GIGANTEA regulates phytochrome A-mediated photomorphogenesis independently of its role in the circadian clock

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

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

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 CBL-CIPK network is involved in the physiological crosstalk between plant growth and stress adaptation

Plants have evolved to deal with different stresses during plant growth, relying on complex interactions or crosstalk between multiple signalling pathways in plant cells. In this sophisticated regulatory network, Ca2+ transients in the cytosol ([Ca2+ ]cyt ) act as major physiological signals to initiate appropriate responses. The CALCINEURIN B-LIKE PROTEIN (CBL)-CBL-INTERACTING PROTEIN KINASE (CIPK) network relays physiological signals characterised by [Ca2+ ]cyt transients during plant development and in response to environmental changes. Many studies are aimed at elucidating the role of the CBL-CIPK network in plant growth and stress responses. This review discusses the involvement of the CBL-CIPK pathways in two levels of crosstalk between plant development and stress adaptation: direct crosstalk through interaction with regulatory proteins, and indirect crosstalk through adaptation of correlated physiological processes that affect both plant development and stress responses. This review thus provides novel insights into the physiological roles of the CBL-CIPK network in plant growth and stress adaptation.

ZmGI2 regulates flowering time through multiple flower development pathways in maize

GIGANTEA (GI) encodes a component of the circadian clock core oscillator and has been identified as a regulatory pathway of the circadian rhythm and photoperiodic flowering in model plants. However, the regulatory pathway of GI affecting flowering time is unknown in maize. Here, we identified that the zmgi2 mutant flowered earlier than the wild type under long day (LD) conditions, whereas the difference in flowering time was not apparent under short day (SD) conditions. The 24 h optimal expression of the gene in the stem apex meristems (SAM) appeared at 9 h after dawn under LD conditions and at 11 h after dawn under SD conditions. DAP-Seq and RNA-Seq further revealed that ZmGI2 delays flowering by directly binding to the upstream regions of ZmVOZs, ZmZCN8 and ZmFPF1 to repress the expression of these genes and by directly binding to the upstream regions of ZmARR11, ZmDOF and ZmUBC11 to promote the expression of these genes. The genetic and biochemical evidence suggests a model for the potential role of ZmGI2 in regulating the flowering time-dependent photoperiodic pathway. This study provides novel insights into the function of ZmGIs in maize and further demonstrates their potential importance for floral transition. These results contribute to a comprehensive understanding of the molecular mechanisms and regulatory networks of GI transcription factors in regulating flowering time in maize.

Transcriptome analysis reveals the roles of phytohormone signaling in tea plant (Camellia sinensis L.) flower development

BACKGROUND

Tea plant (Camellia sinensis (L.) O. Kuntze) is an important economic tea crop, but flowering will consume a lot of nutrients of C. sinensis, which will seriously affect the nutritional growth of C. sinensis. However, there are few studies on the development mechanism of C. sinensis flower, and most studies focus on a single C. sinensis cultivar.

RESULTS

Here, we identified a 92-genes' C. sinensis flower development core transcriptome from the transcriptome of three C. sinensis cultivars ('BaiYe1', 'HuangJinYa' and 'SuChaZao') in three developmental stages (bud stage, white bud stage and blooming stage). In addition, we also reveal the changes in endogenous hormone contents and the expression of genes related to synthesis and signal transduction during the development of C. sinensis flower. The results showed that most genes of the core transcriptome were involved in circadian rhythm and autonomous pathways. Moreover, there were only a few flowering time integrators, only 1 HD3A, 1 SOC1 and 1 LFY, and SOC1 played a dominant role in the development of C. sinensis flower. Furthermore, we screened out 217 differentially expressed genes related to plant hormone synthesis and 199 differentially expressed genes related to plant hormone signal transduction in C. sinensis flower development stage.

CONCLUSIONS

By constructing a complex hormone regulation network of C. sinensis flowering, we speculate that MYC, FT, SOC1 and LFY play key roles in the process of endogenous hormones regulating C. sinensis flowering development. The results of this study can a provide reference for the further study of C. sinensis flowering mechanism.

The BrGI Circadian Clock Gene Is Involved in the Regulation of Glucosinolates in Chinese Cabbage

Circadian clocks integrate environmental cues with endogenous signals to coordinate physiological outputs. Clock genes in plants are involved in many physiological and developmental processes, such as photosynthesis, stomata opening, stem elongation, light signaling, and floral induction. Many Brassicaceae family plants, including Chinese cabbage (Brassica rapa ssp. pekinensis), produce a unique glucosinolate (GSL) secondary metabolite, which enhances plant protection, facilitates the design of functional foods, and has potential medical applications (e.g., as antidiabetic and anticancer agents). The levels of GSLs change diurnally, suggesting a connection to the circadian clock system. We investigated whether circadian clock genes affect the biosynthesis of GSLs in Brassica rapa using RNAi-mediated suppressed transgenic Brassica rapa GIGENTEA homolog (BrGI knockdown; hereafter GK1) Chinese cabbage. GIGANTEA plays an important role in the plant circadian clock system and is related to various developmental and metabolic processes. Using a validated GK1 transgenic line, we performed RNA sequencing and high-performance liquid chromatography analyses. The transcript levels of many GSL pathway genes were significantly altered in GK1 transgenic plants. In addition, GSL contents were substantially reduced in GK1 transgenic plants. We report that the BrGI circadian clock gene is required for the biosynthesis of GSLs in Chinese cabbage plants.

GIGANTEA confers susceptibility to plants during spot blotch attack by regulating salicylic acid signalling pathway

Plants throughout their development are challenged by different abiotic and biotic stresses. Growth and developmental plasticity of a plant is under the strict surveillance of the diurnal and circadian control mechanism, fine-tuned by the biological clock. Success of plant life-cycle resides on the continual battle against pathogen that they encounter at different developmental stages. GIGANTEA (GI), a higher plant specific nuclear protein, has been shown to play a major role in shaping plant development by coupling clock function to the circadian phasing of gene expression in Arabidopsis. Despite the central role of GI in regulating light signalling, clock function, flowering time control and in abiotic stress tolerance, its possible function in pathogen defence is not well known. Here we show that, GI expression positively correlates with susceptibility of plants to the spot blotch pathogen infection in both Arabidopsis and bread wheat. Furthermore, we also show that GI expression promotes disease severity by down regulating the salicylic acid (SA) accumulation and alters the phenylpropanoid pathway, thereby suppressing PR gene expression. It is possible that GI-mediated regulation of SA signalling may be one of the possible ways of coupling the light-temperature input pathway to pathogen defence through circadian clock. Our results indicate that the down-regulation of GI could be beneficial in generating disease tolerant crop plants for sustainable agriculture.

