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

Use of transcriptome sequencing to understand the pistillate flowering in hickory (Carya cathayensis Sarg.)

BACKGROUND

Different from herbaceous plants, the woody plants undergo a long-period vegetative stage to achieve floral transition. They then turn into seasonal plants, flowering annually. In this study, a preliminary model of gene regulations for seasonal pistillate flowering in hickory (Carya cathayensis) was proposed. The genome-wide dynamic transcriptome was characterized via the joint-approach of RNA sequencing and microarray analysis.

RESULTS

Differential transcript abundance analysis uncovered the dynamic transcript abundance patterns of flowering correlated genes and their major functions based on Gene Ontology (GO) analysis. To explore pistillate flowering mechanism in hickory, a comprehensive flowering gene regulatory network based on Arabidopsis thaliana was constructed by additional literature mining. A total of 114 putative flowering or floral genes including 31 with differential transcript abundance were identified in hickory. The locations, functions and dynamic transcript abundances were analyzed in the gene regulatory networks. A genome-wide co-expression network for the putative flowering or floral genes shows three flowering regulatory modules corresponding to response to light abiotic stimulus, cold stress, and reproductive development process, respectively. Totally 27 potential flowering or floral genes were recruited which are meaningful to understand the hickory specific seasonal flowering mechanism better.

CONCLUSIONS

Flowering event of pistillate flower bud in hickory is triggered by several pathways synchronously including the photoperiod, autonomous, vernalization, gibberellin, and sucrose pathway. Totally 27 potential flowering or floral genes were recruited from the genome-wide co-expression network function module analysis. Moreover, the analysis provides a potential FLC-like gene based vernalization pathway and an 'AC' model for pistillate flower development in hickory. This work provides an available framework for pistillate flower development in hickory, which is significant for insight into regulation of flowering and floral development of woody plants.

Dynamics of the shade-avoidance response in Arabidopsis

Shade-intolerant plants perceive the reduction in the ratio of red light (R) to far-red light (FR) as a warning of competition with neighboring vegetation and display a suite of developmental responses known as shade avoidance. In recent years, major progress has been made in understanding the molecular mechanisms underlying shade avoidance. Despite this, little is known about the dynamics of this response and the cascade of molecular events leading to plant adaptation to a low-R/FR environment. By combining genome-wide expression profiling and computational analyses, we show highly significant overlap between shade avoidance and deetiolation transcript profiles in Arabidopsis (Arabidopsis thaliana). The direction of the response was dissimilar at the early stages of shade avoidance and congruent at the late ones. This latter regulation requires LONG HYPOCOTYL IN FAR RED1/SLENDER IN CANOPY SHADE1 and phytochrome A, which function largely independently to negatively control shade avoidance. Gene network analysis highlights a subnetwork containing ELONGATED HYPOCOTYL5 (HY5), a master regulator of deetiolation, in the wild type and not in phytochrome A mutant upon prolonged low R/FR. Network analysis also highlights a direct connection between HY5 and HY5 HOMOLOG (HYH), a gene functionally implicated in the inhibition of hypocotyl elongation and known to be a direct target of the HY5 transcription factor. Kinetics analysis show that the HYH gene is indeed late induced by low R/FR and that its up-regulation depends on the action of HY5, since it does not occur in hy5 mutant. Therefore, we propose that one way plants adapt to a low-R/FR environment is by enhancing HY5 function.

BRANCHED1 interacts with FLOWERING LOCUS T to repress the floral transition of the axillary meristems in Arabidopsis

Plant architecture shows a large degree of developmental plasticity. Some of the key determinants are the timing of the floral transition induced by a systemic flowering signal (florigen) and the branching pattern regulated by key factors such as BRANCHED1 (BRC1). Here, we report that BRC1 interacts with the florigen proteins FLOWERING LOCUS T (FT) and TWIN SISTER OF FT (TSF) but not with TERMINAL FLOWER1, a floral repressor. FT protein induced in leaves moves into the subtended bud, suggesting that FT protein also plays a role in promotion of the floral transition in the axillary meristem (AM). The brc1-2 mutant shows an earlier floral transition in the axillary shoots compared with the wild type, suggesting that BRC1 plays a role in delaying the floral transition of the AMs. Genetic and gene expression analyses suggest that BRC1 interferes with florigen (FT and TSF) function in the AMs. Consistent with this, BRC1 ectopically expressed in the shoot apical meristem delays the floral transition in the main shoot. These results taken together suggest that BRC1 protein interacts with FT and TSF proteins and modulates florigen activity in the axillary buds to prevent premature floral transition of the AMs.

