Phytochrome-mediated light signalling in Arabidopsis

RcOST1L phosphorylates RcPIF4 for proteasomal degradation to promote flowering in rose

Flowering is a vital agronomic trait that determines the economic value of most ornamental plants. The flowering time of rose (Rosa spp.) is photoperiod insensitive and is thought to be tightly controlled by light intensity, although the detailed molecular mechanism remains unclear. Here, we showed that rose plants flower later under low-light (LL) intensity than under high-light (HL) intensity, which is mainly related to the stability of PHYTOCHROME-INTERACTING FACTORs (RcPIFs) mediated by OPEN STOMATA 1-Like (RcOST1L) under different light intensity regimes. We determined that HL conditions trigger the rapid phosphorylation of RcPIFs before their degradation. A yeast two-hybrid screen identified the kinase RcOST1L as interacting with RcPIF4. Moreover, RcOST1L positively regulated rose flowering and directly phosphorylated RcPIF4 on serine 198 to promote its degradation under HL conditions. Additionally, phytochrome B (RcphyB) enhanced RcOST1L-mediated phosphorylation of RcPIF4 via interacting with the active phyB-binding motif. RcphyB was activated upon HL and recruited RcOST1L to facilitate its nuclear accumulation, in turn leading to decreased stability of RcPIF4 and flowering acceleration. Our findings illustrate how RcPIF abundance safeguards proper rose flowering under different light intensities, thus uncovering the essential role of RcOST1L in the RcphyB-RcPIF4 module in flowering.

Comparative and functional analysis unveils the contribution of photoperiod to DNA methylation, sRNA accumulation, and gene expression variations in short-day and long-day grasses

Photoperiod employs complicated networks to regulate various developmental processes in plants, including flowering transition. However, the specific mechanisms by which photoperiod affects epigenetic modifications and gene expression variations in plants remain elusive. In this study, we conducted a comprehensive analysis of DNA methylation, small RNA (sRNA) accumulation, and gene expressions under different daylengths in facultative long-day (LD) grass Brachypodium distachyon and short-day (SD) grass rice. Our results showed that while overall DNA methylation levels were minimally affected by different photoperiods, CHH methylation levels were repressed under their favorable light conditions, particularly in rice. We identified numerous differentially methylated regions (DMRs) that were influenced by photoperiod in both plant species. Apart from differential sRNA clusters, we observed alterations in the expression of key components of the RNA-directed DNA methylation pathway, DNA methyltransferases, and demethylases, which may contribute to the identified photoperiod-influenced CHH DMRs. Furthermore, we identified many differentially expressed genes in response to different daylengths, some of which were associated with the DMRs. Notably, we discovered a photoperiod-responsive gene MYB11 in the transcriptome of B. distachyon, and further demonstrated its role as a flowering inhibitor by repressing FT1 transcription. Together, our comparative and functional analysis sheds light on the effects of daylength on DNA methylation, sRNA accumulation, and gene expression variations in LD and SD plants, thereby facilitating better designing breeding programs aimed at developing high-yield crops that can adapt to local growing seasons.

Responding to light signals: a comprehensive update on photomorphogenesis in cyanobacteria

Cyanobacteria are ancestors of chloroplast and perform oxygen-evolving photosynthesis similar to higher plants and algae. However, an obligatory requirement of photons for their growth results in the exposure of cyanobacteria to varying light conditions. Therefore, the light environment could act as a signal to drive the developmental processes, in addition to photosynthesis, in cyanobacteria. These Gram-negative prokaryotes exhibit characteristic light-dependent developmental processes that maximize their fitness and resource utilization. The development occurring in response to radiance (photomorphogenesis) involves fine-tuning cellular physiology, morphology and metabolism. The best-studied example of cyanobacterial photomorphogenesis is chromatic acclimation (CA), which allows a selected number of cyanobacteria to tailor their light-harvesting antenna called phycobilisome (PBS). The tailoring of PBS under existing wavelengths and abundance of light gives an advantage to cyanobacteria over another photoautotroph. In this work, we will provide a comprehensive update on light-sensing, molecular signaling and signal cascades found in cyanobacteria. We also include recent developments made in other aspects of CA, such as mechanistic insights into changes in the size and shape of cells, filaments and carboxysomes.

PHOTOLYASE/BLUE LIGHT RECEPTOR2 regulates chrysanthemum flowering by compensating for gibberellin perception

The gibberellins (GAs) receptor GA INSENSITIVE DWARF1 (GID1) plays a central role in GA signal perception and transduction. The typical photoperiodic plant chrysanthemum (Chrysanthemum morifolium) only flowers when grown in short-day photoperiods. In addition, chrysanthemum flowering is also controlled by the aging pathway, but whether and how GAs participate in photoperiod- and age-dependent regulation of flowering remain unknown. Here, we demonstrate that photoperiod affects CmGID1B expression in response to GAs and developmental age. Moreover, we identified PHOTOLYASE/BLUE LIGHT RECEPTOR2, an atypical photocleavage synthase, as a CRYPTOCHROME-INTERACTING bHLH1 interactor with which it forms a complex in response to short days to activate CmGID1B transcription. Knocking down CmGID1B raised endogenous bioactive GA contents and GA signal perception, in turn modulating the expression of the aging-related genes MicroRNA156 and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3. We propose that exposure to short days accelerates the juvenile-to-adult transition by increasing endogenous GA contents and response to GAs, leading to entry into floral transformation.

Genome-wide identification and characterization of bZIP gene family and cloning of candidate genes for anthocyanin biosynthesis in pomegranate (Punica granatum)

BACKGROUND

The basic leucine zipper (bZIP) transcription factor is one of the most abundant and conserved gene families in eukaryotes. In addition to participating in plant development and growth, bZIP transcription factors play crucial roles in various abiotic stress responses and anthocyanin accumulation. Up to now, analysis of bZIP gene family members in pomegranate (Punica granatum) has not been reported. Three published pomegranate genome sequences provide valuable resources for further gene function analysis.

RESULTS

Using bioinformatics analysis, 65 PgbZIPs were identified and analyzed from the 'Taishanhong' pomegranate genome. We divided them into 13 groups (A, B, C, D, E, F, G, H, I, J, K, M, and S) according to the phylogenetic relationship with those of Arabidopsis, each containing a different number of genes. The regularity of exon/intron number and distribution was consistent with the classification of groups in the evolutionary tree. Transcriptome analysis of different tissues showed that members of the PgbZIP gene family were differentially expressed in different developmental stages and tissues of pomegranate. Among them, we selected PgbZIP16 and PgbZIP34 as candidate genes which affect anthocyanin accumulation. The full-length CDS region of PgbZIP16 and PgbZIP34 were cloned from pomegranate petals by homologous cloning technique, encoding 170 and 174 amino acids, which were 510 bp and 522 bp, respectively. Subcellular localization assays suggested that both PgbZIP16 and PgbZIP34 were nucleus-localized. Real-time quantitative PCR (qPCR) was used to explore the expression of PgbZIP16 and PgbZIP34 in the petals of three kinds of ornamental pomegranates at the full flowering stage. The results demonstrated that the expression of PgbZIP16 in red petals was 5.83 times of that in white petals, while PgbZIP34 was 3.9 times. The results of transient expression in tobacco showed that consistent trends were observed in anthocyanin concentration and expression levels of related genes, which both increased and then decreased. Both PgbZIP16 and PgbZIP34 could promote anthocyanin accumulation in tobacco leaves. We obtained transgenic strains overexpressing PgbZIP16, and the histochemical staining for GUS activity showed that overexpressed PgbZIP16 seedlings were expressed in the stem. Transgenic experiments indicated that overexpression of PgbZIP16 significantly upregulated UF3GT, ANS and DFR genes in Arabidopsis and enhanced anthocyanin accumulation.