A flowering time locus dependent on E2 in soybean

Soybean [Glycine max (L.) Merrill] is very sensitive to changes in photoperiod as a typical short-day plant. Photoperiodic flowering influences soybean latitudinal adaptability and yield to a considerable degree. Identifying new quantitative trait loci (QTLs) controlling flowering time is a powerful initial approach for elucidating the mechanisms underlying flowering time and adaptation to different latitudes in soybean. In this study, we developed a Recombinant Inbred Lines (RILs) population and recorded flowering time under natural long-day conditions. We also constructed a high-density genetic map by genotyping-by-sequencing and used it for QTL mapping. In total, we detected twelve QTLs, four of which are stable and named by qR1-2, qR1-4, qR1-6.1, and qR1-10, respectively. Among these four QTLs, qR1-4 and qR1-6.1 are novel. QTL mapping in two sub-populations classified by the genotype of the maturity locus E2, genetic interaction evaluation between E2 and qR1-2, and qRT-PCR indicated that E2 has an epistatic effect on qR1-2, and that causal gene of qR1-2 acts upstream of E2. We presumed the most likely candidate genes according to the resequencing data and briefly analyzed the geographic distributions of these genes. These findings will be beneficial for our understanding of the mechanisms underlying photoperiodic flowering in soybean, contribute to further investigate of E2, and provide genetic resources for molecular breeding of soybean.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01224-1.

Gigantea: Uncovering New Functions in Flower Development

GIGANTEA (GI) is a gene involved in multiple biological functions, which have been analysed and are partially conserved in a series of mono- and dicotyledonous plant species. The identified biological functions include control over the circadian rhythm, light signalling, cold tolerance, hormone signalling and photoperiodic flowering. The latter function is a central role of GI, as it involves a multitude of pathways, both dependent and independent of the gene CONSTANS(CO), as well as on the basis of interaction with miRNA. The complexity of the gene function of GI increases due to the existence of paralogs showing changes in genome structure as well as incidences of sub- and neofunctionalization. We present an updated report of the biological function of GI, integrating late insights into its role in floral initiation, flower development and volatile flower production.

Pleiotropy in developmental regulation by flowering-pathway genes: is it an evolutionary constraint?

Pleiotropy occurs when one gene influences more than one trait, contributing to genetic correlations among traits. Consequently, it is considered a constraint on the evolution of adaptive phenotypes because of potential antagonistic selection on correlated traits, or, alternatively, preservation of functional trait combinations. Such evolutionary constraints may be mitigated by the evolution of different functions of pleiotropic genes in their regulation of different traits. Arabidopsis thaliana flowering-time genes, and the pathways in which they operate, are among the most thoroughly studied regarding molecular functions, phenotypic effects, and adaptive significance. Many of them show strong pleiotropic effects. Here, we review examples of pleiotropy of flowering-time genes and highlight those that also influence seed germination. Some genes appear to operate in the same genetic pathways when regulating both traits, whereas others show diversity of function in their regulation, either interacting with the same genetic partners but in different ways or potentially interacting with different partners. We discuss how functional diversification of pleiotropic genes in the regulation of different traits across the life cycle may mitigate evolutionary constraints of pleiotropy, permitting traits to respond more independently to environmental cues, and how it may even contribute to the evolutionary divergence of gene function across taxa.

Multi-level Modulation of Light Signaling by GIGANTEA Regulates Both the Output and Pace of the Circadian Clock

Integration of environmental signals with endogenous biological processes is essential for organisms to thrive in their natural environment. Being entrained by periodic environmental changes, the circadian clock incorporates external information to coordinate physiological processes, phasing them to the optimal time of the day and year. Here, we present a pivotal role for the clock component GIGANTEA (GI) as a genome-wide regulator of transcriptional networks mediating growth and adaptive processes in plants. We provide mechanistic details on how GI integrates endogenous timing with light signaling pathways through the global modulation of PHYTOCHROME-INTERACTING FACTORs (PIFs). Gating of the activity of these transcriptional regulators by GI directly affects a wide array of output rhythms, including photoperiodic growth. Furthermore, we uncover a role for PIFs in mediating light input to the circadian oscillator and show how their regulation by GI is required to set the pace of the clock in response to light-dark cycles.

Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation

The circadian clock regulates physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have integrated RNA-sequencing and protein mass spectrometry data to comparatively analyse the lhycca1, prr7prr9, gi and toc1 circadian clock mutant rosette at the end of day and end of night. Each mutant affects specific sets of genes and proteins, suggesting that the circadian clock regulation is modular. Furthermore, each circadian clock mutant maintains its own dynamically fluctuating transcriptome and proteome profile specific to subcellular compartments. Most of the measured protein levels do not correlate with changes in their corresponding transcripts. Transcripts and proteins that have coordinated changes in abundance are enriched for carbohydrate- and cold-responsive genes. Transcriptome changes in all four circadian clock mutants also affect genes encoding starch degradation enzymes, transcription factors and protein kinases. The comprehensive transcriptome and proteome datasets demonstrate that future system-driven research of the circadian clock requires multi-level experimental approaches. Our work also shows that further work is needed to elucidate the roles of post-translational modifications and protein degradation in the regulation of clock-related processes.

Physiological and molecular mechanisms underlying the integration of light and temperature cues in Arabidopsis thaliana seeds

The relief of dormancy and the promotion of seed germination are of extreme importance for a successful seedling establishment. Although alternating temperatures and light are signals promoting the relief of seed dormancy, the underlying mechanisms of their interaction in seeds are scarcely known. By exposing imbibed Arabidopsis thaliana dormant seeds to two-day temperature cycles previous of a red light pulse, we demonstrate that the germination mediated by phytochrome B requires the presence of functional PSEUDO-RESPONSE REGULATOR 7 (PRR7) and TIMING OF CAB EXPRESSION 1 (TOC1) alleles. In addition, daily cycles of alternating temperatures in darkness reduce the protein levels of DELAY OF GERMINATION 1 (DOG1), allowing the expression of TOC1 to induce seed germination. Our results suggest a functional role for some components of the circadian clock related with the action of DOG1 for the integration of alternating temperatures and light signals in the relief of seed dormancy. The synchronization of germination by the synergic action of light and temperature through the activity of circadian clock might have ecological and adaptive consequences.

