the oscillatory network of the circadian clock. Some elements, such as TOC1 and PRR5 are engaged by a well-described F-box protein, ZEITLUPE, dedicated to their proteolytic turnover to shape their expression profile to a specific time of night. For most other clock components the regulation of their protein abundance is unknown, though turnover is often rapid and often lags the cycling of the respective mRNA. Here we report the design and results of an unbiased genetic screen in Arabidopsis to uncover proteolytic regulatory factors of PSEUDO-RESPONSE REGULATOR 7 (PRR7), a transcriptional repressor that peaks in the late afternoon. We performed EMS mutagenesis on a transgenic line expressing a PRR7::PRR7-luciferase (PRR7-LUC) translational fusion that accurately recapitulates the diurnal and circadian oscillations of the endogenous PRR7 protein. Using continuous luciferase imaging under constant light, we recovered mutants that alter the PRR7-LUC waveform and some that change period. We have identified novel alleles of ELF3 and ELF4, core components of the ELF3-ELF4-LUX Evening Complex (EC), that dampen the oscillation of PRR7-LUC. We report the characterization of two new hypomorphic alleles of ELF3 that help to understand the relationship between molecular potency and phenotype.

Ambient Temperature-Responsive Mechanisms Coordinate Regulation of Flowering Time

In plants, environmental conditions such as temperature affect survival, growth, and fitness, particularly during key stages such as seedling growth and reproduction. To survive and thrive in changing conditions, plants have evolved adaptive responses that tightly regulate developmental processes such as hypocotyl elongation and flowering time in response to environmental temperature changes. Increases in temperature, coupled with increasing fluctuations in local climate and weather, severely affect our agricultural systems; therefore, understanding the mechanisms by which plants perceive and respond to temperature is critical for agricultural sustainability. In this review, we summarize recent findings on the molecular mechanisms of ambient temperature perception as well as possible temperature sensing components in plants. Based on recent publications, we highlight several temperature response mechanisms, including the deposition and eviction of histone variants, DNA methylation, alternative splicing, protein degradation, and protein localization. We discuss roles of each proposed temperature-sensing mechanism that affects plant development, with an emphasis on flowering time. Studies of plant ambient temperature responses are advancing rapidly, and this review provides insights for future research aimed at understanding the mechanisms of temperature perception and responses in plants.

Molecular basis of flowering under natural long-day conditions in Arabidopsis

Plants sense light and temperature changes to regulate flowering time. Here, we show that expression of the Arabidopsis florigen gene, FLOWERING LOCUS T (FT), peaks in the morning during spring, a different pattern than we observe in the laboratory. Providing our laboratory growth conditions with a red/far-red light ratio similar to open-field conditions and daily temperature oscillation is sufficient to mimic the FT expression and flowering time in natural long days. Under the adjusted growth conditions, key light signalling components, such as phytochrome A and EARLY FLOWERING 3, play important roles in morning FT expression. These conditions stabilize CONSTANS protein, a major FT activator, in the morning, which is probably a critical mechanism for photoperiodic flowering in nature. Refining the parameters of our standard growth conditions to more precisely mimic plant responses in nature can provide a powerful method for improving our understanding of seasonal response.

PlantSize Offers an Affordable, Non-destructive Method to Measure Plant Size and Color in Vitro

Plant size, shape and color are important parameters of plants, which have traditionally been measured by destructive and time-consuming methods. Non-destructive image analysis is an increasingly popular technology to characterize plant development in time. High throughput automatic phenotyping platforms can simultaneously analyze multiple morphological and physiological parameters of hundreds or thousands of plants. Such platforms are, however, expensive and are not affordable for many laboratories. Moreover, determination of basic parameters is sufficient for most studies. Here we describe a non-invasive method, which simultaneously measures basic morphological and physiological parameters of in vitro cultured plants. Changes of plant size, shape and color is monitored by repeated photography with a commercial digital camera using neutral white background. Images are analyzed with the MatLab-based computer application PlantSize, which simultaneously calculates several parameters including rosette size, convex area, convex ratio, chlorophyll and anthocyanin contents of all plants identified on the image. Numerical data are exported in MS Excel-compatible format. Subsequent data processing provides information on growth rates, chlorophyll and anthocyanin contents. Proof-of-concept validation of the imaging technology was demonstrated by revealing small but significant differences between wild type and transgenic Arabidopsis plants overexpressing the HSFA4A transcription factor or the hsfa4a knockout mutant, subjected to different stress conditions. While HSFA4A overexpression was associated with better growth, higher chlorophyll and lower anthocyanin content in saline conditions, the knockout hsfa4a mutant showed hypersensitivity to various stresses. Morphological differences were revealed by comparing rosette size, shape and color of wild type plants with phytochrome B (phyB-9) mutant. While the technology was developed with Arabidopsis plants, it is suitable to characterize plants of other species including crops, in a simple, affordable and fast way. PlantSize is publicly available (http://www.brc.hu/pub/psize/index.html).