CONCLUSIONS

The whole genome identification, gene structure, phylogeny, gene cloning, subcellular location and functional verification of the pomegranate bZIP gene family provide a theoretical foundation for the functional study of the PgbZIP gene family and candidate genes for anthocyanin biosynthesis.

Optophysiology: Illuminating cell physiology with optogenetics

Optogenetics combines light and genetics to enable precise control of living cells, tissues, and organisms with tailored functions. Optogenetics has the advantages of noninvasiveness, rapid responsiveness, tunable reversibility, and superior spatiotemporal resolution. Following the initial discovery of microbial opsins as light-actuated ion channels, a plethora of naturally occurring or engineered photoreceptors or photosensitive domains that respond to light at varying wavelengths has ushered in the next chapter of optogenetics. Through protein engineering and synthetic biology approaches, genetically-encoded photoswitches can be modularly engineered into protein scaffolds or host cells to control a myriad of biological processes, as well as to enable behavioral control and disease intervention in vivo. Here, we summarize these optogenetic tools on the basis of their fundamental photochemical properties to better inform the chemical basis and design principles. We also highlight exemplary applications of opsin-free optogenetics in dissecting cellular physiology (designated "optophysiology"), and describe the current progress, as well as future trends, in wireless optogenetics, which enables remote interrogation of physiological processes with minimal invasiveness. This review is anticipated to spark novel thoughts on engineering next-generation optogenetic tools and devices that promise to accelerate both basic and translational studies.

Molecular Genetic Understanding of Photoperiodic Regulation of Flowering Time in Arabidopsis and Soybean

The developmental switch from a vegetative phase to reproduction (flowering) is essential for reproduction success in flowering plants, and the timing of the floral transition is regulated by various environmental factors, among which seasonal day-length changes play a critical role to induce flowering at a season favorable for seed production. The photoperiod pathways are well known to regulate flowering time in diverse plants. Here, we summarize recent progresses on molecular mechanisms underlying the photoperiod control of flowering in the long-day plant Arabidopsis as well as the short-day plant soybean; furthermore, the conservation and diversification of photoperiodic regulation of flowering in these two species are discussed.

Ubiquitin-specific proteases UBP12 and UBP13 promote shade avoidance response by enhancing PIF7 stability

For plants grown in a crowded environment, PHYTOCHROME INTERACTING FACTOR 7 (PIF7) plays a critical role by initiating a series of adaptive growth responses. Here, we demonstrate that, in addition to transcription activity and subcellular localization, the PIF7 protein level, which is stringently regulated, is also important for shade avoidance responses. We identified two ubiquitin-specific proteases, UBP12 and UBP13, which positively regulate rapid plant growth in response to shade light. These two ubiquitin proteases directly interact with PIF7 and protect the latter from destruction by 26S proteasomes. The dynamic changes of PIF7 abundance regulated by UBP12 and UBP13 provide insight into the roles of posttranslational modifications of PIF7 in integrating environmental changes with endogenous responses.

Changes in light quality caused by the presence of neighbor proximity regulate many growth and development processes of plants. PHYTOCHROME INTERACTING FACTOR 7 (PIF7), whose subcellular localization, DNA-binding properties, and protein abundance are regulated in a photoreversible manner, plays a central role in linking shade light perception and growth responses. How PIF7 activity is regulated during shade avoidance responses has been well studied, and many factors involved in this process have been identified. However, the detailed molecular mechanism by which shade light regulates the PIF7 protein level is still largely unknown. Here, we show that the PIF7 protein level regulation is important for shade-induced growth. Two ubiquitin-specific proteases, UBP12 and UBP13, were identified as positive regulators in shade avoidance responses by increasing the PIF7 protein level. The ubp12-2w/13–3 double mutant displayed significantly impaired sensitivity to shade-induced cell elongation and reproduction acceleration. Our genetic and biochemical analysis showed that UBP12 and UBP13 act downstream of phyB and directly interact with PIF7 to maintain PIF7 stability and abundance through deubiquitination.

Calmodulin7: recent insights into emerging roles in plant development and stress

Analyses of the function of Arabidopsis Calmodulin7 (CAM7) in concert with multiple regulatory proteins involved in various signal transduction processes. Calmodulin (CaM) plays various regulatory roles in multiple signaling pathways in eukaryotes. Arabidopsis CALMODULIN 7 (CAM7) is a unique member of the CAM family that works as a transcription factor in light signaling pathways. CAM7 works in concert with CONSTITUTIVE PHOTOMORPHOGENIC 1 and ELONGATED HYPOCOTYL 5, and plays an important role in seedling development. Further, it is involved in the regulation of the activity of various Ca²⁺-gated channels such as cyclic nucleotide gated channel 6 (CNGC6), CNGC14 and auto-inhibited Ca²⁺ ATPase 8. Recent studies further indicate that CAM7 is also an integral part of multiple signaling pathways including hormone, immunity and stress. Here, we review the recent advances in understanding the multifaceted role of CAM7. We highlight the open-ended questions, and also discuss the diverse aspects of CAM7 characterization that need to be addressed for comprehensive understanding of its cellular functions.

Growth Spectrum Complexity Dictates Aromatic Intensity in Coriander (Coriandrum sativum L.)

Advancements in availability and specificity of light-emitting diodes (LEDs) have facilitated trait modification of high-value edible herbs and vegetables through the fine manipulation of spectra. Coriander (Coriandrum sativum L.) is a culinary herb, known for its fresh, citrusy aroma, and high economic value. Studies into the impact of light intensity and spectrum on C. sativum physiology, morphology, and aroma are limited. Using a nasal impact frequency panel, a selection of key compounds associated with the characteristic aroma of coriander was identified. Significant differences (P < 0.05) were observed in the concentration of these aromatics between plants grown in a controlled environment chamber under the same photosynthetic photon flux density (PPFD) but custom spectra: red (100%), blue (100%), red + blue (RB, 50% equal contribution), or red + green + blue (RGB, 35.8% red: 26.4% green: 37.8% blue) wavelengths. In general, the concentration of aromatics increased with increasing numbers of wavelengths emitted alongside selective changes, e.g., the greatest increase in coriander-defining E-(2)-decenal occurred under the RGB spectrum. This change in aroma profile was accompanied by significant differences (P < 0.05) in light saturated photosynthetic CO2 assimilation, water-use efficiency (Wi), and morphology. While plants grown under red wavelengths achieved the greatest leaf area, RB spectrum plants were shortest and had the highest leaf:shoot ratio. Therefore, this work evidences a trade-off between sellable commercial morphologies with a weaker, less desirable aroma or a less desirable morphology with more intense coriander-like aromas. When supplemental trichromatic LEDs were used in a commercial glasshouse, the majority of compounds, with the exception of linalool, also increased showing that even as a supplement additional wavelength can modify the aromatic profile increasing its complexity. Lower levels of linalool suggest these plants may be more susceptible to biotic stress such as herbivory. Finally, the concentration of coriander-defining aromatics E-(2)-decenal and E-(2)-hexenal was significantly higher in supermarket pre-packaged coriander leaves implying that concentrations of aromatics increase after excision. In summary, spectra can be used to co-manipulate aroma profile and plant form with increasing spectral complexity leading to greater aromatic complexity and intensity. We suggest that increasing spectral complexity progressively stimulates signaling pathways giving rise to valuable economic traits.