Insights into the Drought and Heat Avoidance Mechanism in Summer-Dormant Mediterranean Tall Fescue

Summer dormancy is an evolutionary response that some perennial cool-season grasses adopted as an avoidance strategy to escape summer drought and heat. It is correlated with superior survival after severe summer droughts in many perennial grass species originating from Mediterranean environments. Understanding the genetic mechanism and environmental determinants of summer dormancy is important for interpreting the evolutionary history of seasonal dormancy and for the development of genomic tools to improve the efficiency of genetic selection for this important trait. The objectives of this research are to assess morphological and biochemical attributes that seem to be specific for the characterization of summer dormancy in tall fescue, and to validate the hypothesis that genes underlying stem determinacy might be involved in the mechanism of summer dormancy. Our results suggest that vernalization is an important requirement in the onset of summer dormancy in tall fescue. Non-vernalized tall fescue plants do not exhibit summer dormancy as vernalized plants do and behave more like summer-active types. This is manifested by continuation of shoot growth and high root activity in water uptake during summer months. Therefore, summer dormancy in tall fescue should be tested only in plants that underwent vernalization and are not subjected to water deficit during summer months. Total phenolic concentration in tiller bases (antioxidants) does not seem to be related to vernalization. It is most likely an environmental response to protect meristems from oxidative stress. Sequence analysis of the TFL1 homolog CEN gene from tall fescue genotypes belonging to summer-dormant and summer-active tall fescue types showed a unique deletion of three nucleotides specific to the dormant genotypes. Higher tiller bud numbers in dormant plants that were not allowed to flower and complete the reproductive cycle, confirmed that stem determinacy is a major component in the mechanism of summer dormancy. The number of variables identified in these studies as potential players in summer dormancy in tall fescue including vernalization, TFL1/CEN, water status, and protection from oxidative stress are a further confirmation that summer dormancy is a quantitative trait controlled by several genes with varying effects and prone to genotype by environment interactions.

Molecular mechanisms and ecological function of far-red light signalling

Land plants possess the ability to sense and respond to far-red light (700-760 nm), which serves as an important environmental cue. Due to the nature of far-red light, it is not absorbed by chlorophyll and thus is enriched in canopy shade and will also penetrate deeper into soil than other visible wavelengths. Far-red light responses include regulation of seed germination, suppression of hypocotyl growth, induction of flowering and accumulation of anthocyanins, which depend on one member of the phytochrome photoreceptor family, phytochrome A (phyA). Here, we review the current understanding of the underlying molecular mechanisms of how plants sense far-red light through phyA and the physiological responses to this light quality. Light-activated phytochromes act on two primary pathways within the nucleus; suppression of the E3 ubiquitin ligase complex CUL4/DDB1^COP1/SPA and inactivation of the PHYTOCHROME INTERACTING FACTOR (PIF) family of bHLH transcription factors. These pathways integrate with other signal transduction pathways, including phytohormones, for tissue and developmental stage specific responses. Unlike other phytochromes that mediate red-light responses, phyA is transported from the cytoplasm to the nucleus in far-red light by the shuttle proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). However, additional mechanisms must exist that shift the action of phyA to far-red light; current hypotheses are discussed.

ABA-dependent control of GIGANTEA signalling enables drought escape via up-regulation of FLOWERING LOCUS T in Arabidopsis thaliana

One strategy deployed by plants to endure water scarcity is to accelerate the transition to flowering adaptively via the drought escape (DE) response. In Arabidopsis thaliana, activation of the DE response requires the photoperiodic response gene GIGANTEA (GI) and the florigen genes FLOWERING LOCUS T (FT) and TWIN SISTER OF FT (TSF). The phytohormone abscisic acid (ABA) is also required for the DE response, by promoting the transcriptional up-regulation of the florigen genes. The mode of interaction between ABA and the photoperiodic genes remains obscure. In this work we use a genetic approach to demonstrate that ABA modulates GI signalling and consequently its ability to activate the florigen genes. We also reveal that the ABA-dependent activation of FT, but not TSF, requires CONSTANS (CO) and that impairing ABA signalling dramatically reduces the expression of florigen genes with little effect on the CO transcript profile. ABA signalling thus has an impact on the core genes of photoperiodic signalling GI and CO by modulating their downstream function and/or activities rather than their transcript accumulation. In addition, we show that as well as promoting flowering, ABA simultaneously represses flowering, independent of the florigen genes. Genetic analysis indicates that the target of the repressive function of ABA is the flowering-promoting gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), a transcription factor integrating floral cues in the shoot meristem. Our study suggests that variations in ABA signalling provide different developmental information that allows plants to co-ordinate the onset of the reproductive phase according to the available water resources.

A New Insight of Salt Stress Signaling in Plant

Many studies have been conducted to understand plant stress responses to salinity because irrigation-dependent salt accumulation compromises crop productivity and also to understand the mechanism through which some plants thrive under saline conditions. As mechanistic understanding has increased during the last decades, discovery-oriented approaches have begun to identify genetic determinants of salt tolerance. In addition to osmolytes, osmoprotectants, radical detoxification, ion transport systems, and changes in hormone levels and hormone-guided communications, the Salt Overly Sensitive (SOS) pathway has emerged to be a major defense mechanism. However, the mechanism by which the components of the SOS pathway are integrated to ultimately orchestrate plant-wide tolerance to salinity stress remains unclear. A higher-level control mechanism has recently emerged as a result of recognizing the involvement of GIGANTEA (GI), a protein involved in maintaining the plant circadian clock and control switch in flowering. The loss of GI function confers high tolerance to salt stress via its interaction with the components of the SOS pathway. The mechanism underlying this observation indicates the association between GI and the SOS pathway and thus, given the key influence of the circadian clock and the pathway on photoperiodic flowering, the association between GI and SOS can regulate growth and stress tolerance. In this review, we will analyze the components of the SOS pathways, with emphasis on the integration of components recognized as hallmarks of a halophytic lifestyle.