High temperature acclimation through PIF4 signaling

Ambient temperature has direct consequences for plant functioning. Many plant species are able to adjust reproductive timing and development to optimize fitness to changes in ambient temperatures. Understanding the molecular networks of how plants cope with high temperatures is essential to counteract the effects of global warming and to secure future crop productivity. Several recent papers reported that Arabidopsis thaliana responses to changing light conditions and high temperature, and their underlying signaling mechanisms are highly similar and involve the basic helix-loop-helix (bHLH) transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4). In this opinion article we discuss the mechanisms of PIF4-mediated acclimation to increased ambient temperature with focus on timing of flowering and morphological acclimation.

Photoreceptor signaling networks in plant responses to shade

The dynamic light environment of vegetation canopies is perceived by phytochromes, cryptochromes, phototropins, and UV RESISTANCE LOCUS 8 (UVR8). These receptors control avoidance responses to preclude exposure to limiting or excessive light and acclimation responses to cope with conditions that cannot be avoided. The low red/far-red ratios of shade light reduce phytochrome B activity, which allows PHYTOCHROME INTERACTING FACTORS (PIFs) to directly activate the transcription of auxin-synthesis genes, leading to shade-avoidance responses. Direct PIF interaction with DELLA proteins links gibberellin and brassinosteroid signaling to shade avoidance. Shade avoidance also requires CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1), a target of cryptochromes, phytochromes, and UVR8. Multiple regulatory loops and the input of the circadian clock create a complex network able to respond even to subtle threats of competition with neighbors while still compensating for major environmental fluctuations such as the day-night cycles.

PFT1, a transcriptional Mediator complex subunit, controls root hair differentiation through reactive oxygen species (ROS) distribution in Arabidopsis

Root hair morphogenesis is driven by an amalgam of interacting processes controlled by complex signaling events. Redox processes and transcriptional control are critical for root hair development. However, the molecular mechanisms that integrate redox state and transcription are largely unknown. To elucidate a possible role of transcriptional Mediators in root hair formation, we analyzed the Arabidopsis root hair phenotype of T-DNA insertion lines that harbor homozygous mutations in genes encoding Mediator subunits. Genetic evidence indicates that the Mediator subunits PFT1/MED25 and MED8 are critical for root hair differentiation, but act via separate mechanisms. Transcriptional profiling of pft1 roots revealed that PFT1 activates a subset of hydrogen peroxide (H(2)O(2))-producing class III peroxidases. pft1 mutants showed perturbed H(2)O(2) and superoxide (O(2)(·-)) distribution, suggesting that PFT1 is essential to maintain redox homeostasis in the root. Chemical treatments rescued the pft1 mutant phenotype, indicating that correct reactive oxygen species (ROS) distribution is an essential prerequisite for root hair differentiation. In addition, PFT1 positively regulates cell wall remodeling genes that are essential for root hair formation. Our results demonstrate that PFT1 maintains ROS distribution which, in turn, controls root hair differentiation. Thus, our findings reveal a novel mechanism in which the Mediator controls ROS homeostasis by regulating the transcriptional machinery.

Arabidopsis COP1 and SPA genes are essential for plant elongation but not for acceleration of flowering time in response to a low red light to far-red light ratio

Plants sense vegetative shade as a reduction in the ratio of red light to far-red light (R:FR). Arabidopsis (Arabidopsis thaliana) responds to a reduced R:FR with increased elongation of the hypocotyl and the leaf petioles as well as with an acceleration of flowering time. The repressor of light signaling, CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1), has been shown previously to be essential for the shade-avoidance response in seedlings. Here, we have investigated the roles of COP1 and the COP1-interacting SUPPRESSOR OF PHYA-105 (SPA) proteins in seedling and adult facets of the shade-avoidance response. We show that COP1 and the four SPA genes are essential for hypocotyl and leaf petiole elongation in response to low R:FR, in a fashion that involves the COP1/SPA ubiquitination target LONG HYPOCOTYL IN FR LIGHT1 but not ELONGATED HYPOCOTYL5. In contrast, the acceleration of flowering in response to a low R:FR was normal in cop1 and spa mutants, thus demonstrating that the COP1/SPA complex is only required for elongation responses to vegetative shade and not for shade-induced early flowering. We further show that spa mutant seedlings fail to exhibit an increase in the transcript levels of the auxin biosynthesis genes YUCCA2 (YUC2), YUC8, and YUC9 in response to low R:FR, suggesting that an increase in auxin biosynthesis in vegetative shade requires SPA function. Consistent with this finding, expression of the auxin-response marker gene DR5::GUS did not increase in spa mutant seedlings exposed to low R:FR. We propose that COP1/SPA activity, via LONG HYPOCOTYL IN FR LIGHT1, is required for shade-induced modulation of the auxin biosynthesis pathway and thereby enhances cell elongation in low R:FR.