Optogenetic approaches to investigate spatiotemporal signaling during development

Embryogenesis is coordinated by signaling pathways that pattern the developing organism. Many aspects of this process are not fully understood, including how signaling molecules spread through embryonic tissues, how signaling amplitude and dynamics are decoded, and how multiple signaling pathways cooperate to pattern the body plan. Optogenetic approaches can be used to address these questions by providing precise experimental control over a variety of biological processes. Here, we review how these strategies have provided new insights into developmental signaling and discuss how they could contribute to future investigations.

Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship Between Photosynthesis and Leaf Development

Cichorium endivia is a leafy crop closely related to Lactuca sativa that comprises two major botanical varieties characterized by a high degree of intraspecific morphological variation: var. latifolium with broad leaves (escarole) and var. crispum with narrow crisp curly leaves (endive). To investigate the relationship between leaf morphology and photosynthetic activity, escaroles and endives were used as a crop model due to the striking morphological diversity of their leaves. We constructed a leaf database for transcription factors (TFs) and photosynthesis-related genes from a refined C. endivia transcriptome and used RNA-seq transcriptomic data from leaves of four commercial endive and escarole cultivars to explore transcription factor regulatory networks. Cluster and gene co-expression network (GCN) analyses identified two main anticorrelated modules that control photosynthesis. Analysis of the GCN network topological properties identified known and novel hub genes controlling photosynthesis, and candidate developmental genes at the boundaries between shape and function. Differential expression analysis between broad and curly leaves suggested three novel TFs putatively involved in leaf shape diversity. Physiological analysis of the photosynthesis properties and gene expression studies on broad and curly leaves provided new insights into the relationship between leaf shape and function.

Shade Avoidance and Neighbor Detection

Plants detect neighboring vegetation as potential competitors for resources. Vegetation proximity is perceived by changes in the red (R) to far-red (FR) ratio (R:FR) through the phytochrome photoreceptors. To face this challenge, many plants have evolved the strategy to avoid shade, displaying a series of responses known as the shade avoidance syndrome (SAS). The SAS responses have been mostly studied at the seedling stage, and cover hypocotyl elongation as well as cotyledon and primary leaf expansion. In adult stages, SAS responses include an increase in petiole elongation and a decrease in leaf expansion, and an increase in plant height. Thus, the analysis of these responses provides a valuable and simple way to study how vegetation proximity affects plant development in both seedlings and adult plants. Here we describe a simple protocol to simulate shade in the laboratory and to evaluate these responses. Overall, our protocol can be easily used to expand the set of SAS responses of plants at different stages of development.

Transcriptional control of photosynthetic capacity: conservation and divergence from Arabidopsis to rice

Contents 32 I. 32 II. 33 III. 36 IV. 41 43 References 43 SUMMARY: Photosynthesis is one of the most important biological processes on Earth. It provides the consumable energy upon which almost all organisms are dependent, and modulates the composition of the planet's atmosphere. To carry out photosynthesis, plants require a large cohort of genes. These genes encode proteins that capture light energy, store energy in sugars and build the subcellular structures required to facilitate this energy capture. Although the function of many of these genes is known, little is understood about the transcriptional networks that coordinate their expression. This review places our understanding of the transcriptional regulation of photosynthesis in Arabidopsis thaliana in an evolutionary context, to provide new insight into transcriptional regulatory networks that control photosynthesis gene expression in grasses. The similarities and differences between the rice and Arabidopsis networks are highlighted, revealing substantial disparity between the two systems. In addition, avenues are identified that may be exploited for photosynthesis engineering projects in the future.

The G-Protein β Subunit AGB1 Promotes Hypocotyl Elongation through Inhibiting Transcription Activation Function of BBX21 in Arabidopsis

Hypocotyl development in Arabidopsis thaliana is regulated by light and endogenous hormonal cues, making it an ideal model to study the interplay between light and endogenous growth regulators. BBX21, a B-box (BBX)-like zinc-finger transcription factor, integrates light and abscisic acid signals to regulate hypocotyl elongation in Arabidopsis. Heterotrimeric G-proteins are pivotal regulators of plant development. The short hypocotyl phenotype of the G-protein β-subunit (AGB1) mutant (agb1-2) has been previously identified, but the precise role of AGB1 in hypocotyl elongation remains enigmatic. Here, we show that AGB1 directly interacts with BBX21, and the short hypocotyl phenotype of agb1-2 is partially suppressed in agb1-2bbx21-1 double mutant. BBX21 functions in the downstream of AGB1 and overexpression of BBX21 in agb1-2 causes a more pronounced reduction in hypocotyl length, indicating that AGB1 plays an oppositional role in relation to BBX21 during hypocotyl development. Furthermore, we demonstrate that the C-terminal region of BBX21 is important for both its intracellular localization and its transcriptional activation activity that is inhibited by interaction with AGB1. ChIP assays showed that BBX21 specifically associates with its own promoter and with those of BBX22, HY5, and GA2ox1. which is not altered in agb1-2. These data suggest that the AGB1-BBX21 interaction only affects the transcriptional activation activity of BBX21 but has no effect on its DNA binding ability. Taken together, our data demonstrate that AGB1 positively promotes hypocotyl elongation through repressing BBX21 activity.

Role of phytochromes A and B in the regulation of cell death and acclimatory responses to UV stress in Arabidopsis thaliana

Plants coordinate their responses to various biotic and abiotic stresses in order to optimize their developmental and acclimatory programmes. The ultimate response to an excessive amount of stress is local induction of cell death mechanisms. The death of certain cells can help to maintain tissue homeostasis and enable nutrient remobilization, thus increasing the survival chances of the whole organism in unfavourable environmental conditions. UV radiation is one of the environmental factors that negatively affects the photosynthetic process and triggers cell death. The aim of this work was to evaluate a possible role of the red/far-red light photoreceptors phytochrome A (phyA) and phytochrome B (phyB) and their interrelations during acclimatory responses to UV stress. We showed that UV-C treatment caused a disturbance in photosystem II and a deregulation of photosynthetic pigment content and antioxidant enzymes activities, followed by increased cell mortality rate in phyB and phyAB null mutants. We also propose a regulatory role of phyA and phyB in CO2 assimilation, non-photochemical quenching, reactive oxygen species accumulation and salicylic acid content. Taken together, our results suggest a novel role of phytochromes as putative regulators of cell death and acclimatory responses to UV.

Growth and cell cycle of Ulva compressa (Ulvophyceae) under LED illumination

The cell-cycle progression of Ulva compressa is diurnally gated at the G1 phase in accordance with light-dark cycles. The present study was designed to examine the spectral sensitivity of the G1 gating system. When blue, red, and green light-emitting diodes (LEDs) were used for illumination either alone or in combination, the cells divided under all illumination conditions, suggesting that all colors of light were able to open the G1 gate. Although blue light was most effective to open the G1 gate, red light alone or green light alone was also able to open the G1 gate even at irradiance levels lower than the light compensation point of each color. Occurrence of a period of no cell division in the course of a day suggested that the G1 gating system normally functioned as under ordinary illumination by cool-white fluorescent lamps. The rise of the proportion of blue light to green light resulted in increased growth rate. On the other hand, the growth rates did not vary regardless of the proportion of blue light to red light. These results indicate that the difference in growth rate due to light color resulted from the difference in photosynthetic efficiency of the colors of light. However, the growth rates significantly decreased under conditions without blue light. This result suggests that blue light mediates cell elongation and because the spectral sensitivity of the cell elongation regulating system was different from that of the G1 gating system, distinct photoreceptors are likely to mediate the two systems.