DhEFL2, 3 and 4, the three EARLY FLOWERING4-like genes in a Doritaenopsis hybrid regulate floral transition

DhEFL2, 3 and 4 regulate the flowering of Doritaenopsis . These genes could rescue elf4-1 phenotype in Arabidopsis while its overexpression delayed flowering. Phalaenopsis are popular floral plants, and studies on orchid flowering genes could help develop off-season cultivars. Early flowering 4 (ELF4) of A. thaliana has been shown to be involved in photoperiod perception and circadian regulation. We isolated two members of the ELF4 family from Doritaenopsis hybrid (Doritaenopsis 'Tinny Tender' (Doritaenopsis Happy Smile × Happy Valentine)), namely, DhEFL2 and DhEFL3 (DhEFL4 has been previously cloned). Multiple alignment analysis of the deduced amino acid sequences of the three DhEFL homologs showed that DhEFL4 and DhEFL2 are similar with 72% identical amino acids, whereas DhEFL3 is divergent with 72% similarity with DhEFL2 and 68% similarity with DhEFL4. DhEFL3 forms a separate phylogenetic subgroup and is far away from DhEFL2 and DhEFL4. The diurnal expression patterns of DhEFL2, 3, and 4 are similar in the long-day photoperiod conditions; however, in the short-day conditions, DhEFL3 is different from DhEFL2 and 4. For the DhEFL2, 3, and 4 genes, the strongest audience expression organs are the stem, petal and bud, respectively. The ectopic expression of DhEFL2, 3, or 4 in transgenic A. thaliana plants (Ws-2 ecotype) showed novel phenotypes by late flowering and more rosette leaves. The ectopic expression of DhEFL2, 3, or 4 could complement the elf4-1 flowering time and hypocotyl length defects in transgenic A. thaliana elf4-1 mutant plants. These results strongly suggest that DhEFL2, 3, and 4 may be involved in regulation of flower formation and floral induction in Doritaenopsis.

Allelic polymorphism of GIGANTEA is responsible for naturally occurring variation in circadian period in Brassica rapa

GIGANTEA (GI) was originally identified by a late-flowering mutant in Arabidopsis, but subsequently has been shown to act in circadian period determination, light inhibition of hypocotyl elongation, and responses to multiple abiotic stresses, including tolerance to high salt and cold (freezing) temperature. Genetic mapping and analysis of families of heterogeneous inbred lines showed that natural variation in GI is responsible for a major quantitative trait locus in circadian period in Brassica rapa. We confirmed this conclusion by transgenic rescue of an Arabidopsis gi-201 loss of function mutant. The two B. rapa GI alleles each fully rescued the delayed flowering of Arabidopsis gi-201 but showed differential rescue of perturbations in red light inhibition of hypocotyl elongation and altered cold and salt tolerance. The B. rapa R500 GI allele, which failed to rescue the hypocotyl and abiotic stress phenotypes, disrupted circadian period determination in Arabidopsis. Analysis of chimeric B. rapa GI alleles identified the causal nucleotide polymorphism, which results in an amino acid substitution (S264A) between the two GI proteins. This polymorphism underlies variation in circadian period, cold and salt tolerance, and red light inhibition of hypocotyl elongation. Loss-of-function mutations of B. rapa GI confer delayed flowering, perturbed circadian rhythms in leaf movement, and increased freezing and increased salt tolerance, consistent with effects of similar mutations in Arabidopsis. Collectively, these data suggest that allelic variation of GI-and possibly of clock genes in general-offers an attractive target for molecular breeding for enhanced stress tolerance and potentially for improved crop yield.

Probing entrainment of Ostreococcus tauri circadian clock by green and blue light through a mathematical modeling approach

Most organisms anticipate daily environmental variations and orchestrate cellular functions thanks to a circadian clock which entrains robustly to the day/night cycle, despite fluctuations in light intensity due to weather or seasonal variations. Marine organisms are also subjected to fluctuations in light spectral composition as their depth varies, due to differential absorption of different wavelengths by sea water. Studying how light input pathways contribute to circadian clock robustness is therefore important. Ostreococcus tauri, a unicellular picoplanktonic marine green alga with low genomic complexity and simple cellular organization, has become a promising model organism for systems biology. Functional and modeling approaches have shown that a core circadian oscillator based on orthologs of Arabidopsis TOC1 and CCA1 clock genes accounts for most experimental data acquired under a wide range of conditions. Some evidence points at putative light input pathway(s) consisting of a two-component signaling system (TCS) controlled by the only two histidine kinases (HK) of O. tauri. LOV-HK is a blue light photoreceptor under circadian control, that is required for circadian clock function. An involvement of Rhodopsin-HK (Rhod-HK) is also conceivable since rhodopsin photoreceptors mediate blue to green light input in animal circadian clocks. Here, we probe the role of LOV-HK and Rhod-HK in mediating light input to the TOC1-CCA1 oscillator using a mathematical model incorporating the TCS hypothesis. This model agrees with clock gene expression time series representative of multiple environmental conditions in blue or green light, characterizing entrainment by light/dark cycles, free-running in constant light, and resetting. Experimental and theoretical results indicate that both blue and green light can reset O. tauri circadian clock. Moreover, our mathematical analysis suggests that Rhod-HK is a blue-green light receptor and drives the clock together with LOV-HK.

GIGANTEA - an emerging story

GIGANTEA (GI) is a plant specific nuclear protein and functions in diverse physiological processes such as flowering time regulation, light signaling, hypocotyl elongation, control of circadian rhythm, sucrose signaling, starch accumulation, chlorophyll accumulation, transpiration, herbicide tolerance, cold tolerance, drought tolerance, and miRNA processing. It has been five decades since its discovery but the biochemical function of GI and its different domains are still unclear. Although it is known that both GI transcript and GI protein are clock controlled, the regulation of its abundance and functions at the molecular level are still some of the unexplored areas of intensive research. Since GI has many important pleotropic functions as described above scattered through literature, it is worthwhile and about time to encapsulate the available information in a concise review. Therefore, in this review, we are making an attempt to summarize (i) the various interconnected roles that GI possibly plays in the fine-tuning of plant development, and (ii) the known mutations of GI that have been instrumental in understanding its role in distinct physiological processes.

Natural diversity in daily rhythms of gene expression contributes to phenotypic variation

Daily rhythms of gene expression provide a benefit to most organisms by ensuring that biological processes are activated at the optimal time of day. Although temporal patterns of expression control plant traits of agricultural importance, how natural genetic variation modifies these patterns during the day and how precisely these patterns influence phenotypes is poorly understood. The circadian clock regulates the timing of gene expression, and natural variation in circadian rhythms has been described, but circadian rhythms are measured in artificial continuous conditions that do not reflect the complexity of biologically relevant day/night cycles. By studying transcriptional rhythms of the evening-expressed gene gigantea (GI) at high temporal resolution and during day/night cycles, we show that natural variation in the timing of GI expression occurs mostly under long days in 77 Arabidopsis accessions. This variation is explained by natural alleles that alter light sensitivity of GI, specifically in the evening, and that act at least partly independent of circadian rhythms. Natural alleles induce precise changes in the temporal waveform of GI expression, and these changes have detectable effects on phytochrome interacting factor 4 expression and growth. Our findings provide a paradigm for how natural alleles act within day/night cycles to precisely modify temporal gene expression waveforms and cause phenotypic diversity. Such alleles could confer an advantage by adjusting the activity of temporally regulated processes without severely disrupting the circadian system.