Proteasome-mediated turnover of Arabidopsis MED25 is coupled to the activation of FLOWERING LOCUS T transcription

The Mediator complex is a greater than 1-megadalton complex, composed of about 30 subunits and found in most eukaryotes, whose main role is to transmit signals from DNA-bound transcription factors to RNA Polymerase II. The proteasome is emerging as an important regulator of transcription during both initiation and elongation. It is increasing the number of cases where the proteolysis of transcriptional activators by the proteasome activates their function. This counterintuitive phenomenon was called "activation by destruction." Here, we show that, in Arabidopsis (Arabidopsis thaliana), PHYTOCHROME AND FLOWERING TIME1 (PFT1), the MEDIATOR25 (MED25) subunit of the plant Mediator complex, is degraded by the proteasome and that proteasome-mediated PFT1 turnover is coupled to its role in stimulating the transcription of FLOWERING LOCUS T, the plant florigen, which is involved in the process of flowering induction. We further identify two novel RING-H2 proteins that target PFT1 for degradation. We show that MED25-BINDING RING-H2 PROTEIN1 (MBR1) and MBR2 bind to PFT1 in yeast (Saccharomyces cerevisiae) and in vitro, and they promote PFT1 degradation in vivo, in a RING-H2-dependent way, typical of E3 ubiquitin ligases. We further show that both MBR1 and MBR2 also promote flowering by PFT1-dependent and -independent mechanisms. Our findings extend the phenomenon of activation by destruction to a Mediator subunit, adding a new mechanism by which Mediator subunits may regulate downstream genes in specific pathways. Furthermore, we show that two novel RING-H2 proteins are involved in the destruction of PFT1, adding new players to this process in plants.

The mediator complex subunit PFT1 interferes with COP1 and HY5 in the regulation of Arabidopsis light signaling

Arabidopsis (Arabidopsis thaliana) mutants hypersensitive to far-red light were isolated under a light program of alternating red and far-red light pulses and were named eid (for empfindlicher im dunkelroten Licht). The dominant eid3 mutant carries a missense mutation in a conserved domain of PHYTOCHROME AND FLOWERING TIME1 (PFT1), an important component of the plant mediator coactivator complex, which links promoter-bound transcriptional regulators to RNA polymerase II complexes. Epistatic analyses were performed to obtain information about the coaction between the mutated PFT1(eid3) and positively and negatively acting components of light signaling cascades. The data presented here provide clear evidence that the mutation mainly enhances light sensitivity downstream of phytochrome A (phyA) and modulates phyB function. Our results demonstrate that the Mediator component cooperates with CONSTITUTIVE PHOTORMORPHOGENIC1 in the regulation of light responses and that the hypersensitive phenotype strictly depends on the presence of the ELONGATED HYPOCOTYL5 transcription factor, an important positive regulator of light-dependent gene expression. Expression profile analyses revealed that PFT1(eid3) alters the transcript accumulation of light-regulated genes even in darkness. Our data further indicate that PFT1 regulates the floral transition downstream of phyA. The PFT1 missense mutation seems to create a constitutively active transcription factor by mimicking an early step in light signaling.

MEDIATOR25 acts as an integrative hub for the regulation of jasmonate-responsive gene expression in Arabidopsis

The PHYTOCHROME AND FLOWERING TIME1 gene encoding the MEDIATOR25 (MED25) subunit of the eukaryotic Mediator complex is a positive regulator of jasmonate (JA)-responsive gene expression in Arabidopsis (Arabidopsis thaliana). Based on the function of the Mediator complex as a bridge between DNA-bound transcriptional activators and the RNA polymerase II complex, MED25 has been hypothesized to function in association with transcriptional regulators of the JA pathway. However, it is currently not known mechanistically how MED25 functions to regulate JA-responsive gene expression. In this study, we show that MED25 physically interacts with several key transcriptional regulators of the JA signaling pathway, including the APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) transcription factors OCTADECANOID-RESPONSIVE ARABIDOPSIS AP2/ERF59 and ERF1 as well as the master regulator MYC2. Physical interaction detected between MED25 and four group IX AP2/ERF transcription factors was shown to require the activator interaction domain of MED25 as well as the recently discovered Conserved Motif IX-1/EDLL transcription activation motif of MED25-interacting AP2/ERFs. Using transcriptional activation experiments, we also show that OCTADECANOID-RESPONSIVE ARABIDOPSIS AP2/ERF59- and ERF1-dependent activation of PLANT DEFENSIN1.2 as well as MYC2-dependent activation of VEGETATIVE STORAGE PROTEIN1 requires a functional MED25. In addition, MED25 is required for MYC2-dependent repression of pathogen defense genes. These results suggest an important role for MED25 as an integrative hub within the Mediator complex during the regulation of JA-associated gene expression.