Coordinated Regulation of Hypocotyl Cell Elongation by Light and Ethylene through a Microtubule Destabilizing Protein

Precise regulation of hypocotyl cell elongation is essential for plant growth and survival. Light suppresses hypocotyl elongation by degrading transcription factor phytochrome-interacting factor 3 (PIF3), whereas the phytohormone ethylene promotes hypocotyl elongation by activating PIF3. However, the underlying mechanisms regarding how these two pathways coordinate downstream effectors to mediate hypocotyl elongation are largely unclear. In this study, we identified the novel Microtubule-Destabilizing Protein 60 (MDP60), which plays a positive role in hypocotyl cell elongation in Arabidopsis (Arabidopsis thaliana); this effect is mediated through PIF3. Ethylene signaling up-regulates MDP60 expression via PIF3 binding to the MDP60 promoter. MDP60 loss-of-function mutants exhibit much shorter hypocotyls, whereas MDP60 overexpression significantly promotes hypocotyl cell elongation when grown in light compared to the control. MDP60 protein binds to microtubules in vitro and in vivo. The organization of cortical microtubules was significantly disrupted in mdp60 mutant cells and MDP60-overexpressing seedlings. These findings indicate that MDP60 is an important mediator of hypocotyl cell elongation. This study reveals a mechanism in which light and ethylene signaling coordinate MDP60 expression to modulate hypocotyl cell elongation by altering cortical microtubules in Arabidopsis.

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.

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.

Perception and signalling of light and temperature cues in plants

Light and temperature patterns are often correlated under natural plant growth conditions. In this review, we analyse the perception and signalling mechanisms shared by both these environmental cues and discuss the functional implications of their convergence to control plant growth. The first point of integration is the phytochrome B (phyB) receptor, which senses light and temperature. Downstream of phyB, the signalling core comprises two branches, one involving PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and the other CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and ELONGATED HYPOCOTYL 5 (HY5). The dynamics of accumulation and/or localization of each of these core signalling components depend on light and temperature conditions. These pathways are connected through COP1, which enhances the activity of PIF4. The circadian clock modulates this circuit, since EARLY FLOWERING 3 (ELF3), an essential component of the evening complex (EC), represses expression of the PIF4 gene and PIF4 transcriptional activity. Phytochromes are probably not the only entry point of temperature into this network, but other sensors remain to be established. The sharing of mechanisms of action for two distinct environmental cues is to some extent unexpected, as it renders these responses mutually dependent. There are nonetheless many ecological contexts in which such a mutual influence could be beneficial.

Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry

Many species possess an endogenous circadian clock to synchronize internal physiology with an oscillating external environment. In plants, the circadian clock coordinates growth, metabolism and development over daily and seasonal time scales. Many proteins in the circadian network form oscillating complexes that temporally regulate myriad processes, including signal transduction, transcription, protein degradation and post-translational modification. In Arabidopsis thaliana, a tripartite complex composed of EARLY FLOWERING 4 (ELF4), EARLY FLOWERING 3 (ELF3), and LUX ARRHYTHMO (LUX), named the evening complex, modulates daily rhythms in gene expression and growth through transcriptional regulation. However, little is known about the physical interactions that connect the circadian system to other pathways. We used affinity purification and mass spectrometry (AP-MS) methods to identify proteins that associate with the evening complex in A. thaliana. New connections within the circadian network as well as to light signaling pathways were identified, including linkages between the evening complex, TIMING OF CAB EXPRESSION1 (TOC1), TIME FOR COFFEE (TIC), all phytochromes and TANDEM ZINC KNUCKLE/PLUS3 (TZP). Coupling genetic mutation with affinity purifications tested the roles of phytochrome B (phyB), EARLY FLOWERING 4, and EARLY FLOWERING 3 as nodes connecting the evening complex to clock and light signaling pathways. These experiments establish a hierarchical association between pathways and indicate direct and indirect interactions. Specifically, the results suggested that EARLY FLOWERING 3 and phytochrome B act as hubs connecting the clock and red light signaling pathways. Finally, we characterized a clade of associated nuclear kinases that regulate circadian rhythms, growth, and flowering in A. thaliana. Coupling mass spectrometry and genetics is a powerful method to rapidly and directly identify novel components and connections within and between complex signaling pathways.

Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry

Many species possess an endogenous circadian clock to synchronize internal physiology with an oscillating external environment. In plants, the circadian clock coordinates growth, metabolism and development over daily and seasonal time scales. Many proteins in the circadian network form oscillating complexes that temporally regulate myriad processes, including signal transduction, transcription, protein degradation and post-translational modification. In Arabidopsis thaliana, a tripartite complex composed of EARLY FLOWERING 4 (ELF4), EARLY FLOWERING 3 (ELF3), and LUX ARRHYTHMO (LUX), named the evening complex, modulates daily rhythms in gene expression and growth through transcriptional regulation. However, little is known about the physical interactions that connect the circadian system to other pathways. We used affinity purification and mass spectrometry (AP-MS) methods to identify proteins that associate with the evening complex in A. thaliana. New connections within the circadian network as well as to light signaling pathways were identified, including linkages between the evening complex, TIMING OF CAB EXPRESSION1 (TOC1), TIME FOR COFFEE (TIC), all phytochromes and TANDEM ZINC KNUCKLE/PLUS3 (TZP). Coupling genetic mutation with affinity purifications tested the roles of phytochrome B (phyB), EARLY FLOWERING 4, and EARLY FLOWERING 3 as nodes connecting the evening complex to clock and light signaling pathways. These experiments establish a hierarchical association between pathways and indicate direct and indirect interactions. Specifically, the results suggested that EARLY FLOWERING 3 and phytochrome B act as hubs connecting the clock and red light signaling pathways. Finally, we characterized a clade of associated nuclear kinases that regulate circadian rhythms, growth, and flowering in A. thaliana. Coupling mass spectrometry and genetics is a powerful method to rapidly and directly identify novel components and connections within and between complex signaling pathways.