A red light-controlled synthetic gene expression switch for plant systems

On command control of gene expression in time and space is required for the comprehensive analysis of key plant cellular processes. Even though some chemical inducible systems showing satisfactory induction features have been developed, they are inherently limited in terms of spatiotemporal resolution and may be associated with toxic effects. We describe here the first synthetic light-inducible system for the targeted control of gene expression in plants. For this purpose, we applied an interdisciplinary synthetic biology approach comprising mammalian and plant cell systems to customize and optimize a split transcription factor based on the plant photoreceptor phytochrome B and one of its interacting factors (PIF6). Implementation of the system in transient assays in tobacco protoplasts resulted in strong (95-fold) induction in red light (660 nm) and could be instantaneously returned to the OFF state by subsequent illumination with far-red light (740 nm). Capitalizing on this toggle switch-like characteristic, we demonstrate that the system can be kept in the OFF state in the presence of 740 nm-supplemented white light, opening up perspectives for future application of the system in whole plants. Finally we demonstrate the system's applicability in basic research, by the light-controlled tuning of auxin signalling networks in N. tabacum protoplasts, as well as its biotechnological potential for the chemical-inducer free production of therapeutic proteins in the moss P. patens.

Development of fruit color in Solanaceae: a story of two biosynthetic pathways

This review highlights the major differences between the regulation of two important pathways namely anthocyanin and carotenoid pathways, responsible for fruit color generation in Solanaceae mediated by transcription factors (TFs). The anthocyanin pathway is regulated by a common set of TFs (MYB, MYC and WD40) belonging to specific families of DNA-binding proteins. Their regulation is aimed at controlling the type and amount of pigments produced and the physiological conditions (like pH) at which they are finally stored. In the carotenoid pathway, the color diversity depends on the quantity of pigment produced and the point where the pathway is arrested. TFs in the latter case are accordingly found to influence the sequestration and degradation of these pigments, which determines their final concentration in the tissue. TFs (phytochrome interacting factors, MADS-BOX, HB-ZIP and B-ZIP) also regulate important rate-determining steps, which decide the direction in which the pathway proceeds and the point at which it is terminated. In the absence of a clear pattern of TF-mediated regulation, it is suggested that the carotenoid pathway is more significantly influenced by other regulatory methods which need to be explored. It is expected that common factors affecting these pathways are the ones acting much before the initiation of the biosynthesis of respective pigments.

Enhancing the productivity of grasses under high-density planting by engineering light responses: from model systems to feedstocks

The successful commercialization of bioenergy grasses as lignocellulosic feedstocks requires that they be produced, processed, and transported efficiently. Intensive breeding for higher yields in food crops has resulted in varieties that perform optimally under high-density planting but often with high input costs. This is particularly true of maize, where most yield gains in the past have come through increased planting densities and an abundance of fertilizer. For lignocellulosic feedstocks, biomass rather than grain yield and digestibility of cell walls are two of the major targets for improvement. Breeding for high-density performance of lignocellulosic crops has been much less intense and thus provides an opportunity for improving the feedstock potential of these grasses. In this review, we discuss the role of vegetative shade on growth and development and suggest targets for manipulating this response to increase harvestable biomass under high-density planting. To engineer grass architecture and modify biomass properties at increasing planting densities, we argue that new model systems are needed and recommend Setaria viridis, a panicoid grass, closely related to major fuel and bioenergy grasses as a model genetic system.

Arabidopsis CAM7 and HY5 physically interact and directly bind to the HY5 promoter to regulate its expression and thereby promote photomorphogenesis

Arabidopsis thaliana CALMODULIN7 (CAM7), a unique member of the calmodulin gene family, plays a crucial role as a transcriptional regulator in seedling development. The elongated HYPOCOTYL5 (HY5) bZIP protein, an integrator of multiple signaling pathways, also plays an important role in photomorphogenic growth and light-regulated gene expression. CAM7 acts synergistically with HY5 to promote photomorphogenesis at various wavelengths of light. Although the genetic relationships between CAM7 and HY5 in light-mediated seedling development have been demonstrated, the molecular connectivity between CAM7 and HY5 is unknown. Furthermore, whereas HY5-mediated gene regulation has been fairly well investigated, the transcriptional regulation of HY5 is largely unknown. Here, we report that HY5 expression is regulated by HY5 and CAM7 at various wavelengths of light and also at various stages of development. In vitro and in vivo DNA-protein interaction studies suggest that HY5 and CAM7 bind to closely located T/G- and E-box cis-acting elements present in the HY5 promoter, respectively. Furthermore, CAM7 and HY5 physically interact and regulate the expression of HY5 in a concerted manner. Taken together, these results demonstrate that CAM7 and HY5 directly interact with the HY5 promoter to mediate the transcriptional activity of HY5 during Arabidopsis seedling development.

Phytochrome RNAi enhances major fibre quality and agronomic traits of the cotton Gossypium hirsutum L

Simultaneous improvement of fibre quality, early-flowering, early-maturity and productivity in Upland cotton (G. hirsutum) is a challenging task for conventional breeding. The influence of red/far-red light ratio on the fibre length prompted us to examine the phenotypic effects of RNA interference (RNAi) of the cotton PHYA1 gene. Here we show a suppression of up to ~70% for the PHYA1 transcript, and compensatory overexpression of up to ~20-fold in the remaining phytochromes in somatically regenerated PHYA1 RNAi cotton plants. Two independent transformants of three generations exhibited vigorous root and vegetative growth, early-flowering, significantly improved upper half mean fibre length and an improvement in other major fibre characteristics. Small decreases in lint traits were observed but seed cotton yield was increased an average 10-17% compared with controls. RNAi-associated phenotypes were heritable and transferable via sexual hybridization. These results should aid in the development of early-maturing and productive Upland cultivars with superior fibre quality.

Z-box binding transcription factors (ZBFs): a new class of transcription factors in Arabidopsis seedling development

One set of genes encoding diverse groups of transcription factors that interact with the Z-box (ATACGTGT; a potential Z-DNA forming sequence) is called ZBFs (Z-box Binding Factors). ZBFs include ZBF1, ZBF2, and ZBF3, which encode ZBF1/MYC2 (bHLH), ZBF2/GBF1 (bZIP), and ZBF3/CAM7 (Calmodulin) proteins, respectively. With several recent reports, it is becoming increasingly evident that ZBFs play crucial roles in Arabidopsis seedling photomorphogenesis. ZBFs integrate signals from various wavelengths of light to coordinate the regulation of transcriptional networks that affect multiple facets of plant growth and development. The function of each ZBF is qualitatively and quantitatively distinct. The zbf mutants display pleiotropic effects including altered hypocotyl elongation, cotyledon expansion, lateral root development, and flowering time. In this inaugural review, we discuss the identification, molecular functions, and interacting partners of ZBFs in light-mediated Arabidopsis seedling development.