The phytochrome-interacting vascular plant one-zinc finger1 and VOZ2 redundantly regulate flowering in Arabidopsis

The timing of the transition to flowering in plants is regulated by various environmental factors, including daylength and light quality. Although the red/far-red photoreceptor phytochrome B (phyB) represses flowering by indirectly regulating the expression of a key flowering regulator, FLOWERING LOCUS T (FT), the mechanism of phyB signaling for flowering is largely unknown. Here, we identified two Arabidopsis thaliana genes, VASCULAR PLANT ONE-ZINC FINGER1 (VOZ1) and VOZ2, which are highly conserved throughout land plant evolution, as phyB-interacting factors. voz1 voz2 double mutants, but neither single mutant, showed a late-flowering phenotype under long-day conditions, which indicated that VOZ1 and VOZ2 redundantly promote flowering. voz1 voz2 mutations suppressed the early-flowering phenotype of the phyB mutant, and FT expression was repressed in the voz1 voz2 mutant. Green fluorescent protein-VOZ2 signal was observed in the cytoplasm, and interaction of VOZ proteins with phyB was indicated to occur in the cytoplasm under far-red light. However, VOZ2 protein modified to localize constitutively in the nucleus promoted flowering. In addition, the stability of VOZ2 proteins in the nucleus was modulated by light quality in a phytochrome-dependent manner. We propose that partial translocation of VOZ proteins from the cytoplasm to the nucleus mediates the initial step of the phyB signal transduction pathway that regulates flowering.

PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis

Two aspects of light are very important for plant development: the length of the light phase or photoperiod and the quality of incoming light. Photoperiod detection allows plants to anticipate the arrival of the next season, whereas light quality, mainly the red to far-red ratio (R:FR), is an early signal of competition by neighbouring plants. phyB represses flowering by antagonising CO at the transcriptional and post-translational levels. A low R:FR decreases active phyB and consequently increases active CO, which in turn activates the expression of FT, the plant florigen. Other phytochromes like phyD and phyE seem to have redundant roles with phyB. PFT1, the MED25 subunit of the plant Mediator complex, has been proposed to act in the light-quality pathway that regulates flowering time downstream of phyB. However, whether PFT1 signals through CO and its specific mechanism are unclear. Here we show that CO-dependent and -independent mechanisms operate downstream of phyB, phyD and phyE to promote flowering, and that PFT1 is equally able to promote flowering by modulating both CO-dependent and -independent pathways. Our data are consistent with the role of PFT1 as an activator of CO transcription, and also of FT transcription, in a CO-independent manner. Our transcriptome analysis is also consistent with CO and FT genes being the most important flowering targets of PFT1. Furthermore, comparison of the pft1 transcriptome with transcriptomes after fungal and herbivore attack strongly suggests that PFT1 acts as a hub, integrating a variety of interdependent environmental stimuli, including light quality and jasmonic acid-dependent defences.

CRYPTIC PRECOCIOUS/MED12 is a novel flowering regulator with multiple target steps in Arabidopsis

The proper timing of flowering is of crucial importance for reproductive success of plants. Regulation of flowering is orchestrated by inputs from both environmental and endogenous signals such as daylength, light quality, temperature and hormones, and key flowering regulators construct several parallel and interactive genetic pathways. This integrative regulatory network has been proposed to create robustness as well as plasticity of the regulation. Although knowledge of key genes and their regulation has been accumulated, there still remains much to learn about how they are organized into an integrative regulatory network. Here, we have analyzed the CRYPTIC PRECOCIOUS (CRP) gene for the Arabidopsis counterpart of the MED12 subunit of the Mediator. A novel dominant mutant, crp-1D, which causes up-regulation of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), FRUITFULL (FUL) and APETALA1 (AP1) expression in a FLOWERING LOCUS T (FT)-dependent manner, was identified in an enhancer screen of the early-flowering phenotype of 35S::FT. Genetic and molecular analysis of both crp-1D and crp loss-of-function alleles showed that MED12/CRP is required not only for proper regulation of SOC1, FUL and AP1, but also for up-regulation of FT, TWIN SISTER OF FT (TSF) and FD, and down-regulation of FLOWERING LOCUS C (FLC). These observations suggest that MED12/CRP is a novel flowering regulator with multiple regulatory target steps both upstream and downstream of the key flowering regulators including FT florigen. Our work, taken together with recent studies of other Mediator subunit genes, supports an emerging view that the Mediator plays multiple roles in the regulation of flowering.

