Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways

Tomato SlCDF3 Delays Flowering Time by Regulating Different FT-Like Genes Under Long-Day and Short-Day Conditions

Photoperiod is a crucial inducer of plant flowering. Cycling DOF factors (CDFs) play pivotal roles in the flowering of long-day (LD) and short-day (SD) plants. However, the functions of CDFs in the photoperiod regulated flowering remain unclear in day-neutral plants. In the present study, tomato (Solanum lycopersicum L. cv. "Ailsa Craig") seedlings of the wild-type and transgenic lines of overexpressing CDFs were treated with different photoperiods. The flowering time and the expression pattern of SlCDFs and other FT-like genes were investigated. The results showed that tomato SlCDF1, SlCDF2, SlCDF3, SlCDF4, and SlCDF5 are homologs to Arabidopsis cycling DOF factor 1 (AtCDF1). SlCDF1-5 expression levels were influenced by the developmental stage and the tissue location, and notably, the expression patterns throughout light environments showed two opposite trends. Among the SlCDF1-5 overexpression transgenic lines, overexpressing SlCDF3 delayed flowering time in both LD (16 h light/8 h dark) and SD (8 h light/16 h dark) conditions. Furthermore, SlCDF3 led to an increase in the mRNA level of SlSP5G, a tomato FT-like gene, in LD conditions, while the transcription level of the other two FT-like genes, SlSP5G2 and SlSP5G3, were up-regulated in SD conditions. Taken together, at the transcription level, our results demonstrated that SlCDF3 played a significant role in controlling tomato flowering under LD and SD conditions, possibly through directly or indirectly regulating FT-like genes.

Cognitive Disposition to Wine Consumption: How the Brain Is Wired to Select the Perfect Bottle With a Novel Musical Twist

Taste is not a veridical perception: it is modifiable by cognitive and affective processes, as well as by expectations. Even though molecular composition determines the savor, various other factors such as external characteristics and basic assumptions have a sway over perceived pleasantness of food and drink. The rituals associated with wine tastings especially underscore the importance of these subjective ramifications. While auditory stimuli are known to influence drinking experience, the impact of melody on the product itself and on corollary consumer preference is unknown. As routine judgments are also influenced by informational cues, here we evaluated whether description of a unique technological innovation (i.e., serenaded grapes and barrels) as cogent suggestion of quality improves willingness to buy. This project unveils that the belief about music-fed wines, which might be construed as a motivational bias, can alter purchasing decisions; however, further neuro-marketing studies are warranted with this respect.

Darkness-induced effects on gene expression in Cosmarium crenatum (Zygnematophyceae) from a polar habitat

Light is a key environmental regulator in all photosynthetic organisms. Many studies focused on the physiologic response to changes in light availability of species from the Zygnematophyceae, but the impact of the absence of light and the molecular acclimation process on the other side have been poorly understood. Here we present transcriptomic analyses of Cosmarium crenatum from a polar habitat exposed to darkness. The algae were cultured in dark for one week; cell number and quantum yield of photosystem II (Fv/Fm) were monitored. Cell number was stable, but the Fv/Fm decreased in both groups, darkness-treated and control. Gene expression analysis revealed a strong repression of transcripts associated with photosynthesis, photorespiration and cell wall development. General carbohydrate and lipid metabolism were differentially regulated, but starch is shown to be the primary energy source in these conditions. Additionally, C. crenatum induced mRNA responsible for epigenetic modifications which may be a specific response to an adaption and acclimation to polar conditions. Our study sheds light on the molecular acclimation process to darkness and provides ecological implications for new perspectives in this specialized group of green algae.

Sugar accumulation and growth of lettuce exposed to different lighting modes of red and blue LED light

The present study evaluated the growth response and sugar accumulation of lettuce exposed to different lighting modes of red and blue LED light based on the same daily light integral (7.49 μmol·m-2). Six lighting treatments were performed, that were monochromatic red light (R), monochromatic blue light (B), simultaneous red and blue light as the control (RB, R:B = 1:1), mixed modes of R, B and RB (R/RB/B, 4 h R to 4 h RB and then 4 h B), and alternating red and blue light with alternating intervals of 4 h and 1 h respectively recorded as R/B(4 h) and R/B(1 h). The Results showed that different irradiation modes led to obvious morphological changes in lettuce. Among all the treatments, the highest fresh and dry weight of lettuce shoot were both detected with R/B(1 h), significantly higher than the other treatments. Compared with plants treated with RB, the contents of fructose, glucose, crude fiber as well as the total sweetness index (TSI) of lettuce were significantly enhanced by R treatment; meanwhile, monochromatic R significantly promoted the activities of sucrose degrading enzymes such as acid invertase (AI) and neutral invertase (NI), while obviously reduced the activity of sucrose synthesizing enzyme (SPS). Additionally. The highest contents of sucrose and starch accompanied with the strongest activity of SPS were detected in plants treated with R/B(1 h). The alternating treatments R/B(4 h) and R/B(1 h) inhibited the activity of SS, while enhanced that of SPS compared with the other treatments, indicating that different light environment might influence sugar compositions via regulating the activities of sucrose metabolism enzymes. On the whole, R/B(1 h) was the optimal lighting strategy in terms of lettuce yield, taste and energy use efficiency in the present study.