Comparison of the genetic determinism of two key phenological traits, flowering and maturity dates, in three Prunus species: peach, apricot and sweet cherry

The present study investigates the genetic determinism of flowering and maturity dates, two traits highly affected by global climate change. Flowering and maturity dates were evaluated on five progenies from three Prunus species, peach, apricot and sweet cherry, during 3-8 years. Quantitative trait locus (QTL) detection was performed separately for each year and also by integrating data from all years together. High heritability estimates were obtained for flowering and maturity dates. Several QTLs for flowering and maturity dates were highly stable, detected each year of evaluation, suggesting that they were not affected by climatic variations. For flowering date, major QTLs were detected on linkage groups (LG) 4 for apricot and sweet cherry and on LG6 for peach. QTLs were identified on LG2, LG3, LG4 and LG7 for the three species. For maturity date, a major QTL was detected on LG4 in the three species. Using the peach genome sequence data, candidate genes underlying the major QTLs on LG4 and LG6 were investigated and key genes were identified. Our results provide a basis for the identification of genes involved in flowering and maturity dates that could be used to develop cultivar ideotypes adapted to future climatic conditions.

Molecular interactions of GBF1 with HY5 and HYH proteins during light-mediated seedling development in Arabidopsis thaliana

Arabidopsis bZIP transcription factor, GBF1, acts as a differential regulator of cryptochrome-mediated blue light signaling. Whereas the bZIP proteins, HY5 (elongated hypocotyl 5) and HYH (HY5 homologue), are degraded by COP1-mediated proteasomal pathways, GBF1 is degraded by a proteasomal pathway independent of COP1. In this study, we have investigated the functional interrelations of GBF1 with HY5 and HYH in Arabidopsis seedling development. The genetic studies using double and triple mutants reveal that GBF1 largely acts antagonistically with HY5 and HYH in Arabidopsis seedling development. Further, GBF1 and HY5 play more important roles than HYH in blue light-mediated photomorphogenic growth. This study reveals that GBF1 is able to form a G-box-binding heterodimer with HY5 but not with HYH. The in vitro and in vivo studies demonstrate that GBF1 co-localizes with HY5 or HYH in the nucleus and physically interacts with both of the proteins. The protein-protein interaction studies further reveal that the bZIP domain of GBF1 is essential and sufficient for the interaction with HY5 or HYH. Taken together, these data demonstrate the functional interrelations of GBF1 with HY5 and HYH in Arabidopsis seedling development.

Evolution of neutral and flowering genes along pearl millet (Pennisetum glaucum) domestication

Background

Pearl millet landraces display an important variation in their cycle duration. This diversity contributes to the stability of crop production in the Sahel despite inter-annual rainfall fluctuation. Conservation of phenological diversity is important for the future of pearl millet improvement and sustainable use. Identification of genes contributing to flowering time variation is therefore relevant. In this study we focused on three flowering candidate genes, PgHd3a, PgDwarf8 and PgPHYC. We tested for signatures of past selective events within polymorphism patterns of these three genes that could have been associated with pearl millet domestication and/or landraces differentiation. In order to implement ad hoc neutrality tests, a plausible demographic history of pearl millet domestication was inferred through Approximate Bayesian Computation by using eight neutral STS loci.

Results

Domesticated pearl millet exhibited 84% of the nucleotide diversity level found in the wild population. No specific polymorphisms were found either in the wild or in the domestic populations. The Bayesian approach and previous studies suggest that gene flow between wild relatives and domesticated pearl millets is a main factor explaining these results. Early and late landraces did not show significant genetic differentiation at both the neutral and the candidate loci. A positive selection was evidenced in PgHd3a and PgDwarf8 genes of domestic forms but not in the wild population.

Conclusion

Our results strongly suggest that PgHd3a and PgDwarf8 were likely targeted by selection during domestication. However, a potential role of any of the three candidate genes in the phenological differentiation between early and late landraces was not supported by our data. Reasons why these results contrast with previous results that have shown a slight but significant association between PgPHYC polymorphisms and variation in flowering time in pearl millet are discussed.

Advances in upstream players of cytokinin phosphorelay: receptors and histidine phosphotransfer proteins

Cytokinins are a class of plant hormones that have been linked to numerous growth and developmental aspects in plants. The cytokinin signal is perceived by sensor histidine kinase receptors and transmitted via histidine phosphotransfer proteins (HPts) to downstream response regulators. Since their discovery, cytokinin receptors have been a focus of interest for many researchers. Ongoing research on these transmembrane receptors has greatly broadened our knowledge in terms of cytokinin-receptor interaction, receptor specificity, receptor cellular localization, and receptor functions in cytokinin related growth and developmental processes. This review focuses on the recent advances on the cytokinin receptors and HPt proteins in Arabidopsis.

Gene regulation by cytokinin in Arabidopsis

The plant hormone cytokinin realizes at least part of its signaling output through the regulation of gene expression. A great part of the early transcriptional regulation is mediated by type-B response regulators, which are transcription factors of the MYB family. Other transcription factors, such as the cytokinin response factors of the AP2/ERF family, have also been shown to be involved in this process. Additional transcription factors mediate distinct parts of the cytokinin response through tissue- and cell-specific downstream transcriptional cascades. In Arabidopsis, only a single cytokinin response element, to which type-B response regulators bind, has been clearly proven so far, which has 5'-GAT(T/C)-3' as a core sequence. This motif has served to construct a synthetic cytokinin-sensitive two-component system response element, which is useful for monitoring the cellular cytokinin status. Insight into the extent of transcriptional regulation has been gained by genome-wide gene expression analyses following cytokinin treatment and from plants having an altered cytokinin content or signaling. This review presents a meta analysis of such microarray data resulting in a core list of cytokinin response genes. Genes encoding type-A response regulators displayed the most stable response to cytokinin, but a number of cytokinin metabolism genes (CKX4, CKX5, CYP735A2, UGT76C2) also belong to them, indicating homeostatic mechanisms operating at the transcriptional level. The cytokinin core response genes are also the target of other hormones as well as biotic and abiotic stresses, documenting crosstalk of the cytokinin system with other hormonal and environmental signaling pathways. The multiple links of cytokinin to diverse functions, ranging from control of meristem activity, hormonal crosstalk, nutrient acquisition, and various stress responses, are also corroborated by a compilation of genes that have been repeatedly found by independent gene expression profiling studies. Such functions are, at least in part, supported by genetic studies.

Tissue- and isoform-specific phytochrome regulation of light-dependent anthocyanin accumulation in Arabidopsis thaliana

Phytochromes regulate light- and sucrose-dependent anthocyanin synthesis and accumulation in many plants. Mesophyll-specific phyA alone has been linked to the regulation of anthocyanin accumulation in response to far-red light in Arabidopsis thaliana. However, multiple mesophyll-localized phytochromes were implicated in the photoregulation of anthocyanin accumulation in red-light conditions. Here, we report a role for mesophyll-specific phyA in blue-light-dependent regulation of anthocyanin levels and novel roles for individual phy isoforms in the regulation of anthocyanin accumulation under red illumination. These results provide new insight into spatial- and isoform-specific regulation of pigmentation by phytochromes in A. thaliana.