Shade avoidance

The presence of neighboring vegetation modifies the light environment experienced by plants, generating signals that are perceived by phytochromes and cryptochromes. These signals cause large changes in plant body form and function, including enhanced growth of the hypocotyl and petioles, a more erect position of the leaves and early flowering in Arabidopsis thaliana. Collectively, these so-called shade-avoidance responses tend to reduce the degree of current or future shade by neighbors. Shade light signals increase the abundance of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5 proteins, promote the synthesis and redirection of auxin, favor the degradation of DELLA proteins and increase the expression of auxin, gibberellins and brassinosteroid-promoted genes, among other events downstream the photoreceptors. Selectively disrupting these events by genetic or pharmacological approaches affects shade-avoidance responses with an intensity that depends on the developmental context and the environment. Shade-avoidance responses provide a model to investigate the signaling networks used by plants to take advantage of the cues provided by the environment to adjust to the challenges imposed by the environment itself.

The Mediator complex in plants: structure, phylogeny, and expression profiling of representative genes in a dicot (Arabidopsis) and a monocot (rice) during reproduction and abiotic stress

The Mediator (Med) complex relays regulatory information from DNA-bound transcription factors to the RNA polymerase II in eukaryotes. This macromolecular unit is composed of three core subcomplexes in addition to a separable kinase module. In this study, conservation of Meds has been investigated in 16 plant species representing seven diverse groups across the plant kingdom. Using Hidden Markov Model-based conserved motif searches, we have identified all the known yeast/metazoan Med components in one or more plant groups, including the Med26 subunits, which have not been reported so far for any plant species. We also detected orthologs for the Arabidopsis (Arabidopsis thaliana) Med32, -33, -34, -35, -36, and -37 in all the plant groups, and in silico analysis identified the Med32 and Med33 subunits as apparent orthologs of yeast/metazoan Med2/29 and Med5/24, respectively. Consequently, the plant Med complex appears to be composed of one or more members of 34 subunits, as opposed to 25 and 30 members in yeast and metazoans, respectively. Despite low similarity in primary Med sequences between the plants and their fungal/metazoan partners, secondary structure modeling of these proteins revealed a remarkable similarity between them, supporting the conservation of Med organization across kingdoms. Phylogenetic analysis between plant, human, and yeast revealed single clade relatedness for 29 Med genes families in plants, plant Meds being closer to human than to yeast counterparts. Expression profiling of rice (Oryza sativa) and Arabidopsis Med genes reveals that Meds not only act as a basal regulator of gene expression but may also have specific roles in plant development and under abiotic stress conditions.

Control of final organ size by Mediator complex subunit 25 in Arabidopsis thaliana

Control of organ size by cell proliferation and cell expansion is a fundamental developmental process, but the mechanisms that establish the final size of organs and whole organisms remain elusive in plants and animals. We have previously demonstrated that DA1, which encodes a predicted ubiquitin receptor, controls the final size of seeds and organs by restricting cell proliferation in Arabidopsis. Through a genetic screen for mutations that enhance the floral organ size of da1-1, we have identified an enhancer of da1-1 (eod8-1). The eod8-1 mutation was identified, using a map-based cloning approach, in Mediator complex subunit 25 (MED25; also known as PFT1), which is involved in the transcriptional regulation of gene expression. Loss-of-function mutants in MED25 form large organs, with larger and slightly increased numbers of cells as a result of an increased period of cell proliferation and cell expansion, whereas plants overexpressing MED25 have small organs owing to decreases in both cell number and cell size. Our genetic and physiological data suggest that MED25 acts to limit cell and organ growth independently of MED25-mediated phytochrome signaling and the jasmonate pathway. Genetic analyses show that MED25 functions redundantly with DA1 to control organ growth by restricting cell proliferation. Collectively, our findings show that MED25 plays a crucial role in setting final organ size, suggesting that it constitutes an important point of regulation in plant organ size control within the transcriptional machinery.

Flowering and expression of flowering-related genes under long-day conditions with light-emitting diodes

The effects of light quality on flowering time were investigated in Gypsophila paniculata, which is a long-day cut flower, and with Arabidopsis under long-day conditions with light-emitting diodes (LEDs). Gypsophila paniculata plants were grown under natural daylight and flowering was controlled by long-day treatment with a weak LED light of a single color in the night. Flowering was promoted not by blue light, but by far-red light in G. paniculata, while flowering was promoted by both light colors in Arabidopsis. FT homologs of G. paniculata GpFT1 and GpFT2 were differentially expressed under long-day conditions with white light, suggesting that they play roles in flowering at different stages of reproductive development. GpFTs and FT gene expression was not induced by far-red light in G. paniculata or Arabidopsis. Instead, the expression of the SOC1 homolog of G. paniculata GpSOC1 and SOC1 was induced by far-red light in G. paniculata and Arabidopsis. Flowering was promoted by induction of FT and SOC1 expression with blue light in Arabidopsis, whereas GpFTs and GpSOC1 expression was low with blue light induction in G. paniculata. The relationship between flowering and the expression of FT and SOC1 in Arabidopsis was confirmed with ft and soc1 mutants. These results suggest that long-day conditions with far-red light promote flowering through SOC1 and its homologs, while the conditions with blue light do not promote flowering in G. paniculata, because of low expression of GpFTs and GpSOC1 in contrast to that in Arabidopsis.