Circadian Clock Genes Universally Control Key Agricultural Traits

Circadian clocks are endogenous timers that enable plants to synchronize biological processes with daily and seasonal environmental conditions in order to allocate resources during the most beneficial times of day and year. The circadian clock regulates a number of central plant activities, including growth, development, and reproduction, primarily through controlling a substantial proportion of transcriptional activity and protein function. This review examines the roles that alleles of circadian clock genes have played in domestication and improvement of crop plants. The focus here is on three groups of circadian clock genes essential to clock function in Arabidopsis thaliana: PSEUDO-RESPONSE REGULATORs, GIGANTEA, and the evening complex genes early flowering 3, early flowering 4, and lux arrhythmo. homologous genes from each group underlie quantitative trait loci that have beneficial influences on key agricultural traits, especially flowering time but also yield, biomass, and biennial growth habit. Emerging insights into circadian clock regulation of other fundamental plant processes, including responses to abiotic and biotic stresses, are discussed to highlight promising avenues for further crop improvement.

ELF3-PIF4 interaction regulates plant growth independently of the Evening Complex

The circadian clock plays a pivotal role in the control of Arabidopsis hypocotyl elongation by regulating rhythmic expression of the bHLH factors PHYTOCHROME INTERACTING FACTOR 4 and 5 (PIF4 and 5). Coincidence of increased PIF4/PIF5 transcript levels with the dark period allows nuclear accumulation of these factors, and in short days it phases maximal hypocotyl growth at dawn. During early night, PIF4 and PIF5 transcription is repressed by the Evening Complex (EC) proteins EARLY FLOWERING3 (ELF3), EARLY FLOWERING4 (ELF4), and LUX ARRHYTHMO (LUX). While ELF3 has an essential role in EC complex assembly, several lines of evidence indicate that this protein controls plant growth via other mechanisms that are presently unknown. Here, we show that the ELF3 and PIF4 proteins interact in an EC-independent manner, and that this interaction prevents PIF4 from activating its transcriptional targets. We also show that PIF4 overexpression leads to ELF3 protein destabilization, and that this effect is mediated indirectly by negative feedback regulation of photoactive PHYTOCHROME B (phyB). Physical interaction of the phyB photoreceptor with ELF3 has been reported, but its functional relevance remains poorly understood. Our findings establish that phyB is needed for ELF3 accumulation in the light, most likely by competing for CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)-mediated ubiquitination and the proteasomal degradation of ELF3. Our results explain the short hypocotyl phenotype of ELF3 overexpressors, despite their normal clock function, and provide a molecular framework for understanding how warm temperatures promote hypocotyl elongation and affect the endogenous clock.

Phytochrome-interacting transcription factors PIF4 and PIF5 induce leaf senescence in Arabidopsis

Plants initiate senescence to shed photosynthetically inefficient leaves. Light deprivation induces leaf senescence, which involves massive transcriptional reprogramming to dismantle cellular components and remobilize nutrients. In darkness, intermittent pulses of red light can inhibit senescence, likely via phytochromes. However, the precise molecular mechanisms transducing the signals from light perception to the inhibition of senescence remain elusive. Here, we show that in Arabidopsis, dark-induced senescence requires phytochrome-interacting transcription factors PIF4 and PIF5 (PIF4/PIF5). ELF3 and phytochrome B inhibit senescence by repressing PIF4/PIF5 at the transcriptional and post-translational levels, respectively. PIF4/PIF5 act in the signalling pathways of two senescence-promoting hormones, ethylene and abscisic acid, by directly activating expression of EIN3, ABI5 and EEL. In turn, PIF4, PIF5, EIN3, ABI5 and EEL directly activate the expression of the major senescence-promoting NAC transcription factor ORESARA1, thus forming multiple, coherent feed-forward loops. Our results reveal how classical light signalling connects to senescence in Arabidopsis.

Natural variation reveals that intracellular distribution of ELF3 protein is associated with function in the circadian clock

Natural selection of variants within the Arabidopsis thaliana circadian clock can be attributed to adaptation to varying environments. To define a basis for such variation, we examined clock speed in a reporter-modified Bay-0 x Shakdara recombinant inbred line and localized heritable variation. Extensive variation led us to identify EARLY FLOWERING3 (ELF3) as a major quantitative trait locus (QTL). The causal nucleotide polymorphism caused a short-period phenotype under light and severely dampened rhythm generation in darkness, and entrainment alterations resulted. We found that ELF3-Sha protein failed to properly localize to the nucleus, and its ability to accumulate in darkness was compromised. Evidence was provided that the ELF3-Sha allele originated in Central Asia. Collectively, we showed that ELF3 protein plays a vital role in defining its light-repressor action in the circadian clock and that its functional abilities are largely dependent on its cellular localization.