Circadian rhythms of hydraulic conductance and growth are enhanced by drought and improve plant performance

Circadian rhythms enable plants to anticipate daily environmental variations, resulting in growth oscillations under continuous light. Because plants daily transpire up to 200% of their water content, their water status oscillates from favourable during the night to unfavourable during the day. We show that rhythmic leaf growth under continuous light is observed in plants that experience large alternations of water status during an entrainment period, but is considerably buffered otherwise. Measurements and computer simulations show that this is due to oscillations of plant hydraulic conductance and plasma membrane aquaporin messenger RNA abundance in roots during continuous light. A simulation model suggests that circadian oscillations of root hydraulic conductance contribute to acclimation to water stress by increasing root water uptake, thereby favouring growth and photosynthesis. They have a negative effect in favourable hydraulic conditions. Climate-driven control of root hydraulic conductance therefore improves plant performances in both stressed and non-stressed conditions.

Circadian rhythms allow plants to respond to diurnal fluctuations in the environment. Here Caldeira et al. find that circadian control of hydraulic conductance, aquaporin expression and leaf growth are entrained by oscillations of plant water status and promote water uptake in drought-stressed plants.

Light perception and signalling by phytochrome A

In etiolated seedlings, phytochrome A (phyA) mediates very-low-fluence responses (VLFRs), which initiate de-etiolation at the interphase between the soil and above-ground environments, and high-irradiance responses (HIR), which complete de-etiolation under dense canopies and require more sustained activation with far-red light. Light-activated phyA is transported to the nucleus by FAR-RED ELONGATED HYPOCOTYL1 (FHY1). The nuclear pool of active phyA increases under prolonged far-red light of relatively high fluence rates. This condition maximizes the rate of FHY1-phyA complex assembly and disassembly, allowing FHY1 to return to the cytoplasm to translocate further phyA to the nucleus, to replace phyA degraded in the proteasome. The core signalling pathways downstream of nuclear phyA involve the negative regulation of CONSTITUTIVE PHOTOMORPHOGENIC 1, which targets for degradation transcription factors required for photomorphogenesis, and PHYTOCHROME-INTERACTING FACTORs, which are transcription factors that repress photomorphogenesis. Under sustained far-red light activation, released FHY1 can also be recruited with active phyA to target gene promoters as a transcriptional activator, and nuclear phyA signalling activates a positive regulatory loop involving BELL-LIKE HOMEODOMAIN 1 that reinforces the HIR.

The circadian clock-associated gene gigantea1 affects maize developmental transitions

The circadian clock is an internal timing mechanism that allows plants to make developmental decisions in accordance with environmental conditions. In model plants, circadian clock-associated gigantea (gi) genes are directly involved in control of growth and developmental transitions. The maize gigantea1 (gi1) gene is the more highly expressed of the two gi homeologs, and its function is uncharacterized. To understand the role of gi1 in the regulatory networks of the maize circadian clock system, gi1 mutants were evaluated for changes in flowering time, phase change and growth control. When grown in long-day (LD) photoperiods, gi1 mutants flowered earlier than non-mutant plants, but this difference was not apparent in short-day (SD) photoperiods. Therefore, gi1 participates in a pathway that suppresses flowering in LD photoperiods, but not in SD. Part of the underlying cause of early flowering was up-regulated expression of the FT-like floral activator gene zea mays centroradialis8 (zcn8) and the CONSTANS-like flowering regulatory gene constans of zea mays1 (conz1). gi1 mutants also underwent vegetative phase change earlier and grew taller than non-mutant plants. These findings indicate gi1 has a repressive function in multiple regulatory pathways that govern maize growth and development.

Release of SOS2 kinase from sequestration with GIGANTEA determines salt tolerance in Arabidopsis

Environmental challenges to plants typically entail retardation of vegetative growth and delay or cessation of flowering. Here we report a link between the flowering time regulator, GIGANTEA (GI), and adaptation to salt stress that is mechanistically based on GI degradation under saline conditions, thus retarding flowering. GI, a switch in photoperiodicity and circadian clock control, and the SNF1-related protein kinase SOS2 functionally interact. In the absence of stress, the GI:SOS2 complex prevents SOS2-based activation of SOS1, the major plant Na(+)/H(+)-antiporter mediating adaptation to salinity. GI overexpressing, rapidly flowering, plants show enhanced salt sensitivity, whereas gi mutants exhibit enhanced salt tolerance and delayed flowering. Salt-induced degradation of GI confers salt tolerance by the release of the SOS2 kinase. The GI-SOS2 interaction introduces a higher order regulatory circuit that can explain in molecular terms, the long observed connection between floral transition and adaptive environmental stress tolerance in Arabidopsis.

Crosstalk between the circadian clock and innate immunity in Arabidopsis

The circadian clock integrates temporal information with environmental cues in regulating plant development and physiology. Recently, the circadian clock has been shown to affect plant responses to biotic cues. To further examine this role of the circadian clock, we tested disease resistance in mutants disrupted in CCA1 and LHY, which act synergistically to regulate clock activity. We found that cca1 and lhy mutants also synergistically affect basal and resistance gene-mediated defense against Pseudomonas syringae and Hyaloperonospora arabidopsidis. Disrupting the circadian clock caused by overexpression of CCA1 or LHY also resulted in severe susceptibility to P. syringae. We identified a downstream target of CCA1 and LHY, GRP7, a key constituent of a slave oscillator regulated by the circadian clock and previously shown to influence plant defense and stomatal activity. We show that the defense role of CCA1 and LHY against P. syringae is at least partially through circadian control of stomatal aperture but is independent of defense mediated by salicylic acid. Furthermore, we found defense activation by P. syringae infection and treatment with the elicitor flg22 can feedback-regulate clock activity. Together this data strongly supports a direct role of the circadian clock in defense control and reveal for the first time crosstalk between the circadian clock and plant innate immunity.