The interplay between light and jasmonate signalling during defence and development

During their evolution, plants have acquired diverse capabilities to sense their environment and modify their growth and development as required. The versatile utilization of solar radiation for photosynthesis as well as a signal to coordinate developmental responses to the environment is an excellent example of such a capability. Specific light quality inputs are converted to developmental outputs mainly through hormonal signalling pathways. Accordingly, extensive interactions between light and the signalling pathways of every known plant hormone have been uncovered in recent years. One such interaction that has received recent attention and forms the focus of this review occurs between light and the signalling pathway of the jasmonate hormone with roles in regulating plant defence and development. Here the recent research that revealed new mechanistic insights into how plants might integrate light and jasmonate signals to modify their growth and development, especially when defending themselves from either pests, pathogens, or encroaching neighbours, is discussed.

Transcriptomic, proteomic and metabolomic analysis of UV-B signaling in maize

Background

Under normal solar fluence, UV-B damages macromolecules, but it also elicits physiological acclimation and developmental changes in plants. Excess UV-B decreases crop yield. Using a treatment twice solar fluence, we focus on discovering signals produced in UV-B-irradiated maize leaves that translate to systemic changes in shielded leaves and immature ears.

Results

Using transcriptome and proteomic profiling, we tracked the kinetics of transcript and protein alterations in exposed and shielded organs over 6 h. In parallel, metabolic profiling identified candidate signaling molecules based on rapid increase in irradiated leaves and increased levels in shielded organs; pathways associated with the synthesis, sequestration, or degradation of some of these potential signal molecules were UV-B-responsive. Exposure of just the top leaf substantially alters the transcriptomes of both irradiated and shielded organs, with greater changes as additional leaves are irradiated. Some phenylpropanoid pathway genes are expressed only in irradiated leaves, reflected in accumulation of pathway sunscreen molecules. Most protein changes detected occur quickly: approximately 92% of the proteins in leaves and 73% in immature ears changed after 4 h UV-B were altered by a 1 h UV-B treatment.

Conclusions

There were significant transcriptome, proteomic, and metabolomic changes under all conditions studied in both shielded and irradiated organs. A dramatic decrease in transcript diversity in irradiated and shielded leaves occurs between 0 h and 1 h, demonstrating the susceptibility of plants to short term UV-B spikes as during ozone depletion. Immature maize ears are highly responsive to canopy leaf exposure to UV-B.

The Arabidopsis thaliana Med25 mediator subunit integrates environmental cues to control plant development

Development in plants is controlled by abiotic environmental cues such as day length, light quality, temperature, drought, and salinity. These signals are sensed by a variety of systems and transmitted by different signal transduction pathways. Ultimately, these pathways are integrated to control expression of specific target genes, which encode proteins that regulate development and differentiation. The molecular mechanisms for such integration have remained elusive. We here show that a linear 130-amino-acids-long sequence in the Med25 subunit of the Arabidopsis thaliana Mediator is a common target for the drought response element binding protein 2A, zinc finger homeodomain 1, and Myb-like transcription factors which are involved in different stress response pathways. In addition, our results show that Med25 together with drought response element binding protein 2A also function in repression of PhyB-mediated light signaling and thus integrate signals from different regulatory pathways.

A high-throughput screening system for Arabidopsis transcription factors and its application to Med25-dependent transcriptional regulation

The activities of transcription factors (TFs) require interactions with specific DNA sequences and other regulatory proteins. To detect such interactions in Arabidopsis, we developed a high-throughput screening system with a Gateway-compatible Gal4-AD-TF library of 1589 Arabidopsis TFs, which can be easily screened by mating-based yeast-one-hybrid (Y1H) and yeast-two-hybrid (Y2H) methods. The efficiency of the system was validated by examining two well-characterized TF-DNA and TF-protein interactions: the CHE-CCA1 promoter interaction by Y1H and NPR1-TGAs interactions by Y2H. We used this system to identify eight TFs that interact with a Mediator subunit, Med25, a key regulator in JA signaling. We identified five TFs that interacted with the GCC-box cis-element in the promoter of PDF1.2, a downstream gene of Med25. We found that three of these TFs, all from the AP2-EREBP family, interact directly both with Med25 and the GCC-box of PDF1.2, suggesting that Med25 regulates PDF1.2 expression through these three TFs. These results demonstrate that this high-throughput Y1H/Y2H screening system is an efficient tool for studying transcriptional regulation networks in Arabidopsis. This system will be available for other Arabidopsis researchers, and thus it provides a vital resource for the Arabidopsis community.