The Arabidopsis Myb genes MYR1 and MYR2 are redundant negative regulators of flowering time under decreased light intensity

Changes in the duration, quality and intensity of light affect flowering time. Compared with the effects of light duration and quality, less is known about the effects of light intensity on flowering. Here we describe two paralogous single Myb domain genes, MYB-RELATED PROTEIN 1 (MYR1) and MYB-RELATED PROTEIN 2 (MYR2), and their roles as repressors of responses to decreased light intensity in Arabidopsis. Homozygous myr1 myr2 double mutants flowered early under low light intensities. Additionally, myr1 myr2 mutants exhibited increases in petiole length, leaf angle and apical dominance. Genetic analyses involving mutants in the long-day, gibberellin (GA) and phyB flowering pathways indicated that all aspects of the myr1 myr2 phenotype required GA biosynthesis. The early-flowering phenotype of myr1 myr2 also required FLOWERING LOCUS T, and myr1 myr2 mutants showed an epistatic interaction with the phyB-9 mutant. Over-expression of MYR1 or MYR2 produced GA-deficiency symptoms that were rescued by application of gibberellic acid (GA₃). Loss of MYR1 and MYR2 function was associated with a twofold increase in GA20ox2 expression and a 30% increase in GA₄ levels, while over-expression of MYR2 led to a threefold decrease in GA20ox2 expression and a 50% decrease in GA₄ levels. Considered together, these results suggest that the ability of MYR1 and MYR2 to repress flowering and organ elongation is at least partly due to their negative effect on levels of bioactive GA.

A novel phototropic response to red light is revealed in microgravity

The aim of this study was to investigate phototropism in plants grown in microgravity conditions without the complications of a 1-g environment. Experiments performed on the International Space Station (ISS) were used to explore the mechanisms of both blue-light- and red-light-induced phototropism in plants. This project utilized the European Modular Cultivation System (EMCS), which has environmental controls for plant growth as well as centrifuges for gravity treatments used as a 1-g control. Images captured from video tapes were used to analyze the growth, development, and curvature of Arabidopsis thaliana plants that developed from seed in space. A novel positive phototropic response to red light was observed in hypocotyls of seedlings that developed in microgravity. This response was not apparent in seedlings grown on Earth or in the 1-g control during the space flight. In addition, blue-light-based phototropism had a greater response in microgravity compared with the 1-g control. Although flowering plants are generally thought to lack red light phototropism, our data suggest that at least some flowering plants may have retained a red light sensory system for phototropism. Thus, this discovery may have important implications for understanding the evolution of light sensory systems in plants.

A focus on natural variation for abiotic constraints response in the model species Arabidopsis thaliana

Plants are particularly subject to environmental stress, as they cannot move from unfavourable surroundings. As a consequence they have to react in situ. In any case, plants have to sense the stress, then the signal has to be transduced to engage the appropriate response. Stress response is effected by regulating genes, by turning on molecular mechanisms to protect the whole organism and its components and/or to repair damage. Reactions vary depending on the type of stress and its intensity, but some are commonly turned on because some responses to different abiotic stresses are shared. In addition, there are multiple ways for plants to respond to environmental stress, depending on the species and life strategy, but also multiple ways within a species depending on plant variety or ecotype. It is regularly accepted that populations of a single species originating from diverse geographic origins and/or that have been subjected to different selective pressure, have evolved retaining the best alleles for completing their life cycle. Therefore, the study of natural variation in response to abiotic stress, can help unravel key genes and alleles for plants to cope with their unfavourable physical and chemical surroundings. This review is focusing on Arabidopsis thaliana which has been largely adopted by the global scientific community as a model organism. Also, tools and data that facilitate investigation of natural variation and abiotic stress encountered in the wild are set out. Characterization of accessions, QTLs detection and cloning of alleles responsible for variation are presented.

Right place, right time: Spatiotemporal light regulation of plant growth and development

Recent advances in our understanding of the roles of photoreceptors in light-dependent regulation of plant growth and development have been rapid and significant. Developments have been reported for numerous plant photoreceptor signaling pathways, yet researchers have made the most progress in increasing our comprehension of the roles of phytochrome family members, as well as the intracellular roles of phytochromes and phytochrome-interacting proteins in light-dependent signaling. An understudied, but vitally important, area of phytochrome biology centers on the roles phytochromes play in intercellular and interorgan signaling at the molecular level that results in the coordination of growth responses between distinct tissues and organs. This frontier of research into the spatiotemporal roles of phytochromes, and more generally plant photoreceptors, which is only beginning to be investigated and understood at the molecular genetic level, has a rich history of physiological data.

GBF1, a transcription factor of blue light signaling in Arabidopsis, is degraded in the dark by a proteasome-mediated pathway independent of COP1 and SPA1

Arabidopsis GBF1/ZBF2 is a bZIP transcription factor that plays dual but opposite regulatory roles in cryptochrome-mediated blue light signaling. Here, we show the genetic and molecular interrelation of GBF1 with two well characterized negative regulators of light signaling, COP1 and SPA1, in photomorphogenic growth and light-regulated gene expression. Our results further reveal that GBF1 protein is less abundant in the dark-grown seedlings and is degraded by a proteasome-mediated pathway independent of COP1 and SPA1. Furthermore, COP1 physically interacts with GBF1 and is required for the optimum accumulation of GBF1 protein in light-grown seedlings. Taken together, this study provides a mechanistic view of concerted function of three important regulators in Arabidopsis seedling development.

The role of phytochrome C in gravitropism and phototropism in Arabidopsis thaliana

The phytochrome (phy) photoreceptors, which consist of a small gene family PHYA-E in dicot plants, play important roles in regulating many light-induced responses in plants. Although the best characterised phytochromes are phytochrome A (phyA) and phytochrome (phyB), the functions of phyD and phyE have been increasingly studied. Phytochrome C (phy C) has been the most poorly understood member of the photoreceptor family, since isolation of phyC mutants only has been accomplished within the last few years. Recent reports show that phyC functions in hypocotyl elongation, rosette leaf morphology, and timing of flowering. In the present study, we show that phyC plays a role in tropisms in seedlings and inflorescence stems of light-grown Arabidopsis thaliana (L.) Heynh. (Wassilewskija ecotype). Phytochrome C has a positive effect on gravitropism in hypocotyls and stems, but it has a limited role in root gravitropism. In contrast, phyC attenuates the positive phototropic response to blue light in hypocotyls and the red-light-based positive phototropism in roots. Phytochrome D (phy D) also mediates gravitropism in hypocotyls and inflorescence stems and attenuates positive phototropism in response to blue in hypocotyls and stems. Thus, phyC can be added to the list of the other four phytochromes, which play various roles in both gravitropism and phototropism in plant organs. This report also supports the growing body of evidence demonstrating cross talk between phytochromes and blue-light photoreceptors.

PKS1 plays a role in red-light-based positive phototropism in roots

Aerial parts of plants curve towards the light (i.e. positive phototropism), and roots typically grow away from the light (i.e. negative phototropism). In addition, Arabidopsis roots exhibit positive phototropism relative to red light (RL), and this response is mediated by phytochromes A and B (phyA and phyB). Upon light stimulation, phyA and phyB interact with the phytochrome kinase substrate (PKS1) in the cytoplasm. In this study, we investigated the role of PKS1, along with phyA and phyB, in the positive phototropic responses to RL in roots. Using a high-resolution feedback system, we studied the phenotypic responses of roots of phyA, phyB, pks1, phyA pks1 and phyB pks1 null mutants as well as the PKS1-overexpressing line in response to RL. PKS1 emerged as an intermediary in the signalling pathways and appears to promote a negative curvature to RL in roots. In addition, phyA and phyB were both essential for a positive response to RL and act in a complementary fashion. However, either photoreceptor acting without the other results in negative curvature in response to red illumination so that the mode of action differs depending on whether phyA and phyB act independently or together. Our results suggest that PKS1 is part of a signalling pathway independent of phyA and phyB and that PKS1 modulates RL-based root phototropism.