DOI:http://dx.doi.org/10.7554/eLife.02206.001

Life on Earth tends to follow a daily rhythm: some animals are awake during the day and asleep at night, whilst others are more active at night, or during the twilight around dawn and dusk. For many living things, these cycles of activity are driven by an internal body clock that helps the organism to adapt to the daily cycle of light and dark—and similar internal clocks also exist in plants.

These internal clocks define daily—or circadian—cycles whereby multiple genes are switched ‘on’ or ‘off’ at different time points in every 24-hr period. And, because light and ambient temperatures also vary with time of the day, many organisms use these external signals as cues to reset their own internal clocks. Moreover, the hours of daylight and temperature vary around the world, and also with the seasons, so plants and animals must be able to change how these external signals influence their internal clocks so that they stay in tune with the day/night cycle. However, it is not clear how they do this.

To explore this question, Anwer et al. grew plants that were from a cross between two types of the model plant Arabidopsis thaliana from different environments: one from Germany, and the other from Tajikistan in Central Asia. These offspring were also genetically engineered so that an enzyme that could give off light was produced under the control of the internal clock. Anwer et al. found that the plants continued to glow and fade with an almost daily rhythm even after external cues, such as changes in temperature or light, had been removed.

Different offspring plants consistently glowed and faded with different rhythms such that some had, for example, a 21-hr day and others a 28-hr day. These differences were caused by many genes that differed from the original German and Tajikistan parent plants, and Anwer et al. ‘mapped’ one of these genetic differences to a single gene. Offspring that inherited a version of a gene called ELF3 from the Tajikistan parent had internal clocks that ran faster when the plant was under the light. These plants also gradually stopped glowing as brightly as the German parent when they were kept in the dark, suggesting that their internal clocks were ‘ticking more softly’. It was already known that the ELF3 gene affected the circadian clock in plants, and Anwer et al. thus concluded that the plants with Tajikistan version of this gene, called ELF3-Sha, were also less able to reset their internal clocks to synchronize in response to external cues.

Anwer et al. also showed that the normal ELF3 protein is more likely to be found in the nucleus of a plant cell than the ELF3-Sha version, which might suggest that this protein is involved in switching genes off. Further research is now needed to uncover exactly how the ELF3 protein does this to keep the plant's internal clock ‘ticking’ correctly.

DOI:http://dx.doi.org/10.7554/eLife.02206.002

OsELF3 is involved in circadian clock regulation for promoting flowering under long-day conditions in rice

Heading date is a critical trait that determines cropping seasons and regional adaptability in rice (Oryza sativa). Research efforts during the last decade have identified some important photoperiod pathway genes that are conserved between Arabidopsis and rice. In this study, we identified a novel gene, Oryza sativa ELF3 (OsELF3), which is a putative homolog of the ELF3 gene in Arabidopsis thaliana. OsELF3 was required for the control of heading date under long-day conditions. Its Tos17-tagging mutants exhibited a delayed heading date phenotype only under long-day, but not short-day, conditions. OsELF3 was highly expressed in leaf blades, and the OsELF3 protein was localized in the nucleolus. An obvious diurnal rhythm of OsELF3 transcript level was observed, with a trough in the early day and a peak in the late night in wild-type plants. However, this expression pattern was disrupted in oself3 mutants. Further investigations showed that the expression of OsGI and Ghd7 was up-regulated in the oself3 mutant, indicating that OsELF3 acts as a negative regulator upstream of OsGI and Ghd7 in the flowering-time control under long-day conditions. The rhythmic expression of circadian clock-related genes, including some OsPRR members, was obviously affected in oself3 mutants. Our results indicated that OsELF3 acts as a floral activator in the long-day photoperiodic pathway via its crosstalk with the circadian clock in rice.

Genetic interactions between brassinosteroid-inactivating P450s and photomorphogenic photoreceptors in Arabidopsis thaliana

Plants use light as a source of information via a suite of photomorphogenic photoreceptors to optimize growth in response to their light environment. Growth-promoting hormones such as brassinosteroids also can modulate many of these responses. BAS1 and SOB7 are brassinosteroid-catabolizing P450s in Arabidopsis thaliana that synergistically/redundantly modulate photomorphogenic traits such as flowering time. The role of BAS1 and SOB7 in photomorphogenesis has been investigated by studying null-mutant genetic interactions with the photoreceptors phyA, phyB, and cry1 with regard to seed germination and flowering time. The removal of BAS1 and/or SOB7 rescued the low germination rate of the phyA-211 phyB-9 double-null mutant. With regard to floral induction, bas1-2 and sob7-1 showed a complex set of genetic interactions with photoreceptor-null mutants. Histochemical analysis of transgenic plants harboring BAS1:BAS1-GUS and SOB7:SOB7-GUS translational fusions under the control of their endogenous promoters revealed overlapping and distinct expression patterns. BAS1’s expression in the shoot apex increases during the phase transition from short-to-long-day growth conditions and requires phyB in red light. In summary, BAS1 and SOB7 displayed both simple and complex genetic interactions with the phytochromes in a plant-stage specific manner.