Mathematical modeling of an oscillating gene circuit to unravel the circadian clock network of Arabidopsis thaliana

The Arabidopsis thaliana circadian clock is an interconnected network highly tractable to systems approaches. Most elements in the transcriptional-translational oscillator were identified by genetic means and the expression of clock genes in various mutants led to the founding hypothesis of a positive-negative feedback loop being the core clock. The identification of additional clock genes beyond those defined in the core led to the use of systems approaches to decipher this angiosperm oscillator circuit. Kinetic modeling was first used to explain periodicity effects of various circadian mutants. This conformed in a flexible way to experimental details. Such observations allowed a recursive use of hypothesis generating from modeling, followed by experimental corroboration. More recently, the biochemical finding of new description of a DNA-binding activity for one class of clock components directed improvements in feature generation, one of which revealed that the core of the oscillator is a negative-negative feedback loop. The recursive use of modeling and experimental validation has thus revealed many essential transcriptional components that drive negative arms in the circadian oscillator. What awaits is to more fully describe the positive arms and an understanding of how additional pathways converge on the clock.

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.

A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering

Flowering is indicative of the transition from vegetative to reproductive phase, a critical event in the life cycle of plants. In soybean (Glycine max), a flowering quantitative trait locus, FT2, corresponding to the maturity locus E2, was detected in recombinant inbred lines (RILs) derived from the varieties "Misuzudaizu" (ft2/ft2; JP28856) and "Moshidou Gong 503" (FT2/FT2; JP27603). A map-based cloning strategy using the progeny of a residual heterozygous line (RHL) from the RIL was employed to isolate the gene responsible for this quantitative trait locus. A GIGANTEA ortholog, GmGIa (Glyma10g36600), was identified as a candidate gene. A common premature stop codon at the 10th exon was present in the Misuzudaizu allele and in other near isogenic lines (NILs) originating from Harosoy (e2/e2; PI548573). Furthermore, a mutant line harboring another premature stop codon showed an earlier flowering phenotype than the original variety, Bay (E2/E2; PI553043). The e2/e2 genotype exhibited elevated expression of GmFT2a, one of the florigen genes that leads to early flowering. The effects of the E2 allele on flowering time were similar among NILs and constant under high (43°N) and middle (36°N) latitudinal regions in Japan. These results indicate that GmGIa is the gene responsible for the E2 locus and that a null mutation in GmGIa may contribute to the geographic adaptation of soybean.

Light-regulated nuclear import and degradation of Arabidopsis phytochrome-A N-terminal fragments

The photoreceptor phytochrome-A (phyA) regulates germination and seedling establishment by mediating very low fluence (VLFR) and far-red high irradiance (FR-HIR) responses in Arabidopsis thaliana. In darkness, phyA homodimers exist in the biologically inactive Pr form and are localized in the cytoplasm. Light induces formation of the biologically active Pfr form and subsequent rapid nuclear import. PhyA Pfr, in contrast to the Pr form, is labile and has a half-life of ∼30 min. We produced transgenic plants in a phyA-201 null background that express the PHYA-yellow fluorescent protein (YFP) or the PHYA686-YFP-dimerization domain (DD) and PHYA686-YFP-DD-nuclear localization signal (NLS) or PHYA686-YFP-DD-nuclear exclusion signal (NES) fusion proteins. The PHYA686-YFP fusion proteins contained the N-terminal domain of phyA (686 amino acid residues), a short DD and the YFP. Here we report that (i) PHYA686-YFP-DD fusion protein is imported into the nucleus in a light-dependent fashion; (ii) neither of the PHYA686 fusion proteins is functional in FR-HIR and nuclear VLFR; and (iii) the phyA-dependent, blue light-induced inhibition of hypocotyl growth is mediated by the PHYA686-YFP-DD-NES but not by the PHYA686-YFP-DD-NLS and PHYA686-YFP-DD fusion proteins. We demonstrate that (i) light induces degradation of all PHYA N-terminal-containing fusion proteins and (ii) these N-terminal domain-containing fusion proteins including the constitutively nuclear PHYA686-YFP-DD-NLS and predominantly cytoplasmic PHYA686-YFP-DD-NES degrade at comparable rates but markedly more slowly than PHYA-YFP, whereas (iii) light-induced degradation of the native phyA is faster compared with PHYA-YFP.

Network news: prime time for systems biology of the plant circadian clock

Whole-transcriptome analyses have established that the plant circadian clock regulates virtually every plant biological process and most prominently hormonal and stress response pathways. Systems biology efforts have successfully modeled the plant central clock machinery and an iterative process of model refinement and experimental validation has contributed significantly to the current view of the central clock machinery. The challenge now is to connect this central clock to the output pathways for understanding how the plant circadian clock contributes to plant growth and fitness in a changing environment. Undoubtedly, systems approaches will be needed to integrate and model the vastly increased volume of experimental data in order to extract meaningful biological information. Thus, we have entered an era of systems modeling, experimental testing, and refinement. This approach, coupled with advances from the genetic and biochemical analyses of clock function, is accelerating our progress towards a comprehensive understanding of the plant circadian clock network.

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.

Expression, purification and characterisation of GIGANTEA: a circadian clock-controlled regulator of photoperiodic flowering in plants

The Arabidopsis thaliana (Arabidopsis) GIGANTEA (GI) gene is a central component of the photoperiodic flowering pathway. While it has been 40 years since the first mutant alleles of GI were described much is still unknown about the molecular mechanism of GI action. To investigate the biochemistry and domain organisation (and ultimately to give a greater understanding of the role of GI in floral induction), it is first necessary to produce significant quantities of purified protein. Soluble affinity-tagged full-length GI was expressed in Escherichia coli (E. coli) and was stabilised by the addition of the detergent n-dodecyl-β-D-maltoside (DDM) to storage and purification buffers. Stabilised GI was purified using a variety of chromatographic methods, and characterised using a selection of biochemical techniques including circular dichroism, and dynamic light scattering. This showed that purified GI contained secondary structure, but was polydisperse in solution. Electron microscopy suggests a possible tetramer arrangement of GI. Limited proteolytic digests and mass spectrometry were used to identify potential GI domains. This led to the identification of a predicted 46 kDa amino-terminal GI domain. GI was also expressed in Sf9 insect cells using the baculovirus expression system. GI produced via this route gave insoluble protein.