SHORT HYPOCOTYL IN WHITE LIGHT1, a serine-arginine-aspartate-rich protein in Arabidopsis, acts as a negative regulator of photomorphogenic growth

Light is an important factor for plant growth and development. We have identified and functionally characterized a regulatory gene SHORT HYPOCOTYL IN WHITE LIGHT1 (SHW1) involved in Arabidopsis (Arabidopsis thaliana) seedling development. SHW1 encodes a unique serine-arginine-aspartate-rich protein, which is constitutively localized in the nucleus of hypocotyl cells. Transgenic analyses have revealed that the expression of SHW1 is developmentally regulated and is closely associated with the photosynthetically active tissues. Genetic and molecular analyses suggest that SHW1 acts as a negative regulator of light-mediated inhibition of hypocotyl elongation, however, plays a positive regulatory role in light-regulated gene expression. The shw1 mutants also display shorter hypocotyl in dark, and analyses of shw1 cop1 double mutants reveal that SHW1 acts nonredundantly with COP1 to control hypocotyl elongation in the darkness. Taken together, this study provides evidences that SHW1 is a regulatory protein that is functionally interrelated to COP1 and plays dual but opposite regulatory roles in photomorphogenesis.

DIURNAL CELL DIVISION REGULATED BY GATING THE G1 /S TRANSITION IN ENTEROMORPHA COMPRESSA (CHLOROPHYTA)(1)

The cell-cycle progression of Enteromorpha compressa (L.) Nees (=Ulva compressa L.) was diurnally regulated by gating the G1 /S transition. When the gate was open, the cells were able to divide if they had attained a sufficient size. However, the cells were not able to divide while the gate was closed, even if the cells had attained sufficient size. The diurnal rhythm of cell division immediately disappeared when the thalli were transferred to continuous light or darkness. When the thalli were transferred to a shifted photoperiod, the rhythm of cell division immediately and accurately synchronized with the shifted photoperiod. These data support a gating-system model regulated by light:dark (L:D) cycles rather than an endogenous circadian clock. A dark phase of 6 h or longer was essential for gate closing, and a light phase of 14 h was required to renew cell division after a dark phase of >6 h.

LZF1, a HY5-regulated transcriptional factor, functions in Arabidopsis de-etiolation

We surveyed differential gene expression patterns during early photomorphogenesis in both wild-type and mutant Arabidopsis defective in HY5, an influential positive regulator of the responses of gene expression to a light stimulus, to identify light-responsive genes whose expression was HY5 dependent. These gene-expression data identified light-regulated zinc finger protein 1 (LZF1), a gene encoding a previously uncharacterized C2C2-CO B-box transcriptional regulator. HY5 has positive trans-activating activity toward LZF1 and binding affinity to LZF1 promoter in vivo. HY5 is needed but not sufficient for the induction of LZF1 expression. Anthocyanin content is significantly diminished in lzf1 under far red, which is the most efficient light for the induction of LZF1. The expression of PAP1/MYB75 is elevated in plants overexpressing LZF1, which leads to the hyperaccumulation of anthocyanin in transgenic Arabidopsis. The transition from etioplast to chloroplast and the accumulation of chlorophyll were notably compromised in the lzf1 mutant. We provide molecular evidence that LZF1 influences chloroplast biogenesis and function via regulating genes encoding chloroplast proteins. In the absence of HY5, mutation of LZF1 leads to further reduced light sensitivity for light-regulated inhibition of hypocotyl elongation and anthocyanin and chlorophyll accumulation. Our data indicate that LZF1 is a positive regulator functioning in Arabidopsis de-etiolation.

EGY1 plays a role in regulation of endodermal plastid size and number that are involved in ethylene-dependent gravitropism of light-grown Arabidopsis hypocotyls

Egy1 was isolated as an ethylene-dependent gravitropism-deficient Arabidopsis mutant. Molecular studies reveal that EGY1 gene encodes a 59-kDa plastid-targeted metalloprotease. It is actively expressed in hypocotyl tissue and targets to endodermal and cortex plastid. Its protein level is up-regulated by both ethylene and light. CAB protein accumulation and chlorophyll level is severely reduced in hypocotyls and endodermal cells, respectively. Sucrose is able to restore the severely reduced starch and lipid contents as well as the deficient endodermal plastid size found in light-grown egy1 hypocotyls yet it fails to rescue the reduced plastid number and chlorophyll level in egy1 endodermal cells. The loss-of-function egy1 mutation results in a smaller size (1.9 +/- 0.3 microm in diameter) and less number (5 +/- 1) of plastids in endodermal cells, which are nearly 50% of the wild-type. EGY1 is specially required for the development of full-size endodermal plastid in seedlings that are grown on sucrose-free media under light. It plays a direct role in controlling the light-induced chlorophyll production, grana formation and plastid replication in endodermal cell. However, it plays an indirect role in regulation of endodermal plastid size. It is likely that the ethylene-dependent gravitropism-deficient phenotype of egy1 hypocotyls may result from the smaller size and less number of endodermal plastids. Gravicurvature assays performed on ethylene-insensitive mutants, etr1-1, etr2-1, ers2-1, ein4-1 and ein2-5, have clearly demonstrated the necessary role for ethylene in vigorous gravitropism of light-grown hypocotyls. The degree of ethylene-dependent gravicurvature is positively correlated with the combined state of endodermal plastid mass and number. Neither ethylene nor EGY1-regulated full-size endodermal plastid is sufficient for promotion of vigorous hypocotyl gravitropism. Presence of 4 full-size plastids per endodermal cell together with ethylene pretreatment of hypocotyls becomes sufficient to trigger vigorous gravicurvature in light-grown seedlings. A model is therefore proposed to address the role of EGY1 in regulation of endodermal plastid size and number as well as the stimulatory effect of ethylene on hypocotyl gravitropism.

An inositol polyphosphate 5-phosphatase functions in PHOTOTROPIN1 signaling in Arabidopis by altering cytosolic Ca2+

Inositol polyphosphate 5-phosphatase (5PTase) is a key enzyme in the phosphatidylinositol metabolic pathway, which plays critical roles in a number of cellular processes in plants. Our previous work implicated the role of 5PTase13, which encodes a WD40-containing type II 5PTase, in hormone-mediated cotyledon vein development. Here, we show that 5PTase13 is also involved in blue light responses in Arabidopsis thaliana. Compared with that in darkness, the expression of 5PTase13 was suppressed by blue light irradiation, and disruption of the gene resulted in shortened hypocotyls and expanded cotyledons. Genetic analysis showed that 5PTase13 acted independently from CRYPTOCHROME1 and CONSTITUTIVE PHOTOMORPHOGENIC1 but interacted functionally with PHOTOTROPIN1 (PHOT1). The expression level of 5PTase13 was significantly enhanced in phot1 single or phot1 phot2 double mutants under blue light, and suppression of 5PTase13 expression rescued the elongated hypocotyls in the phot1 or phot1 phot2 mutants. Further analysis showed that the blue light-induced elevation of cytosolic Ca2+ was inhibited in the phot1 mutant but enhanced in the 5pt13 mutant, suggesting that 5PTase13 antagonizes PHOT1-mediated effects on calcium signaling under blue light.