OsELF3-1, an ortholog of Arabidopsis early flowering 3, regulates rice circadian rhythm and photoperiodic flowering

Arabidopsis thaliana early flowering 3 (ELF3) as a zeitnehmer (time taker) is responsible for generation of circadian rhythm and regulation of photoperiodic flowering. There are two orthologs (OsELF3-1 and OsELF3-2) of ELF3 in rice (Oryza sativa), but their roles have not yet been fully identified. Here, we performed a functional characterization of OsELF3-1 and revealed it plays a more predominant role than OsELF3-2 in rice heading. Our results suggest OsELF3-1 can affect rice circadian systems via positive regulation of OsLHY expression and negative regulation of OsPRR1, OsPRR37, OsPRR73 and OsPRR95 expression. In addition, OsELF3-1 is involved in blue light signaling by activating early heading date 1 (Ehd1) expression to promote rice flowering under short-day (SD) conditions. Moreover, OsELF3-1 suppresses a flowering repressor grain number, plant height and heading date 7 (Ghd7) to indirectly accelerate flowering under long-day (LD) conditions. Taken together, our results indicate OsELF3-1 is essential for circadian regulation and photoperiodic flowering in rice.

TIME FOR COFFEE represses accumulation of the MYC2 transcription factor to provide time-of-day regulation of jasmonate signaling in Arabidopsis

Plants are confronted with predictable daily biotic and abiotic stresses that result from the day-night cycle. The circadian clock provides an anticipation mechanism to respond to these daily stress signals to increase fitness. Jasmonate (JA) is a phytohormone that mediates various growth and stress responses. Here, we found that the circadian-clock component TIME FOR COFFEE (TIC) acts as a negative factor in the JA-signaling pathway. We showed that the tic mutant is hypersensitive to growth-repressive effects of JA and displays altered JA-regulated gene expression. TIC was found to interact with MYC2, a key transcription factor of JA signaling. From this, we discovered that the circadian clock rhythmically regulates JA signaling. TIC is a key determinant in this circadian-gated process, and as a result, the tic mutant is defective in rhythmic JA responses to pathogen infection. TIC acts here by inhibiting MYC2 protein accumulation and by controlling the transcriptional repression of CORONATINE INSENSITIVE1 in an evening-phase-specific manner. Taken together, we propose that TIC acts as an output component of the circadian oscillator to influence JA signaling directly.

The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops

Circadian clocks synchronise biological processes with the day/night cycle, using molecular mechanisms that include interlocked, transcriptional feedback loops. Recent experiments identified the evening complex (EC) as a repressor that can be essential for gene expression rhythms in plants. Integrating the EC components in this role significantly alters our mechanistic, mathematical model of the clock gene circuit. Negative autoregulation of the EC genes constitutes the clock's evening loop, replacing the hypothetical component Y. The EC explains our earlier conjecture that the morning gene Pseudo-Response Regulator 9 was repressed by an evening gene, previously identified with Timing Of CAB Expression1 (TOC1). Our computational analysis suggests that TOC1 is a repressor of the morning genes Late Elongated Hypocotyl and Circadian Clock Associated1 rather than an activator as first conceived. This removes the necessity for the unknown component X (or TOC1mod) from previous clock models. As well as matching timeseries and phase-response data, the model provides a new conceptual framework for the plant clock that includes a three-component repressilator circuit in its complex structure.

HSP90 functions in the circadian clock through stabilization of the client F-box protein ZEITLUPE

The autoregulatory loops of the circadian clock consist of feedback regulation of transcription/translation circuits but also require finely coordinated cytoplasmic and nuclear proteostasis. Although protein degradation is important to establish steady-state levels, maturation into their active conformation also factors into protein homeostasis. HSP90 facilitates the maturation of a wide range of client proteins, and studies in metazoan clocks implicate HSP90 as an integrator of input or output. Here we show that the Arabidopsis circadian clock-associated F-box protein ZEITLUPE (ZTL) is a unique client for cytoplasmic HSP90. The HSP90-specific inhibitor geldanamycin and RNAi-mediated depletion of cytoplasmic HSP90 reduces levels of ZTL and lengthens circadian period, consistent with ztl loss-of-function alleles. Transient transfection of artificial microRNA targeting cytoplasmic HSP90 genes similarly lengthens period. Proteolytic targets of SCF(ZTL), TOC1 and PRR5, are stabilized in geldanamycin-treated seedlings, whereas the levels of closely related clock proteins, PRR3 and PRR7, are unchanged. An in vitro holdase assay, typically used to demonstrate chaperone activity, shows that ZTL can be effectively bound, and aggregation prevented, by HSP90. GIGANTEA, a unique stabilizer of ZTL, may act in the same pathway as HSP90, possibly linking these two proteins to a similar mechanism. Our findings establish maturation of ZTL by HSP90 as essential for proper function of the Arabidopsis circadian clock. Unlike metazoan systems, HSP90 functions here within the core oscillator. Additionally, F-box proteins as clients may place HSP90 in a unique and more central role in proteostasis.