Jasmonate-induced defenses: a tale of intelligence, collaborators and rascals

Plants have sophisticated defense systems to protect their tissues against the attack of herbivorous organisms. Many of these defenses are orchestrated by the oxylipin jasmonate. A growing body of evidence indicates that the expression of jasmonate-induced responses is tightly regulated by the ecological context of the plant. Ecological information is provided by molecular signals that indicate the nature of the attacker, the value of the attacked organs, phytochrome status and thereby proximity of competing plants, association with beneficial organisms and history of plant interactions with pathogens and herbivores. This review discusses recent advances in this field and highlights the need to map the activities of informational modulators to specific control points within our emerging model of jasmonate signaling.

The plant Mediator and its role in noncoding RNA production

Mediator, a conserved multiprotein complex in animals, plants, and fungi, is a cofactor of RNA Polymerase II (Pol II). It is known to promote basal Pol II-mediated transcription as well as bridge sequence-specific transcriptional regulators and Pol II to integrate regulatory information. Pol II transcribes not only protein-coding genes but also intergenic regions to generate noncoding RNAs such as small RNAs (microRNAs and small interfering RNAs) and long noncoding RNAs. Intriguingly, two plant-specific polymerases, Pol IV and Pol V, have evolved from Pol II and play a role in the production of small interfering RNAs and long noncoding RNAs at heterochromatic regions to maintain genome stability through transcriptional gene silencing (TGS). Recent studies have defined the composition of the plant Mediator and evaluated its role in noncoding RNA production in relationship to Pol II, Pol IV and Pol V. Here, we review the functions of Mediator and that of noncoding RNAs generated by Pol II, Pol IV and Pol V in plants, and discuss a role of Mediator in epigenetic regulation via noncoding RNA production.

Involvement of brassinosteroid signals in the floral-induction network of Arabidopsis

The transition to flowering is known to be regulated by numerous interacting endogenous and environmental cues, of which brassinosteroids (BRs), a group of polyhydroxylated steroid phytohormones, appear to be linked to the regulation of flowering time. In Arabidopsis, BR biosynthetic det2 mutants exhibited delayed flowering time by at least 10 d compared with the wild type. The levels of endogenous BRs in det2 were below 10% of the wild type. The timing of flowering was also delayed in the BR biosynthetic dwf4 and cpd mutants and in the BR-insensitive bri1 mutants. Because brassinolide (BL) and different BL precursors were over-accumulated in BR biosynthetic mutants and BR-insensitive bri1 mutants, this showed that alterations in the endogenous BL content and the level of different BL precursors affect flowering time in Arabidopsis. The late-flowering phenotypes of bri1 also showed that components of the BR signal transduction pathway affect flowering time. So far, reports on a connection between BRs and flowering time are limited. This review summarizes recent advances regarding the action of BRs in the transition to flowering.

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.

The flowering time regulator CONSTANS is recruited to the FLOWERING LOCUS T promoter via a unique cis-element

CONSTANS is an evolutionarily-conserved central component of the genetic pathway that controls the onset of flowering in response to daylength. However, the specific biochemical mechanism by which the CONSTANS protein regulates the expression of its target genes remains largely unknown. *By using a combination of cell-based expression analysis and in vitro DNA binding studies, we have demonstrated that CONSTANS possesses transcriptional activation potential and is capable of directly binding to DNA. *CONSTANS was found to bind DNA via a unique sequence element containing a consensus TGTG(N2-3)ATG motif. This element is present in tandem within the FLOWERING LOCUS T promoter and is sufficient for CO binding and activity. The conserved CCT (CONSTANS, CONSTANS-like and TOC1) domain of CONSTANS was shown to be required for its recruitment to the DNA motif and other CCT-containing proteins were also found to have the ability to regulate gene expression via this element. *The CCAAT box, which has been previously hypothesized as a recruitment site for complexes containing the CONSTANS protein, potentiated CONSTANS-mediated activation but was not essential for CONSTANS recruitment to a target promoter or for its activity as a transcriptional factor.

Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses

Brachypodium distachyon (Brachypodium) is a model for the temperate grasses which include important cereals such as barley, wheat and oats. Comparison of the Brachypodium genome (accession Bd21) with those of the model dicot Arabidopsis thaliana and the tropical cereal rice (Oryza sativa) provides an opportunity to compare and contrast genetic pathways controlling important traits. We analysed the homologies of genes controlling the induction of flowering using pathways curated in Arabidopsis Reactome as a starting point. Pathways include those detecting and responding to the environmental cues of day length (photoperiod) and extended periods of low temperature (vernalization). Variation in these responses has been selected during cereal domestication, providing an interesting comparison with the wild genome of Brachypodium. Brachypodium Bd21 has well conserved homologues of circadian clock, photoperiod pathway and autonomous pathway genes defined in Arabidopsis and homologues of vernalization pathway genes defined in cereals with the exception of VRN2 which was absent. Bd21 also lacked a member of the CO family (CO3). In both cases flanking genes were conserved showing that these genes are deleted in at least this accession. Segmental duplication explains the presence of two CO-like genes in temperate cereals, of which one (Hd1) is retained in rice, and explains many differences in gene family structure between grasses and Arabidopsis. The conserved fine structure of duplications shows that they largely evolved to their present structure before the divergence of the rice and Brachypodium. Of four flowering-time genes found in rice but absent in Arabidopsis, two were found in Bd21 (Id1, OsMADS51) and two were absent (Ghd7, Ehd1). Overall, results suggest that an ancient core photoperiod pathway promoting flowering via the induction of FT has been modified by the recruitment of additional lineage specific pathways that promote or repress FT expression.

Arabidopsis thaliana life without phytochromes

Plants use light as a source of energy for photosynthesis and as a source of environmental information perceived by photoreceptors. Testing whether plants can complete their cycle if light provides energy but no information about the environment requires a plant devoid of phytochromes because all photosynthetically active wavelengths activate phytochromes. Producing such a quintuple mutant of Arabidopsis thaliana has been challenging, but we were able to obtain it in the flowering locus T (ft) mutant background. The quintuple phytochrome mutant does not germinate in the FT background, but it germinates to some extent in the ft background. If germination problems are bypassed by the addition of gibberellins, the seedlings of the quintuple phytochrome mutant exposed to red light produce chlorophyll, indicating that phytochromes are not the sole red-light photoreceptors, but they become developmentally arrested shortly after the cotyledon stage. Blue light bypasses this blockage, rejecting the long-standing idea that the blue-light receptors cryptochromes cannot operate without phytochromes. After growth under white light, returning the quintuple phytochrome mutant to red light resulted in rapid senescence of already expanded leaves and severely impaired expansion of new leaves. We conclude that Arabidopsis development is stalled at several points in the presence of light suitable for photosynthesis but providing no photomorphogenic signal.

Interaction between the light quality and flowering time pathways in Arabidopsis

Flowering in Arabidopsis is accelerated by a reduced ratio of red light to far-red light (R/FR), which indicates the proximity of competitive vegetation. By exploiting the natural genetic variation in flowering time responses to low R/FR, we obtained further insight into the complex pathways that fine-tune the transition to flowering in Arabidopsis. The Bla-6 ecotype does not flower significantly earlier in response to low R/FR, but is still able to display other features of shade avoidance, suggesting branching of low R/FR signalling. Here we show that the muted flowering response of Bla-6 is due to high levels of the floral repressor FLOWERING LOCUS C (FLC), conferred by a combination of functional FLC and FRIGIDA (FRI) alleles with a 'weak'FY allele. The Bla-6 FY allele encodes a protein with a corrupted WW binding domain, and we provide evidence that this locus plays a key role in the natural variation in light quality-induced flowering in Arabidopsis. In Bla-6, FLC blocks promotion to flowering by reduced R/FR by inhibiting expression of the floral integrator FLOWERING LOCUS T (FT) in a dose-dependent manner. Reduction of FLC removes this obstruction, and Bla6 plants then exhibit strong induction of FT and flower early in response to a low R/FR signal. This paper illustrates the intricate interaction of environmental signals and genetic factors to regulate flowering in Arabidopsis.

The mediator complex subunit PFT1 is a key regulator of jasmonate-dependent defense in Arabidopsis

Jasmonate signaling plays an important role in both plant defense and development. Here, we have identified a subunit of the Mediator complex as a regulator of the jasmonate signaling pathway in Arabidopsis thaliana. The Mediator complex is a conserved multiprotein complex that acts as a universal adaptor between transcription factors and the RNA polymerase II transcriptional machinery. We report that the PHYTOCHROME AND FLOWERING TIME1 (PFT1) gene, which encodes the MEDIATOR25 subunit of Mediator, is required for jasmonate-dependent defense gene expression and resistance to leaf-infecting necrotrophic fungal pathogens. Conversely, PFT1 appears to confer susceptibility to Fusarium oxysporum, a root-infecting hemibiotrophic fungal pathogen known to hijack jasmonate responses for disease development. Consistent with this, jasmonate gene expression was suppressed in the pft1 mutant during infection with F. oxysporum. In addition, a wheat (Triticum aestivum) homolog of PFT1 complemented the defense and the developmental phenotypes of the pft1 mutant, suggesting that the jasmonate signaling functions of PFT1 may be conserved in higher plants. Overall, our results identify an important control point in the regulation of the jasmonate signaling pathway within the transcriptional machinery.