Identification and molecular characterization of a Brachypodium distachyon GIGANTEA gene: functional conservation in monocot and dicot plants

Developmental phase change and flowering transition are emerging as potential targets for biomass agriculture in recent years. The GIGANTEA (GI) gene is one of the central regulators that direct flowering promotion and phase transition. In this work, we isolated a GI gene orthologue from the small annual grass Brachypodium distachyon inbred line Bd21 (Brachypodium), which is perceived as a potential model monocot for studies on bioenergy grass species. A partial GI gene sequence was identified from a Brachypodium expressed sequence tag library, and a full-size gene (BdGI) was amplified from a Brachypodium cDNA library using specific primer sets designed through analysis of monocot GI gene sequences. The BdGI gene was up-regulated by light and cold. A circadian rhythm set by light-dark transition also regulated the expression of the BdGI gene. The deduced amino acid sequence of the BdGI protein shares higher than 70% of sequence identity with the GI proteins in monocots and Arabidopsis. In addition, the BdGI protein is constitutively targeted to the nucleus and physically interacts with the ZEITLUPE (ZTL) and CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) proteins, like the Arabidopsis GI protein. Interestingly, heterologous expression of the BdGI gene in a GI-deficient Arabidopsis mutant rescued efficiently the late flowering phenotype. Together, our data indicate that the role of the GI gene in flowering induction is conserved in Arabidopsis and Brachypodium. It is envisioned that the GI genes of bioenergy grasses as well as Brachypodium could be manipulated to improve biomass by engineering developmental timing of phase transitions.

Analysis of a post-translational steroid induction system for GIGANTEA in Arabidopsis

BACKGROUND

To investigate the link between the flowering time gene GIGANTEA (GI) and downstream genes, an inducible GI system was developed in Arabidopsis thaliana L. Heynh. Transgenic Arabidopsis plant lines were generated with a steroid-inducible post-translational control system for GI. The gene expression construct consisted of the coding region of the GI protein fused to that of the ligand binding domain of the rat glucocorticoid receptor (GR). This fusion gene was expressed from the constitutive cauliflower mosaic virus 35S promoter and was introduced into plants carrying the gi-2 mutation. Application of the steroid dexamethasone (DEX) was expected to result in activation of the GI-GR protein and its relocation from the cytoplasm to the nucleus.

RESULTS

Application of DEX to the transgenic plant lines rescued the late flowering phenotype conferred by the gi-2 mutation. However, despite their delayed flowering in the absence of steroid, the transgenic lines expressed predicted GI downstream genes such as CONSTANS (CO) to relatively high levels. Nevertheless, increased CO and FLOWERING LOCUS T (FT) transcript accumulation was observed in transgenic plants within 8 h of DEX treatment compared to controls which was consistent with promotion of flowering by DEX. Unlike CO and FT, there was no change in the abundance of transcript of two other putative GI downstream genes HEME ACTIVATOR PROTEIN 3A (HAP3A) or TIMING OF CHLOROPHYLL A/B BINDING PROTEIN 1 (TOC1) after DEX application.

CONCLUSION

The post-translational activation of GI and promotion of flowering by steroid application supports a nuclear role for GI in the floral transition. Known downstream flowering time genes CO and FT were elevated by DEX treatment, but not other proposed targets HAP3A and TOC1, indicating that the expression of these genes may be less directly regulated by GI.

OWL1: an Arabidopsis J-domain protein involved in perception of very low light fluences

To sense ambient light conditions in order to optimize their growth and development, plants employ a battery of photoreceptors responsive to light quality and quantity. Essential for the sensing of red and far-red (FR) light is the phytochrome family of photoreceptors. Among them, phytochrome A is special because it mediates responses to different light conditions, including both very low fluences (very low fluence response [VLFR]) and high irradiances (high irradiance response [HIR]). In contrast with the FR-HIR signaling pathway, in which several intermediates of the signaling pathway have been identified, specific components of the VLFR pathway remain unknown. Here, we describe owl1 (for orientation under very low fluences of light), a mutant that is specific for the VLFR, suggesting that VLFR and HIR pathways are genetically distinct, although some common mechanisms can be observed. OWL1 codes for a ubiquitous J-domain protein essential for germination, cotyledon opening, hypocotyl elongation, and deviation of the direction of hypocotyl growth from the vertical under very low light conditions. Additionally, we observed a flowering phenotype suggesting a role for the VLFR during the whole life cycle of a plant. OWL1 interacts with the basic helix-loop-helix HFR1 (LONG HYPOCOTYL IN FAR-RED) transcription factor, previously characterized as a component of the FR-HIR pathway. Both proteins are involved in the agravitropic response under FR light. We propose a central function of OWL1 in the VLFR pathway, which is essential for plant survival under unfavorable light conditions.

Towards a systems biology approach to understanding seed dormancy and germination

Seed germination is the first adaptive decision in the development of many land plants. Advances in genetics and molecular physiology have taught us much about the control of germination using the model plant Arabidopsis thaliana. Here we review the current state of the art with an emphasis on mechanistic considerations and explore the potential impact of a systems biology approach to the problem.

Fragments of the key flowering gene GIGANTEA are associated with helitron-type sequences in the Pooideae grass Lolium perenne

BACKGROUND

Helitrons are a class of transposable elements which have been identified in a number of species of plants, animals and fungi. They are unique in their proposed rolling-circle mode of replication, have a highly variable copy-number and have been implicated in the restructuring of coding sequences both by their insertion into existing genes and by their incorporation of transcriptionally competent gene fragments. Helitron discovery depends on identifying associated DNA signature sequences and comprehensive evaluation of helitron contribution to a particular genome requires detailed computational analysis of whole genome sequence. Therefore, the role which helitrons have played in modelling non-model plant genomes is largely unknown.

RESULTS

Cloning of the flowering gene GIGANTEA (GI) from a BAC library of the Pooideae grass Lolium perenne (perennial ryegrass) identified the target gene and several GI pseudogene fragments spanning the first five exons. Analysis of genomic sequence 5' and 3' of one these GI fragments revealed motifs consistent with helitron-type transposon insertion, specifically a putative 5'-A (downward arrow) T-3' insertion site containing 5'-TC and CTAG-3' borders with a sub-terminal 16 bp hairpin. Screening of a BAC library of the closely related grass species Festuca pratensis (meadow fescue) indicated similar helitron-associated GI fragments present in this genome, as well as non-helitron associated GI fragments derived from the same region of GI. In order to investigate the possible extent of ancestral helitron-activity in L. perenne, a methylation-filtered GeneThresher genomic library developed from this species was screened for potential helitron 3' hairpin sequences associated with a 3'-CTRR motif. This identified 7 potential helitron hairpin-types present between at least 9 and 51 times within the L. perenne methylation-filtered library.

CONCLUSION

This represents evidence for a possible ancestral role for helitrons in modelling the genomes of Lolium and related species.