Exploration of the Effect of Blue Light on Functional Metabolite Accumulation in Longan Embryonic Calli via RNA Sequencing

Light is an important factor that affects the synthesis of functional metabolites in longan embryogenic calli (ECs). However, analysis of the effect of light on functional metabolites in longan ECs via RNA sequencing has rarely been reported and their light regulation network is unclear. The contents of various functional metabolites as well as the enzymatic activities of superoxide dismutase and peroxidase and the level of H₂O₂ in longan ECs were significantly higher under blue light treatment than under the other treatments (dark, white). In this study, we sequenced three mRNA libraries constructed from longan ECs subjected to different treatments. A total of 4463, 1639 and 1806 genes were differentially expressed in the dark versus blue (DB), dark versus white (DW) and white versus blue (WB) combinations, respectively. According to GO and KEGG analyses, most of the differentially expressed genes (DEGs) identified were involved in transmembrane transport, taurine and hypotaurine metabolism, calcium transport and so forth. Mapman analysis revealed that more DEGs were identified in each DB combination pathway than in DW combination pathways, indicating that blue light exerts a significantly stronger regulatory effect on longan EC metabolism than the other treatments. Based on previous research and transcriptome data mining, a blue light signaling network of genes that affect longan functional metabolites was constructed and HY5, PIF4 and MYC2 were shown to be the key regulatory genes in the network. The results of this study demonstrate that the expression levels of phase-specific genes vary with changes in longan EC functional metabolites.

Carotenoid biosynthesis of pak choi (Brassica rapa ssp. chinensis) sprouts grown under different light-emitting diodes during the diurnal course

Light-emitting diodes (LEDs) are considered the future of greenhouse lighting. This study investigates the carotenoid concentrations of pak choi sprouts after growth under blue, red and white LEDs at six different time points. Furthermore, the diurnal changes of RNA transcripts of key genes of the carotenoid biosynthesis pathway as well as of the carotenoid cleavage dioxygenase 4 (CCD4) gene and of the transcription factor genes elongated hypocotyl 5 (HY5) and circadian clock associated 1 (CCA1) were investigated. The carotenoid concentrations were steady throughout the day, but showed a small maximum in the afternoon. An average total carotenoid concentration of 536 ± 29 ng mg-1 DM produced under white LEDs was measured, which is comparable to previously described field-grown levels. The carotenoid concentrations were slightly lower under blue or red LEDs. Moreover, the diurnal RNA transcript rhythms of most of the carotenoid biosynthesis genes showed an increase during the light period, which can be correlated to the carotenoid maxima in the afternoon. Blue LEDs caused the highest transcriptional induction of biosynthetic genes as well as of CCD4, thereby indicating an increased flux through the pathway. In addition, the highest levels of HY5 transcripts and CCA1 transcripts were determined under blue LEDs.

Supplementary Light Source Affects the Growth and Development of Codonopsis lanceolata Seedlings

Codonopsis lanceolata is widely used in traditional medicine and diets. However, there is no optimal protocol for the commercial production of C. lanceolata seedlings. This study was carried out to find the optimum supplementary light source for the production of C. lanceolata seedlings. Seedlings were grown for four weeks in a glasshouse with an average daily light intensity of 490 μmol·m⁻²·s⁻¹ photosynthetic photon flux density (PPFD) coming from the sun and a 16-h daily supplementary lighting at 120 μmol·m⁻²·s⁻¹ PPFD from either high-pressure sodium (HPS), metal halide (MH), far-red (FR), white LED (LED-w), or mixed (white: red: blue = 1:2:1) LEDs (LED-mix). The results showed that the greatest total biomass, stem diameter, ratio of shoot weight to shoot length, root biomass, and ratio of root weight to shoot weight were found in seedlings grown under supplementary LED-mix. Meanwhile, the stomatal properties and soluble sugar contents were improved for seedlings in LED-mix. The contents of starch, total phenols, and flavonoids were the greatest for seedlings in LED-w and LED-mix. The expression of photosynthetic proteins and genes in seedlings was also enhanced by LED-mix. Overall, these results suggest that LED-mix is advantageous to the photosynthetic potential and the accumulation of biomass, carbohydrates and secondary metabolites in C. lanceolata.

Role of Mitochondria in Regulating Lutein and Chlorophyll Biosynthesis in Chlorella pyrenoidosa under Heterotrophic Conditions

The green alga Chlorella pyrenoidosa can accumulate lutein and chlorophyll under heterotrophic conditions. We propose that the mitochondrial respiratory electron transport chain (mRET) may be involved in this process. To verify this hypothesis, algal cells were treated with different mRET inhibitors. The biosynthesis of lutein and chlorophyll was found to be significantly stimulated by salicylhydroxamic acid (SHAM), whereas their contents substantially decreased after treatment with antimycin A and sodium azide (NaN₃). Proteomic studies revealed profound protein alterations related to the redox and energy states, and a network was proposed: The up-regulation of peroxiredoxin reduces oxidized glutathione (GSSG) to reduced glutathione (GSH); phosphoenolpyruvate carboxykinase (PEPCK) catalyzes the conversion of oxaloacetic acid to phosphoenolpyruvate, and after entering the methylerythritol phosphate (MEP) pathway, 4-hydroxy-3-methylbut-2-en-1yl diphosphate synthase reduces 2-C-methyl-d-erythritol-2,4-cyclodiphosphate (ME-Cpp) to 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP), which is closely related to the synthesis of lutein; and coproporphyrinogen III oxidase and ChlI play important roles in the chlorophyll biosynthetic pathway. These results supported that for the heterotrophic C. pyrenoidosa, the signaling, oriented from mRET, may regulate the nuclear genes encoding the enzymes involved in photosynthetic pigment biosynthesis.