A reduced-function allele reveals that EARLY FLOWERING3 repressive action on the circadian clock is modulated by phytochrome signals in Arabidopsis

Arabidopsis thaliana EARLY FLOWERING3 (ELF3) is essential for the generation of circadian rhythms. ELF3 has been proposed to restrict light signals to the oscillator through phytochrome photoreceptors, but that has not been explicitly shown. Furthermore, the genetic action of ELF3 within the clock had remained elusive. Here, we report a functional characterization of ELF3 through the analysis of the elf3-12 allele, which encodes an amino acid replacement in a conserved domain. Circadian oscillations persisted, and unlike elf3 null alleles, elf3-12 resulted in a short circadian period only under ambient light. The period shortening effect of elf3-12 was enhanced by the overexpression of phytochromes phyA and phyB. We found that elf3-12 was only modestly perturbed in resetting of the oscillator and in gating light-regulated gene expression. Furthermore, elf3-12 essentially displayed wild-type development. We identified targets of ELF3 transcriptional repression in the oscillator, highlighting the action at the morning gene PSEUDO-RESPONSE REGULATOR9. Taken together, we identified two separable roles for ELF3, one affecting the circadian network and the other affecting light input to the oscillator. This is consistent with a dual function of ELF3 as both an integrator of phytochrome signals and a repressor component of the core oscillator.

Phytochrome signaling mechanisms

Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.

Double loss-of-function mutation in EARLY FLOWERING 3 and CRYPTOCHROME 2 genes delays flowering under continuous light but accelerates it under long days and short days: an important role for Arabidopsis CRY2 to accelerate flowering time in continuous light

The photoperiodic response is one of the adaptation mechanisms to seasonal changes of lengths of day and night. The circadian clock plays pivotal roles in this process. In Arabidopsis, LHY, CCA1, ELF3, and other clock proteins play major roles in maintaining circadian rhythms. lhy;cca1 double mutants with severe defects in circadian rhythms showed accelerated flowering under short days (SDs), but delayed flowering under continuous light (LL). The protein level of the floral repressor SVP increased in lhy;cca1 mutants under LL, and the late-flowering phenotype of lhy;cca1 mutants was partially suppressed by svp, flc, or elf3. ELF3 interacted with both CCA1 and SVP, and elf3 suppressed the SVP accumulation in lhy;cca1 under LL. These results suggest that the unique mechanism of the inversion of the flowering response of lhy;cca1 under LL may involve both the ELF3-SVP/FLC-dependent and -independent pathways. In this work, elf3-1 seeds were mutagenized with heavy-ion beams and used to identify mutation(s) that delayed flowering under LL but not long days (LDs) or SDs even without ELF3. In this screening, seven candidate lines named suppressor of elf3 1 (self1), sel3, sel5, sel7, sel14, sel15, and sel20 were identified. Genetic analysis indicated that sel20 was a new deletion allele of a mutation in the blue light receptor, CRY2. A late-flowering phenotype and decrease of FT expression in the elf3;sel20 double mutant was obvious under LL but not under SDs or LDs. These results indicated that the late-flowering phenotype in the double mutant elf3;sel20 as well as in lhy;cca1 was affected by the presence of darkness. The results suggest that CRY2 may play more essential roles in the acceleration of flowering under LL than LDs or SDs.

Phytochrome signaling mechanisms

Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.

Genetic mapping of natural variation in a shade avoidance response: ELF3 is the candidate gene for a QTL in hypocotyl growth regulation

When plants become shaded by neighbouring plants, they perceive a decrease in the red/far-red (R/FR) ratio of the light environment, which provides an early and unambiguous warning of the presence of competing vegetation. The mechanistic bases of the natural genetic variation in response to shade signals remain largely unknown. This study demonstrates that a wide range of genetic variation for hypocotyl elongation in response to an FR pulse at the end of day (EOD), a light signal that simulates natural shade, exists between Arabidopsis accessions. A quantitative trait locus (QTL) mapping analysis was done in the Bayreuth×Shahdara recombinant inbred line population. EODINDEX1 is the most significant QTL identified in response to EOD. The Shahdara alleles at EODINDEX1 caused a reduced response to shade as a consequence of an impaired hypocotyl inhibition under white light, and an accelerated leaf movement rhythm, which correlated positively with the pattern of circadian expression of clock genes such as PRR7 and PRR9. Genetic and quantitative complementation analyses demonstrated that ELF3 is the most likely candidate gene underlying natural variation at EODINDEX1. In conclusion, ELF3 is proposed as a component of the shade avoidance signalling pathway responsible for the phenotypic differences between Arabidopsis populations in relation to adaptation in a changing light environment.

Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis

Quantitative Trait Loci (QTL) analyses in immortal populations are a powerful method for exploring the genetic mechanisms that control interactions of organisms with their environment. However, QTL analyses frequently do not culminate in the identification of a causal gene due to the large chromosomal regions often underlying QTLs. A reasonable approach to inform the process of causal gene identification is to incorporate additional genome-wide information, which is becoming increasingly accessible. In this work, we perform QTL analysis of the shade avoidance response in the Bayreuth-0 (Bay-0, CS954) x Shahdara (Sha, CS929) recombinant inbred line population of Arabidopsis. We take advantage of the complex pleiotropic nature of this trait to perform network analysis using co-expression, eQTL and functional classification from publicly available datasets to help us find good candidate genes for our strongest QTL, SAR2. This novel network analysis detected EARLY FLOWERING 3 (ELF3; AT2G25930) as the most likely candidate gene affecting the shade avoidance response in our population. Further genetic and transgenic experiments confirmed ELF3 as the causative gene for SAR2. The Bay-0 and Sha alleles of ELF3 differentially regulate developmental time and circadian clock period length in Arabidopsis, and the extent of this regulation is dependent on the light environment. This is the first time that ELF3 has been implicated in the shade avoidance response and that different natural alleles of this gene are shown to have phenotypic effects. In summary, we show that development of networks to inform candidate gene identification for QTLs is a promising technique that can significantly accelerate the process of QTL cloning.