Phytochrome induces rapid PIF5 phosphorylation and degradation in response to red-light activation

The phytochrome (phy) family of sensory photoreceptors (phyA-phyE in Arabidopsis thaliana) induces changes in target-gene expression upon light-induced translocation to the nucleus, where certain members interact with selected members of the constitutively nuclear basic helix-loop-helix transcription factor family, such as PHYTOCHROME-INTERACTING FACTOR3 (PIF3). Previous evidence indicates that the binding of the photoactivated photoreceptor molecule to PIF3 induces rapid phosphorylation of the transcription factor in the cell prior to its degradation via the ubiqitin-proteosome system. To investigate whether this apparent primary signaling mechanism can be generalized to other phy-interacting partners, we have examined the molecular behavior of a second related phy-interacting member of the basic helix-loop-helix family, PIF5, during early deetiolation, immediately following initial exposure of dark-grown seedlings to light. The data show that red light induces very rapid phosphorylation and subsequent degradation (t(1/2) < 5 min) of PIF5 via the proteosome system upon irradiation. Photobiological and genetic evidence indicates that the photoactivated phy molecule acts within 60 s to induce this phosphorylation of PIF5, and that phyA and phyB redundantly dominate this process, with phyD playing an apparently minor role. Collectively, the data support the proposal that the rapid phy-induced phosphorylation of PIF3 and PIF5 may represent the biochemical mechanism of primary signal transfer from photoactivated photoreceptor to binding partner, and that phyA and phyB (and possibly phyD) may signal to multiple, shared partners utilizing this common mechanism.

Arabidopsis fhl/fhy1 double mutant reveals a distinct cytoplasmic action of phytochrome A

Phytochrome A (phyA) plays an important role during germination and early seedling development. Because phyA is the primary photoreceptor for the high-irradiance response and the very-low-fluence response, it can trigger development not only in red and far-red (FR) light but also in a wider range of light qualities. Although phyA action is generally associated with translocation to the nucleus and regulation of transcription, there is evidence for additional cytoplasmic functions. Because nuclear accumulation of phyA has been shown to depend on far-red-elongated hypocotyl 1 (FHY1) and FHL (FHY1-like), investigation of phyA function in a double fhl/fhy1 mutant might be valuable in revealing the mechanism of phyA translocation and possible cytoplasmic functions. In fhl/fhy1, the FR-triggered nuclear translocation of phyA could no longer be detected but could be restored by transgenic expression of CFP:FHY1. Whereas the fhl/fhy1 mutant showed a phyA phenotype in respect to hypocotyl elongation and cotyledon opening under high-irradiance response conditions as well as a typical phyA germination phenotype under very-low-fluence response conditions, fhl/fhy1 showed no phenotype with respect to the phyA-dependent abrogation of negative gravitropism in blue light and in red-enhanced phototropism, demonstrating clear cytoplasmic functions of phyA. Disturbance of phyA nuclear import in fhl/fhy1 led to formation of FR-induced phyA:GFP cytoplasmic foci resembling the sequestered areas of phytochrome. FHY1 and FHL play crucial roles in phyA nuclear translocation and signaling. Thus the double-mutant fhl/fhy1 allows nuclear and cytoplasmic phyA functions to be separated, leading to the novel identification of cytoplasmic phyA responses.

Plant protein phosphorylation monitored by capillary liquid chromatography--element mass spectrometry

Many essential cellular functions such as growth rate, motility, and metabolic activity are linked to reversible protein phosphorylation, since they are controlled by signaling cascades based mainly on phosphorylation/dephosphorylation events. Quantification of global or site-specific protein phosphorylation is not straightforward with standard proteomic techniques. The coupling of capillary liquid chromatography (microLC) with ICP-MS (inductively coupled plasma-mass spectrometry) is a method which allows a quantitative screening of protein extracts for their phosphorus and sulfur content, and thus provides access to the protein phosphorylation degree. In extension of a recent pilot study, we analyzed protein extracts from the model organisms Arabidopsis thaliana and Chlamydomonas reinhardtii as representatives for multicellular and unicellular green photosynthetically active organisms. The results indicate that the average protein phosphorylation level of the algae C. reinhardtii is higher than that of A. thaliana. Both the average phosphorylation levels were found to be between the extreme values determined so far for prokaryotes (C. glutamicum, lowest levels) and eukaryotes (Mus musculus, highest levels). Tissue samples of A. thaliana representing different stages of plant development showed varying levels of protein phosphorylation indicating a different adjustment of the kinase/phosphatase system. We also utilized the microLC-ICP-MS technology to estimate the efficiency of a novel phosphoprotein enrichment method based on aluminum hydroxide, since the enrichment of phosphorylated species is often an essential step for their molecular characterization.

A Basic Leucine Zipper Transcription Factor, G-box-binding Factor 1, Regulates Blue Light-mediated Photomorphogenic Growth in Arabidopsis

Several transcriptional regulators have been identified and demonstrated to play either positive or negative regulatory roles in seedling development. However, the regulatory coordination between hypocotyl elongation and cotyledon expansion during early seedling development in plants remains unknown. We report the identification of a Z-box binding factor (ZBF2) and its functional characterization in cryptochrome-mediated blue light signaling. ZBF2 encodes a G-box binding factor (GBF1), which is a basic leucine zipper transcription factor. Our DNA-protein interaction studies reveal that ZBF2/GBF1 also interacts with the Z-box light-responsive element of light-regulated promoters. Genetic analyses of gbf1 mutants and overexpression studies suggest that GBF1 acts as a repressor of blue light-mediated inhibition in hypocotyl elongation, however, it acts as a positive regulator of cotyledon expansion during photomorphogenic growth. Furthermore, whereas GBF1 acts as a positive regulator of lateral root formation, it differentially regulates the expression of light-inducible genes. Taken together, these results demonstrate that GBF1 is a unique transcriptional regulator of photomorphogenesis in blue light.

How to be early flowering: an evolutionary perspective

In wild and cultivated annual plant species, flowering time is an important life-history trait that coordinates the life cycle with local environmental conditions. Extensive studies on the genetic basis of flowering time in the model species Arabidopsis thaliana have revealed a complex genetic network that can detect environmental and internal signals. Based on this knowledge and on known pleiotropic effects associated with flowering time genes, we suggest that a natural shift towards an early-flowering life cycle might involve only particular functional regions in a limited number of genes. Our predictions are supported by genetic theories of adaptation and by recent data about genes associated with natural variation. We analyse the extent to which these predictions can also apply to crop species.

Proteomic identification of potential target proteins regulated by an ASK1-mediated proteolysis pathway

The ASK1 (ARABIDOPSIS SKP1-LIKE) protein is a critical component of the SCF (Skp1-Cullin-F box protein) ubiquitin ligase complexes that recruit target proteins for degradation by the 26S proteosome. To investigate proteins that are affected by the ASK1-mediated proteolysis pathway in Arabidopsis flowers, we compared the proteomes of the Arabidopsis wild type and ask1 mutant flower buds using two-dimensional electrophoresis (2-DE). Ten protein spots with higher or lower abundance in the ask1 mutant flowers compared to wild type flowers were excised and subjected to further mass spectrometry (MS) analysis. The results showed that they were proteins involved in photomorphogenesis, circadian oscillation, post-translation process, stress-responses and cell expansion or elongation, suggesting that those processes were affected in the ask1 mutant. The transcript levels of these genes were also compared based on the Affymetrix gene chip microarray data. No significant difference was observed for most of the genes, suggesting that the proteins with elevated levels of accumulation in the ask1 mutant could be candidate targets regulated by an ASK1-mediated proteolysis pathway. These results help to elucidate the pleiotropic functions of ASK1 in Arabidopsis developmental processes and also demonstrate the importance and necessity of studying protein levels with respect to gene functions.