Using light to improve commercial value

The plasticity of plant morphology has evolved to maximize reproductive fitness in response to prevailing environmental conditions. Leaf architecture elaborates to maximize light harvesting, while the transition to flowering can either be accelerated or delayed to improve an individual's fitness. One of the most important environmental signals is light, with plants using light for both photosynthesis and as an environmental signal. Plants perceive different wavelengths of light using distinct photoreceptors. Recent advances in LED technology now enable light quality to be manipulated at a commercial scale, and as such opportunities now exist to take advantage of plants' developmental plasticity to enhance crop yield and quality through precise manipulation of a crops' lighting regime. This review will discuss how plants perceive and respond to light, and consider how these specific signaling pathways can be manipulated to improve crop yield and quality.

Transcriptional and translational responses of rapeseed leaves to red and blue lights at the rosette stage

Under different red (R):blue (B) photon flux ratios, the growth performance of rapeseed (Brassica napus L.) is significantly different. Rapeseed under high R ratios shows shade response, while under high B ratios it shows sun-type morphology. Rapeseed under monochromatic red or blue light is seriously stressed. Transcriptomic and proteomic methods were used to analyze the metabolic pathway change of rapeseed (cv. "Zhongshuang 11") leaves under different R:B photon flux ratios (including 100R:0B%, 75R:25B%, 25R:75B%, and 0R:100B%), based on digital gene expression (DGE) and two-dimensional gel electrophoresis (2-DE). For DGE analysis, 2054 differentially expressed transcripts (|log₂(fold change)|≥1, q<0.005) were detected among the treatments. High R ratios (100R:0B% and 75R:25B%) enhanced the expression of cellular structural components, mainly the cell wall and cell membrane. These components participated in plant epidermis development and anatomical structure morphogenesis. This might be related to the shade response induced by red light. High B ratios (25R:75B% and 0R:100B%) promoted the expression of chloroplast-related components, which might be involved in the formation of sun-type chloroplast induced by blue light. For 2-DE analysis, 37 protein spots showed more than a 2-fold difference in expression among the treatments. Monochromatic light (ML; 100R:0B% and 0R:100B%) stimulated accumulation of proteins associated with antioxidation, photosystem II (PSII), DNA and ribosome repairs, while compound light (CL; 75R:25B% and 25R:75B%) accelerated accumulation of proteins associated with carbohydrate, nucleic acid, amino acid, vitamin, and xanthophyll metabolisms. These findings can be useful in understanding the response mechanisms of rapeseed leaves to different R:B photon flux ratios.

The redox state of the apoplast influences the acclimation of photosynthesis and leaf metabolism to changing irradiance

The redox state of the apoplast is largely determined by ascorbate oxidase (AO) activity. The influence of AO activity on leaf acclimation to changing irradiance was explored in wild-type (WT) and transgenic tobacco (Nicotiana tobaccum) lines containing either high [pumpkin AO (PAO)] or low [tobacco AO (TAO)] AO activity at low [low light (LL); 250 μmol m-2  s-1 ] and high [high light (HL); 1600 μmol m-2  s-1 ] irradiance and following the transition from HL to LL. AO activities changed over the photoperiod, particularly in the PAO plants. AO activity had little effect on leaf ascorbate, which was significantly higher under HL than under LL. Apoplastic ascorbate/dehydroascorbate (DHA) ratios and threonate levels were modified by AO activity. Despite decreased levels of transcripts encoding ascorbate synthesis enzymes, leaf ascorbate increased over the first photoperiod following the transition from HL to LL, to much higher levels than LL-grown plants. Photosynthesis rates were significantly higher in the TAO leaves than in WT or PAO plants grown under HL but not under LL. Sub-sets of amino acids and fatty acids were lower in TAO and WT leaves than in the PAO plants under HL, and following the transition to LL. Light acclimation processes are therefore influenced by the apoplastic as well as chloroplastic redox state.

Nitric oxide promotes light-initiated seed germination by repressing PIF1 expression and stabilizing HFR1

Seed germination is a crucial stage in the life cycle of plants and is tightly controlled by internal and external signals. Phytochrome photoreceptors perceive light stimulation to promote seed germination. Previous studies have shown that PHYTOCHROME-INTERACTION FACTOR 1 (PIF1) is a negative regulatory factor and represses seed germination, while LONG HYPOCOTYL IN FAR-RED (HFR1) sequesters PIF1 by forming a heterodimer to relieve the inhibitory effect of seed germination during the initial phase. Nitric oxide (NO) has been reported to break seed dormancy, but the underlying mechanism is not well understood. Here, we report that NO signal enhances phytochrome B (PHYB)-dependent seed germination, and PHYB perceives red light stimulation to activate NR activity and NO accumulation. NO signal not only downregulates the transcription of PIF1, but also stabilize HFR1 proteins to intensify the interaction of the HFR1-PIF1 heterodimer, and compensate for the inhibitory effect of PIF1 on its target genes associated with hormone metabolism and cell wall loosening, consequently initiating seed germination. Thus, our results reveal a new mechanism for NO signals in modulating PHYB-mediated seed germination by repressing PIF1 expression at the transcriptional level as well as preventing PIF1 activity by stabilizing HFR1 protein.

Redox regulation of PEP activity during seedling establishment in Arabidopsis thaliana

Activation of the plastid-encoded RNA polymerase is tightly controlled and involves a network of phosphorylation and, as yet unidentified, thiol-mediated events. Here, we characterize PLASTID REDOX INSENSITIVE2, a redox-regulated protein required for full PEP-driven transcription. PRIN2 dimers can be reduced into the active monomeric form by thioredoxins through reduction of a disulfide bond. Exposure to light increases the ratio between the monomeric and dimeric forms of PRIN2. Complementation of prin2-2 with different PRIN2 protein variants demonstrates that the monomer is required for light-activated PEP-dependent transcription and that expression of the nuclear-encoded photosynthesis genes is linked to the activity of PEP. Activation of PEP during chloroplast development likely is the source of a retrograde signal that promotes nuclear LHCB expression. Thus, regulation of PRIN2 is the thiol-mediated mechanism required for full PEP activity, with PRIN2 monomerization via reduction by TRXs providing a mechanistic link between photosynthetic electron transport and activation of photosynthetic gene expression.