Ambient temperature response establishes ELF3 as a required component of the core Arabidopsis circadian clock

Circadian clocks synchronize internal processes with environmental cycles to ensure optimal timing of biological events on daily and seasonal time scales. External light and temperature cues set the core molecular oscillator to local conditions. In Arabidopsis, EARLY FLOWERING 3 (ELF3) is thought to act as an evening-specific repressor of light signals to the clock, thus serving a zeitnehmer function. Circadian rhythms were examined in completely dark-grown, or etiolated, null elf3-1 seedlings, with the clock entrained by thermocycles, to evaluate whether the elf3 mutant phenotype was light-dependent. Circadian rhythms were absent from etiolated elf3-1 seedlings after exposure to temperature cycles, and this mutant failed to exhibit classic indicators of entrainment by temperature cues, consistent with global clock dysfunction or strong perturbation of temperature signaling in this background. Warm temperature pulses failed to elicit acute induction of temperature-responsive genes in elf3-1. In fact, warm temperature-responsive genes remained in a constitutively "ON" state because of clock dysfunction and, therefore, were insensitive to temperature signals in the normal time of day-specific manner. These results show ELF3 is broadly required for circadian clock function regardless of light conditions, where ELF3 activity is needed by the core oscillator to allow progression from day to night during either light or temperature entrainment. Furthermore, robust circadian rhythms appear to be a prerequisite for etiolated seedlings to respond correctly to temperature signals.

A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature

Plants regulate their time to flowering by gathering information from the environment. Photoperiod and temperature are among the most important environmental variables. Sub-optimal, but not near-freezing, temperatures regulate flowering through the thermosensory pathway, which overlaps with the autonomous pathway. Here we show that ambient temperature regulates flowering by two genetically distinguishable pathways, one requiring TFL1 and another requiring ELF3. The delay in flowering time observed at lower temperatures was partially suppressed in single elf3 and tfl1 mutants, whereas double elf3 tfl1 mutants were insensitive to temperature. tfl1 mutations abolished the temperature response in cryptochrome mutants that are deficient in photoperiod perception, but not in phyB mutants, which have a constitutive photoperiodic response. In contrast to tfl1, elf3 mutations were able to suppress the temperature response in phyB mutants, but not in cryptochrome mutants. Gene expression profiles revealed that the tfl1 and elf3 effects are due to the activation of different sets of genes, and identified CCA1 and SOC1/AGL20 as being important cross-talk points. Finally, genome-wide gene expression analysis strongly suggests a general and complementary role for ELF3 and TFL1 in temperature signalling.

Diurnal and circadian rhythms in the tomato transcriptome and their modulation by cryptochrome photoreceptors

BACKGROUND

Circadian clocks are internal molecular time-keeping mechanisms that provide living organisms with the ability to adjust their growth and physiology and to anticipate diurnal environmental changes. Circadian clocks, without exception, respond to light and, in plants, light is the most potent and best characterized entraining stimulus. The capacity of plants to respond to light is achieved through a number of photo-perceptive proteins including cryptochromes and phytochromes. There is considerable experimental evidence demonstrating the roles of photoreceptors in providing light input to the clock.

METHODOLOGY

In order to identify genes regulated by diurnal and circadian rhythms, and to establish possible functional relations between photoreceptors and the circadian clock in tomato, we monitored the temporal transcription pattern in plants entrained to long-day conditions, either by large scale comparative profiling, or using a focused approach over a number of photosensory and clock-related genes by QRT-PCR. In parallel, focused transcription analyses were performed in cry1a- and in CRY2-OX tomato genotypes.

CONCLUSIONS

We report a large series of transcript oscillations that shed light on the complex network of interactions among tomato photoreceptors and clock-related genes. Alteration of cryptochrome gene expression induced major changes in the rhythmic oscillations of several other gene transcripts. In particular, over-expression of CRY2 had an impact not only on day/night fluctuations but also on rhythmicity under constant light conditions. Evidence was found for widespread diurnal oscillations of transcripts encoding specific enzyme classes (e.g. carotenoid biosynthesis enzymes) as well as for post-transcriptional diurnal and circadian regulation of the CRY2 transcript.

Modulation of environmental responses of plants by circadian clocks

Circadian clocks are signalling networks that enhance an organism's relationship with the rhythmic environment. The plant circadian clock modulates a wide range of physiological and biochemical events, such as stomatal and organ movements, photosynthesis and induction of flowering. Environmental signals regulate the phase and period of the plant circadian clock, which results in an approximate synchronization of clock outputs with external events. One of the consequences of circadian control is that stimuli of the same strength applied at different times of the day can result in responses of different intensities. This is known as 'gating'. Gating of a signal may allow plants to better process and react to the wide range and intensities of environmental signals to which they are constantly subjected. Light signalling, stomatal movements and low-temperature responses are examples of signalling pathways that are gated by the circadian clock. In this review, we describe the many levels at which the circadian clock interacts with responses to the environment. We discuss how environmental rhythms of temperature and light intensity entrain the circadian clock, how photoperiodism may be regulated by the relationship between environmental rhythms and the phasing of clock outputs, and how gating modulates the sensitivity of the clock and other responses to environmental and physiological signals. Finally, we describe evidence that the circadian clock can increase plant fitness.