A role for multiple circadian clock genes in the response to signals that break seed dormancy in Arabidopsis

Plant seeds can sense diverse environmental signals and integrate the information to regulate developmental responses, such as dormancy and germination. The circadian clock confers a growth advantage on plants and uses environmental information for entrainment. Here, we show that normal circadian clock gene function is essential for the response to dormancy-breaking signals in seeds. We show that mutations in the clock genes LATE ELONGATED HYPOCOTYL, CIRCADIAN CLOCK ASSOCIATED1 (CCA1), and GIGANTEA (GI) cause germination defects in response to low temperature, alternating temperatures, and dry after-ripening. We demonstrate that the transcriptional clock is arrested in an evening-like state in dry seeds but rapidly entrains to light/dark cycles in ambient temperatures upon imbibition. Consistent with a role for clock genes in seed dormancy control, CCA1 expression is transcriptionally induced in response to dry after-ripening and that after-ripening affects the amplitude of subsequent transcriptional clock gene oscillations. Control of abscisic acid- and gibberellin-related gene expression in seeds requires normal circadian function, and GI and TIMING OF CAB EXPRESSION1 regulate the response to ABA and GA in seeds. We conclude that circadian clock genes play a key role in the integration of environmental signaling controlling dormancy release in plants.

Comparative genomic analysis of light-regulated transcripts in the Solanaceae

Background

Plants use different light signals to adjust their growth and development to the prevailing environmental conditions. Studies in the model species Arabidopsis thaliana and rice indicate that these adjustments are mediated by large changes in the transcriptome. Here we compared transcriptional responses to light in different species of the Solanaceae to investigate common as well as species-specific changes in gene expression.

Results

cDNA microarrays were used to identify genes regulated by a transition from long days (LD) to short days (SD) in the leaves of potato and tobacco plants, and by phytochrome B (phyB), the photoreceptor that represses tuberization under LD in potato. We also compared transcriptional responses to photoperiod in Nicotiana tabacum Maryland Mammoth (MM), which flowers only under SD, with those of Nicotiana sylvestris, which flowers only under LD conditions. Finally, we identified genes regulated by red compared to far-red light treatments that promote germination in tomato.

Conclusion

Most of the genes up-regulated in LD were associated with photosynthesis, the synthesis of protective pigments and the maintenance of redox homeostasis, probably contributing to the acclimatization to seasonal changes in irradiance. Some of the photoperiodically regulated genes were the same in potato and tobacco. Others were different but belonged to similar functional categories, suggesting that conserved as well as convergent evolutionary processes are responsible for physiological adjustments to seasonal changes in the Solanaceae. A β-ZIP transcription factor whose expression correlated with the floral transition in Nicotiana species with contrasting photoperiodic responses was also regulated by photoperiod and phyB in potato, and is a candidate gene to act as a general regulator of photoperiodic responses. Finally, GIGANTEA, a gene that controls flowering time in Arabidopsis thaliana and rice, was regulated by photoperiod in the leaves of potato and tobacco and by red compared to far-light treatments that promote germination in tomato seeds, suggesting that a conserved light signaling cascade acts across developmental contexts and species.

The circadian system in higher plants

The circadian clock regulates diverse aspects of plant growth and development and promotes plant fitness. Molecular identification of clock components, primarily in Arabidopsis, has led to recent rapid progress in our understanding of the clock mechanism in higher plants. Using mathematical modeling and experimental approaches, workers in the field have developed a model of the clock that incorporates both transcriptional and posttranscriptional regulation of clock genes. This cell-autonomous clock, or oscillator, generates rhythmic outputs that can be monitored at the cellular and whole-organism level. The clock not only confers daily rhythms in growth and metabolism, but also interacts with signaling pathways involved in plant responses to the environment. Future work will lead to a better understanding of how the clock and other signaling networks are integrated to provide plants with an adaptive advantage.

Gene expression analysis of light-modulated germination in tomato seeds

Tomato (Solanum lycopersicum) seed germination can be inhibited by continuous irradiation with far-red light (FRc) and re-induced by a subsequent red light pulse. In this study, we carried out a global transcript analysis of seeds subjected to FRc inhibitory treatment, with and without a subsequent red light pulse, using potato cDNA microarrays. We also identified and characterized genes involved in light-modulated germination as elements of the phytochrome signalling pathway. Microarray data showed that the inhibition of germination by FRc involves the induction of a large number of genes and the repression of a significantly smaller quantity. Multivariate analysis established an underlying pattern of expression dependent on physiological treatment and incubation time, and identified different groups of genes associated with dormancy maintenance, inhibition and promotion of germination. We showed that ELIP, CSN6, SOS2 and RBP are related to the photocontrol of germination. These genes are known to participate in other physiological processes, but their participation in germination has not been suggested previously. Light quality regulates the tomato seed transcriptome during phytochrome-modulated germination through changes in the expression of certain sets of genes. In addition, ELIP and GIGANTEA were confirmed as components of the phytochrome A signalling pathway during FRc inhibition of germination.

Acceleration of flowering during shade avoidance in Arabidopsis alters the balance between FLOWERING LOCUS C-mediated repression and photoperiodic induction of flowering

The timing of the floral transition in Arabidopsis (Arabidopsis thaliana) is influenced by a number of environmental signals. Here, we have focused on acceleration of flowering in response to vegetative shade, a condition that is perceived as a decrease in the ratio of red to far-red radiation. We have investigated the contributions of several known flowering-time pathways to this acceleration. The vernalization pathway promotes flowering in response to extended cold via transcriptional repression of the floral inhibitor FLOWERING LOCUS C (FLC); we found that a low red to far-red ratio, unlike cold treatment, lessened the effects of FLC despite continued FLC expression. A low red to far-red ratio required the photoperiod-pathway genes GIGANTEA (GI) and CONSTANS (CO) to fully accelerate flowering in long days and did not promote flowering in short days. Together, these results suggest a model in which far-red enrichment can bypass FLC-mediated late flowering by shifting the balance between FLC-mediated repression and photoperiodic induction of flowering to favor the latter. The extent of this shift was dependent upon environmental parameters, such as the length of far-red exposure. At the molecular level, we found that far-red enrichment generated a phase delay in GI expression and enhanced CO expression and activity at both dawn and dusk. Finally, our analysis of the contribution of PHYTOCHROME AND FLOWERING TIME1 (PFT1) to shade-mediated rapid flowering has led us to suggest a new model for the involvement of PFT1 in light signaling.