The plastid-encoded RNA polymerase PEP is regulated according to plastid redox state. Here, the authors show that the redox-regulated PRIN2 protein is reduced to monomeric form in a thiol-dependent manner in response to light and that PRIN2 monomers are required for PEP activity and retrograde signaling.

Dynamic N-glycoproteome analysis of maize seedling leaves during de-etiolation using Concanavalin A lectin affinity chromatography and a nano-LC-MS/MS-based iTRAQ approach

The identification of N -glycosylated proteins with information about changes in the level of N -glycosylation during de-etiolation provides a database that will aid further research on plant N -glycosylation and de-etiolation. N-glycosylation is one of the most prominent and abundant protein post-translational modifications in all eukaryotes and in plants it plays important roles in development, stress tolerance and immune responses. Because light-induced de-etiolation is one of the most dramatic developmental processes known in plants, seedlings undergoing de-etiolation are an excellent model for investigating dynamic proteomic profiles. Here, we present a comprehensive, quantitative N-glycoproteomic profile of maize seedlings undergoing 12 h of de-etiolation obtained using Concanavalin A (Con A) lectin affinity chromatography enrichment coupled with a nano-LC-MS/MS-based iTRAQ approach. In total, 1084 unique N-glycopeptides carrying 909 N-glycosylation sites and corresponding to 609 proteins were identified and quantified, including 186 N-glycosylation sites from 162 proteins that were significantly regulated over the course of the 12 h de-etiolation period. Based on hierarchical clustering analysis, the significantly regulated N-glycopeptides were divided into seven clusters that showed different N-glycosylation patterns during de-etiolation. We found no obvious difference in the enriched MapMan bincode categories for each cluster, and these clustered significantly regulated N-glycoproteins (SRNPs) are enriched in miscellaneous, protein, cell wall and signaling, indicating that although the N-glycosylation regulation patterns of these SRNPs might differ, they are involved in similar biological processes. Overall, this study represents the first large-scale quantitative N-glycoproteome of the model C4 plant, maize, which is one of the most important cereal and biofuel crops. Our results greatly expand the maize N-glycoproteomic database and also shed light on the potential roles of N-glycosylation modification during the greening of maize leaves.

Blue-light induced biosynthesis of ROS contributes to the signaling mechanism of Arabidopsis cryptochrome

Cryptochromes are evolutionarily conserved blue light receptors with many roles throughout plant growth and development. They undergo conformational changes in response to light enabling interaction with multiple downstream signaling partners. Recently, it has been shown that cryptochromes also synthesize reactive oxygen species (ROS) in response to light, suggesting the possibility of an alternate signaling mechanism. Here we show by fluorescence imaging and microscopy that H₂0₂ and ROS accumulate in the plant nucleus after cryptochrome activation. They induce ROS-regulated transcripts including for genes implicated in pathogen defense, biotic and abiotic stress. Mutant cryptochrome alleles that are non-functional in photomorphogenesis retain the capacity to induce ROS-responsive phenotypes. We conclude that nuclear biosynthesis of ROS by cryptochromes represents a new signaling paradigm that complements currently known mechanisms. This may lead to novel applications using blue light induced oxidative bursts to prime crop plants against the deleterious effects of environmental stresses and toxins.

Identification of HDA15-PIF1 as a key repression module directing the transcriptional network of seed germination in the dark

Light is a major external factor in regulating seed germination. Photoreceptor phytochrome B (PHYB) plays a predominant role in promoting seed germination in the initial phase after imbibition, partially by repressing phytochrome-interacting factor1 (PIF1). However, the mechanism underlying the PHYB-PIF1-mediated transcription regulation remains largely unclear. Here, we identified that histone deacetylase15 (HDA15) is a negative component of PHYB-dependent seed germination. Overexpression of HDA15 in Arabidopsis inhibits PHYB-dependent seed germination, whereas loss of function of HDA15 increases PHYB-dependent seed germination. Genetic evidence indicated that HDA15 acts downstream of PHYB and represses seed germination dependent on PIF1. Furthermore, HDA15 interacts with PIF1 both in vitro and in vivo. Genome-wide transcriptome analysis revealed that HDA15 and PIF1 co-regulate the transcription of the light-responsive genes involved in multiple hormonal signaling pathways and cellular processes in germinating seeds in the dark. In addition, PIF1 recruits HDA15 to the promoter regions of target genes and represses their expression by decreasing the histone H3 acetylation levels in the dark. Taken together, our analysis uncovered the role of histone deacetylation in the light-regulated seed germination process and identified that HDA15-PIF1 acts as a key repression module directing the transcription network of seed germination.

COP1 regulates plant growth and development in response to light at the post-translational level

Photoreceptors perceive different wavelengths of light and transduce light signals downstream via a range of proteins. COP1, an E3 ubiquitin ligase, regulates light signaling by mediating the ubiquitination and subsequent proteasomal degradation of photoreceptors such as phytochromes and cryptochromes, as well as various development-related proteins including other light-responsive proteins. COP1 is itself regulated by direct interactions with several signaling molecules that modulate its activity. The control of photomorphogenesis by COP1 is also regulated by its localization to the cytoplasm in response to light. COP1 thus acts as a tightly regulated switch that determines whether development is skotomorphogenic or photomorphogenic. In this review, we discuss the effects of COP1 on the abundance and activity of various development-related proteins, including photoreceptors, and summarize the regulatory mechanisms that influence COP1 activity and stability in plants.