The GRAS protein SCL13 is a positive regulator of phytochrome-dependent red light signaling, but can also modulate phytochrome A responses

Phytochrome photoreceptors enable plants to perceive divergent light signals leading to adaptive changes in response to differing environmental conditions. However, the mechanism of light signal transduction is not fully understood. Here we report the identification of a new signaling intermediate from Arabidopsis thaliana, Scarecrow-like (SCL)13, which serves as a positive regulator of continuous red light signals downstream of phytochrome B (phyB). SCL13 antisense lines exhibit reduced sensitivity towards red light, but only a distinct subset of phyB-mediated responses is affected, indicating that SCL13 executes its major role in hypocotyl elongation during de-etiolation. Genetic evidence suggests that SCL13 is also needed to modulate phytochrome A (phyA) signal transduction in a phyB-independent way. The SCL13 protein is localized in the cytoplasm, but can also be detected in the nucleus. Overexpression of both a nuclear and cytoplasmic localized SCL13 protein leads to a hypersensitive phenotype under red light indicating that SCL13 is biologically active in both compartments. SCL13 is a member of the plant-specific GRAS protein family, which is involved in various different developmental and signaling pathways. A previously identified phytochrome A signaling intermediate, PAT1, belongs to the same subbranch of GRAS proteins as SCL13. Although both proteins are involved in phytochrome signaling, each is specific for a different light condition and regulates a different subset of responses.

Independent roles for EARLY FLOWERING 3 and ZEITLUPE in the control of circadian timing, hypocotyl length, and flowering time

The circadian clock regulates many aspects of plant development, including hypocotyl elongation and photoperiodic induction of flowering. ZEITLUPE (ZTL) is a clock-related F-box protein, and altered ZTL expression causes fluence rate-dependent circadian period effects, and altered hypocotyl elongation and flowering time. EARLY FLOWERING 3 (ELF3) is a novel protein of unknown biochemical function. elf3 mutations cause light-dependent circadian dysfunction, elongated hypocotyls, and early flowering. Although both genes affect similar processes, their relationship is unclear. Here we show that the effects of ZTL and ELF3 on circadian clock function and early photomorphogenesis are additive. The long period of ztl mutations and ELF3 overexpressors are more severe than either alone. Dark-release experiments showing additivity in phase advances suggest that the arrthymicity caused by ZTL overexpression and that of the elf3-1 mutation arise through independent pathways. A similar additive effect on hypocotyl elongation in red and blue light is also observed. In contrast, ELF3 and ZTL overexpressors act similarly to control flowering time in long days through the CONSTANS/FLOWERING LOCUS T (CO/FT) pathway. ZTL overexpression does not delay flowering through changes in GIGANTEA or FLAVIN-BINDING, KELCH REPEAT, F-BOX levels, but through a ZTL-mediated reduction in CO expression. In contrast, ELF3 negatively regulates CO, FT, and GIGANTEA transcript levels, as the expression of all three genes is increased in elf3-1. The elf3-1 co-1 double mutant flowers much earlier in long days than co-1, although FT message levels remain very low. These results show that elf3-1 can derepress late flowering through a CO-independent mechanism. ELF3 may act at more than one juncture, possibly posttranscriptionally.

PIL5, a phytochrome-interacting basic helix-loop-helix protein, is a key negative regulator of seed germination in Arabidopsis thaliana

The first decision made by an angiosperm seed, whether to germinate or not, is based on integration of various environmental signals such as water and light. The phytochromes (Phys) act as red and far-red light (Pfr) photoreceptors to mediate light signaling through yet uncharacterized pathways. We report here that the PIF3-like 5 (PIL5) protein, a basic helix-loop-helix transcription factor, is a key negative regulator of phytochrome-mediated seed germination. PIL5 preferentially interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB). Analyses of a pil5 mutant in conjunction with phyA and phyB mutants, a pif3 pil5 double mutant, and PIL5 overexpression lines indicate that PIL5 is a negative factor in Phy-mediated promotion of seed germination, inhibition of hypocotyl negative gravitropism, and inhibition of hypocotyl elongation. Our data identify PIL5 as the first Phy-interacting protein that regulates seed germination.

Phenotypic characterization of a photomorphogenic mutant

Light is arguably the most important abiotic factor controlling plant growth and development throughout their life cycle. Plants have evolved sophisticated light-sensing mechanisms to monitor fluctuations in light quality, intensity, direction and periodicity (day length). In Arabidopsis, three families of photoreceptors have been identified by molecular genetic studies. The UV-A/blue light receptors cryptochromes and the red/far-red receptors phytochromes control an overlapping set of responses including photoperiodic flowering induction and de-etiolation. Phototropins are the primary photoreceptors for a set of specific responses to UV-A/blue light such as phototropism, chloroplast movement and stomatal opening. Mutants affecting a photoreceptor have a characteristic phenotype. It is therefore possible to determine the specific developmental responses and the photoreceptor pathway(s) affected in a mutant by performing an appropriate set of photobiological and genetic experiments. In this paper, we outline the principal and easiest experiments that can be performed to obtain a first indication about the nature of the photobiological defect in a given mutant.