Unraveling multifaceted contributions of small regulatory RNAs to photomorphogenic development in Arabidopsis

Background

Post-transcriptional control of gene expression mediated by small regulatory RNAs (sRNAs) is vital for growth and development of diverse organisms. The biogenesis of sRNAs is regulated by both positive and negative regulators known to regulate photomorphogenic development. Two microRNAs (miRNAs), miR157 and miR319, also regulate photomorphogenesis. However, genome-wide profiling of sRNAs and their regulation of target genes during photomorphogenesis has been missing. We provide a comprehensive view of sRNA-controlled gene expression in this developmental process.

Results

By profiling sRNAs and the 5′ ends of degraded mRNAs during the first 24 h of photomorphogenic development in Arabidopsis, we identified 335 sRNA-mediated mRNA cleavage events in de-etiolating seedlings. These cleavage events are primarily resulted from actions of highly expressed miRNAs and irrelevant to the abundance of target mRNAs. In the light, the expression of the slicer protein gene ARGONAUTE1 in the miRNA functioning pathway could be fine-tuned by miRNA168a/b. We also found that miR396a/b positively regulates de-etiolation by suppressing GROWTH REGULATING FACTORs. Our results suggest that the miRNAs are required to tune down the target mRNAs and regulate photomorphogenesis.

Conclusion

sRNAs may have a broad impact on gene expression regulation for optimized photomorphogenic development. With both positive and negative regulators under the control of sRNAs, young Arabidopsis seedlings can have a timely but not exaggerated developmental adaptation to light.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3937-6) contains supplementary material, which is available to authorized users.

Metabolomics and Integrative Omics for the Development of Thai Traditional Medicine

In recent years, interest in studies of traditional medicine in Asian and African countries has gradually increased due to its potential to complement modern medicine. In this review, we provide an overview of Thai traditional medicine (TTM) current development, and ongoing research activities of TTM related to metabolomics. This review will also focus on three important elements of systems biology analysis of TTM including analytical techniques, statistical approaches and bioinformatics tools for handling and analyzing untargeted metabolomics data. The main objective of this data analysis is to gain a comprehensive understanding of the system wide effects that TTM has on individuals. Furthermore, potential applications of metabolomics and systems medicine in TTM will also be discussed.

Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome during Photomorphogenesis

The switch from skotomorphogenesis to photomorphogenesis is a key developmental transition in the life of seed plants. While much of the underpinning proteome remodeling is driven by light-induced changes in gene expression, the proteolytic removal of specific proteins by the ubiquitin-26S proteasome system is also likely paramount. Through mass spectrometric analysis of ubiquitylated proteins affinity-purified from etiolated Arabidopsis seedlings before and after red-light irradiation, we identified a number of influential proteins whose ubiquitylation status is modified during this switch. We observed a substantial enrichment for proteins involved in auxin, abscisic acid, ethylene, and brassinosteroid signaling, peroxisome function, disease resistance, protein phosphorylation and light perception, including the phytochrome (Phy) A and phototropin photoreceptors. Soon after red-light treatment, PhyA becomes the dominant ubiquitylated species, with ubiquitin attachment sites mapped to six lysines. A PhyA mutant protected from ubiquitin addition at these sites is substantially more stable in planta upon photoconversion to Pfr and is hyperactive in driving photomorphogenesis. However, light still stimulates ubiquitylation and degradation of this mutant, implying that other attachment sites and/or proteolytic pathways exist. Collectively, we expand the catalog of ubiquitylation targets in Arabidopsis and show that this post-translational modification is central to the rewiring of plants for photoautotrophic growth.

Seed-specific transcription factor HSFA9 links late embryogenesis and early photomorphogenesis

HSFA9 is a seed-specific transcription factor that in sunflower (Helianthus annuus) is involved in desiccation tolerance and longevity. Here we show that the constitutive overexpression of HSFA9 in tobacco (Nicotiana tabacum) seedlings attenuated hypocotyl growth under darkness and accelerated the initial photosynthetic development. Plants overexpressing HSFA9 increased accumulation of carotenoids, chlorophyllide, and chlorophyll, and displayed earlier unfolding of the cotyledons. HSFA9 enhanced phytochrome-dependent light responses, as shown by an intensified hypocotyl length reduction after treatments with continuous far-red or red light. This observation indicated the involvement of at least two phytochromes: PHYA and PHYB. Reduced hypocotyl length under darkness did not depend on phytochrome photo-activation; this was inferred from the lack of effect observed using far-red light pulses applied before the dark treatment. HSFA9 increased the expression of genes that activate photomorphogenesis, including PHYA, PHYB, and HY5. HSFA9 might directly upregulate PHYA and indirectly affect PHYB transcription, as suggested by transient expression assays. Converse effects on gene expression, greening, and cotyledon unfolding were observed using a dominant-negative form of HSFA9, which was overexpressed under a seed-specific promoter. This work uncovers a novel transcriptional link, through HSFA9, between seed maturation and early photomorphogenesis. In all, our data suggest that HSFA9 enhances photomorphogenesis via early transcriptional effects that start in seeds under darkness.

Cryptochromes Orchestrate Transcription Regulation of Diverse Blue Light Responses in Plants

Blue light affects many aspects of plant growth and development throughout the plant lifecycle. Plant cryptochromes (CRYs) are UV-A/blue light photoreceptors that play pivotal roles in regulating blue light-mediated physiological responses via the regulated expression of more than one thousand genes. Photoactivated CRYs regulate transcription via two distinct mechanisms: indirect promotion of the activity of transcription factors by inactivation of the COP1/SPA E3 ligase complex or direct activation or inactivation of at least two sets of basic helix-loop-helix transcription factor families by physical interaction. Hence, CRYs govern intricate mechanisms that modulate activities of transcription factors to regulate multiple aspects of blue light-responsive photomorphogenesis. Here, we review recent progress in dissecting the pathways of CRY signaling and discuss accumulating evidence that shows how CRYs regulate broad physiological responses to blue light.

Early changes of gene activity in developing seedlings of Arabidopsis hybrids relative to parents may contribute to hybrid vigour

Hybrid vigour (heterosis) has been used for decades in crop industries, especially in the production of maize and rice. Hybrid varieties usually exceed their parents in plant biomass and seed yield. But the molecular basis of hybrid vigour is not fully understood. In this project, we studied heterosis at early stages of seedling development in Arabidopsis hybrids derived from crossing Ler and C24 accessions. We found that early heterosis is associated with non-additive gene expression that resulted from earlier changes in gene expression in the hybrids relative to the parents. The non-additively expressed genes are involved in metabolic pathways, including photosynthesis, critical for plant growth. The early increased expression levels of genes involved in energy production in hybrids is associated with heterosis in the young seedlings that could be essential for biomass heterosis at later developmental stages of the plant.

NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana

Recent reports suggest that NF-Y transcription factors are positive regulators of skotomorphogenesis in Arabidopsis thaliana. Three NF-YC genes (NF-YC3, NF-YC4, and NF-YC9) are known to have overlapping functions in photoperiod dependent flowering and previous studies demonstrated that they interact with basic leucine zipper (bZIP) transcription factors. This included ELONGATED HYPOCOTYL 5 (HY5), which has well-demonstrated roles in photomorphogenesis. Similar to hy5 mutants, we report that nf-yc3 nf-yc4 nf-yc9 triple mutants failed to inhibit hypocotyl elongation in all tested light wavelengths. Surprisingly, nf-yc3 nf-yc4 nf-yc9 hy5 mutants had synergistic defects in light perception, suggesting that NF-Ys represent a parallel light signaling pathway. As with other photomorphogenic transcription factors, nf-yc3 nf-yc4 nf-yc9 triple mutants also partially suppressed the short hypocotyl and dwarf rosette phenotypes of CONSTITUTIVE PHOTOMORPHOGENIC 1 (cop1) mutants. Thus, our data strongly suggest that NF-Y transcription factors have important roles as positive regulators of photomorphogenesis, and in conjunction with other recent reports, implies that the NF-Y are multifaceted regulators of early seedling development.

Light perception is critically important for the fitness of plants in both natural and agricultural settings. Plants not only use light for photosynthesis, but also as a cue for proper development. As a seedling emerges from soil it must determine the light environment and adopt an appropriate growth habit. When blue and red wavelengths are the dominant sources of light, plants will undergo photomorphogenesis. Photomorphogenesis describes a number of developmental responses initiated by light in a seedling, and includes shortened stems and establishing the ability to photosynthesize. The genes regulating photomorphogenesis have been studied extensively, but a complete picture remains elusive. Here we describe the finding that NUCLEAR FACTOR-Y (NF-Y) genes are positive regulators of photomorphogenesis—i.e., in plants where NF-Y genes are mutated, they display some characteristics of dark grown plants, even though they are in the light. Our data suggests that the roles of NF-Y genes in light perception do not fit in easily with those of other described pathways. Thus, studying these genes promises to help develop a more complete picture of how light drives plant development.

Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L

Light is a major environmental factor that affects metabolic pathways and stimulates the production of secondary metabolites in potato. However, adaptive changes in potato metabolic pathways and physiological functions triggered by light are partly explained by gene expression changes. Regulation of secondary metabolic pathways in potato has been extensively studied at transcriptional level, but little is known about the mechanisms of post-transcriptional regulation by miRNAs. To identify light-responsive miRNAs/mRNAs and construct putative metabolism pathways regulated by the miRNA-mRNA pairs, an integrated omics (sRNAome and transcriptome) analysis was performed to potato under light stimulus. A total of 31 and 48 miRNAs were identified to be differentially expressed in the leaves and tubers, respectively. Among the DEGs, 1353 genes in the leaves and 1841 genes in the tubers were upregulated, while 1595 genes in the leaves and 897 genes in the tubers were downregulated by light. Mapman enrichment analyses showed that genes related to MVA pathway, alkaloids-like, phenylpropanoids, flavonoids, and carotenoids metabolism were significantly upregulated, while genes associated with major CHO metabolism were repressed in the leaves and tubers. Integrated miRNA and mRNA profiles revealed that light-responsive miRNAs are important regulators in alkaloids metabolism, UMP salvage, lipid biosynthesis, and cellulose catabolism. Moreover, several miRNAs may participate in glycoalkaloids metabolism via JA signaling pathway, UDP-glucose biosynthesis and hydroxylation reaction. This study provides a global view of miRNA and mRNA expression profiles in potato response to light, our results suggest that miRNAs might play important roles in secondary metabolic pathways, especially in glycoalkaloid biosynthesis. The findings will enlighten us on the genetic regulation of secondary metabolite pathways and pave the way for future application of genetically engineered potato.

Arabidopsis FHY3 and FAR1 Regulate Light-Induced myo-Inositol Biosynthesis and Oxidative Stress Responses by Transcriptional Activation of MIPS1

myo-Inositol-1-phosphate synthase (MIPS) catalyzes the limiting step of inositol biosynthesis and has crucial roles in plant growth and development. In response to stress, the transcription of MIPS1 is induced and the biosynthesis of inositol or inositol derivatives is promoted by unknown mechanisms. Here, we found that the light signaling protein FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1) regulate light-induced inositol biosynthesis and oxidative stress responses by activating the transcription of MIPS1. Disruption of FHY3 and FAR1 caused light-induced cell death after dark-light transition, precocious leaf senescence, and increased sensitivity to oxidative stress. Reduction of salicylic acid (SA) accumulation by overexpression of SALICYLIC ACID 3-HYDROXYLASE largely suppressed the cell death phenotype of fhy3 far1 mutant plants, suggesting that FHY3- and FAR1-mediated cell death is dependent on SA. Furthermore, comparative analysis of chromatin immunoprecipitation sequencing and microarray results revealed that FHY3 and FAR1 directly target both MIPS1 and MIPS2. The fhy3 far1 mutant plants showed severely decreased MIPS1/2 transcript levels and reduced inositol levels. Conversely, constitutive expression of MIPS1 partially rescued the inositol contents, caused reduced transcript levels of SA-biosynthesis genes, and prevented oxidative stress in fhy3 far1. Taken together, our results indicate that the light signaling proteins FHY3 and FAR1 directly bind the promoter of MIPS1 to activate its expression and thereby promote inositol biosynthesis to prevent light-induced oxidative stress and SA-dependent cell death.

Signaling mechanisms of plant cryptochromes in Arabidopsis thaliana

Cryptochromes (CRY) are flavoproteins that direct a diverse array of developmental processes in response to blue light in plants. Conformational changes in CRY are induced by the absorption of photons and result in the propagation of light signals to downstream components. In Arabidopsis, CRY1 and CRY2 serve both distinct and partially overlapping functions in regulating photomorphogenic responses and photoperiodic flowering. For example, both CRY1 and CRY2 regulate the abundance of transcription factors by directly reversing the activity of E3 ubiquitin ligase on CONSTITUTIVE PHOTOMORPHOGENIC 1 and SUPPRESSOR OF PHYA-105 1 complexes in a blue light-dependent manner. CRY2 also specifically governs a photoperiodic flowering mechanism by directly interacting with a transcription factor called CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX. Recently, structure/function analysis of CRY1 revealed that the CONSTITUTIVE PHOTOMORPHOGENIC 1 independent pathway is also involved in CRY1-mediated inhibition of hypocotyl elongation. CRY1 and CRY2 thus not only share a common pathway but also relay light signals through distinct pathways, which may lead to altered developmental programs in plants.

Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination

BACKGROUND

Light plays an important role in plant growth and development. In this study, the impact of light on physiology of 20-d-old Arabidopsis leaves was examined through transcriptomic, proteomic and metabolomic analysis. Since the energy-generating electron transport chains in chloroplasts and mitochondria are encoded by both nuclear and organellar genomes, sequencing total RNA after removal of ribosomal RNAs provides essential information on transcription of organellar genomes. The changes in the levels of ADP, ATP, NADP(+), NADPH and 41 metabolites upon illumination were also quantified.

RESULTS

Upon illumination, while the transcription of the genes encoded by the plastid genome did not change significantly, the transcription of nuclear genes encoding different functional complexes in the photosystem are differentially regulated whereas members of the same complex are co-regulated with each other. The abundance of mRNAs and proteins encoded by all three genomes are, however, not always positively correlated. One such example is the negative correlation between mRNA and protein abundances of the photosystem components, which reflects the importance of post-transcriptional regulation in plant physiology.

CONCLUSION

This study provides systems-wide datasets which allow plant researchers to examine the changes in leaf transcriptomes, proteomes and key metabolites upon illumination and to determine whether there are any correlations between changes in transcript and protein abundances of a particular gene or pathway upon illumination. The integration of data of the organelles and the photosystems, Calvin-Benson cycle, carbohydrate metabolism, glycolysis, the tricarboxylic acid cycle and respiratory chain, thereby provides a more complete picture to the changes in plant physiology upon illumination than has been attained to date.

The cold responsive mechanism of the paper mulberry: decreased photosynthesis capacity and increased starch accumulation

Background

Most studies on the paper mulberry are mainly focused on the medicated and pharmacology, fiber quality, leaves feed development, little is known about its mechanism of adaptability to abiotic stress. Physiological measurement, transcriptomics and proteomic analysis were employed to understand its response to cold stress in this study.

Methods

The second to fourth fully expanded leaves from up to down were harvested at different stress time points forthe transmission electron microscope (TEM) observation. Physiological characteristics measurement included the relative electrolyte leakage (REL), SOD activity assay, soluble sugar content, and Chlorophyll fluorescence parameter measurement. For screening of differentially expressed genes, the expression level of every transcript in each sample was calculated by quantifying the number of Illumina reads. To identify the differentially expressed protein, leaves of plants under 0, 6, 12, 24, 48 and 72 h cold stress wereharvested for proteomic analysis. Finally, real time PCR was used to verify the DEG results of the RNA-seq and the proteomics data.

Results

Results showed that at the beginning of cold stress, respiratory metabolism was decreased and the transportation and hydrolysis of photosynthetic products was inhibited, leading to an accumulation of starch in the chloroplasts. Total of 5800 unigenes and 38 proteins were affected, including the repressed expression of photosynthesis and the enhanced expression in signal transduction, stress defense pathway as well as secondary metabolism. Although the transcriptional level of a large number of genes has been restored after 12 h, sustained cold stress brought more serious injury to the leaf cells, including the sharp rise of the relative electrolyte leakage, the declined Fv/Fm value, swelled chloroplast and the disintegrated membrane system.

Conclusion

The starch accumulation and the photoinhibition might be the main adaptive mechanism of the paper mulberry responded to cold stress. Most of important, enhancing the transport and hydrolysis of photosynthetic products could be the potential targets for improving the cold tolerance of the paper mulberry.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2047-6) contains supplementary material, which is available to authorized users.

Seeing the world differently: variability in the photosensory mechanisms of two model fungi

Light plays an important role for most organisms on this planet, serving either as a source of energy or information for the adaptation of biological processes to specific times of day. The fungal kingdom is estimated to contain well over a million species, possibly 10-fold more, and it is estimated that a majority of the fungi respond to light, eliciting changes in several physiological characteristics including pathogenesis, development and secondary metabolism. Two model organisms for photobiological studies have taken centre-stage over the last few decades--Neurospora crassa and Aspergillus nidulans. In this review, we will first discuss our understanding of the light response in N. crassa, about which the most is known, and will then juxtapose N. crassa with A. nidulans, which, as will be described below, provides an excellent template for understanding photosensory cross-talk. Finally, we will end with a commentary on the variability of the light response among other relevant fungi, and how our molecular understanding in the aforementioned model organisms still provides a strong base for dissecting light responses in such species.

Let there be light: regulation of gene expression in plants

Gene expression regulation relies on a variety of molecular mechanisms affecting different steps of a messenger RNA (mRNA) life: transcription, processing, splicing, alternative splicing, transport, translation, storage and decay. Light induces massive reprogramming of gene expression in plants. Differences in alternative splicing patterns in response to environmental stimuli suggest that alternative splicing plays an important role in plant adaptation to changing life conditions. In a recent publication, our laboratories showed that light regulates alternative splicing of a subset of Arabidopsis genes encoding proteins involved in RNA processing by chloroplast retrograde signals. The light effect on alternative splicing is also observed in roots when the communication with the photosynthetic tissues is not interrupted, suggesting that a signaling molecule travels through the plant. These results point at alternative splicing regulation by retrograde signals as an important mechanism for plant adaptation to their environment.

Transcriptome Analysis Reveals that Red and Blue Light Regulate Growth and Phytohormone Metabolism in Norway Spruce [Picea abies (L.) Karst]

The mechanisms by which different light spectra regulate plant shoot elongation vary, and phytohormones respond differently to such spectrum-associated regulatory effects. Light supplementation can effectively control seedling growth in Norway spruce. However, knowledge of the effective spectrum for promoting growth and phytohormone metabolism in this species is lacking. In this study, 3-year-old Norway spruce clones were illuminated for 12 h after sunset under blue or red light-emitting diode (LED) light for 90 d, and stem increments and other growth traits were determined. Endogenous hormone levels and transcriptome differences in the current needles were assessed to identify genes related to the red and blue light regulatory responses. The results showed that the stem increment and gibberellin (GA) levels of the seedlings illuminated by red light were 8.6% and 29.0% higher, respectively, than those of the seedlings illuminated by blue light. The indoleacetic acid (IAA) level of the seedlings illuminated by red light was 54.6% lower than that of the seedlings illuminated by blue light, and there were no significant differences in abscisic acid (ABA) or zeatin riboside [ZR] between the two groups of seedlings. The transcriptome results revealed 58,736,166 and 60,555,192 clean reads for the blue-light- and red-light-illuminated samples, respectively. Illumina sequencing revealed 21,923 unigenes, and 2744 (approximately 93.8%) out of 2926 differentially expressed genes (DEGs) were found to be upregulated under blue light. The main KEGG classifications of the DEGs were metabolic pathway (29%), biosynthesis of secondary metabolites (20.49%) and hormone signal transduction (8.39%). With regard to hormone signal transduction, AUXIN-RESISTANT1 (AUX1), AUX/IAA genes, auxin-inducible genes, and early auxin-responsive genes [(auxin response factor (ARF) and small auxin-up RNA (SAUR)] were all upregulated under blue light compared with red light, which might have yielded the higher IAA level. DELLA and phytochrome-interacting factor 3 (PIF3), involved in negative GA signaling, were also upregulated under blue light, which may be related to the lower GA level. Light quality also affects endogenous hormones by influencing secondary metabolism. Blue light promoted phenylpropanoid biosynthesis, phenylalanine metabolism, flavonoid biosynthesis and flavone and flavonol biosynthesis, accompanied by upregulation of most of the genes in their pathways. In conclusion, red light may promote stem growth by regulating biosynthesis of GAs, and blue light may promote flavonoid, lignin, phenylpropanoid and some hormones (such as jasmonic acid) which were related to plant defense in Norway spruce, which might reduce the primary metabolites available for plant growth.

Molecular Cloning and Functional Analysis of UV RESISTANCE LOCUS 8 (PeUVR8) from Populus euphratica

Ultraviolet-B (UV-B; 280–315 nm) light, which is an integral part of the solar radiation reaching the surface of the Earth, induces a broad range of physiological responses in plants. The UV RESISTANCE LOCUS 8 (UVR8) protein is the first and only light photoreceptor characterized to date that is specific for UV-B light and it regulates various aspects of plant growth and development in response to UV-B light. Despite its involvement in the control of important plant traits, most studies on UV-B photoreceptors have focused on Arabidopsis and no data on UVR8 function are available for forest trees. In this study, we isolated a homologue of the UV receptor UVR8 of Arabidopsis, PeUVR8, from Populus euphratica (Euphrates poplar) and analyzed its structure and function in detail. The deduced PeUVR8 amino acid sequence contained nine well-conserved regulator of chromosome condensation 1 (RCC1) repeats and the region 27 amino acids from the C terminus (C27) that interact with COP1 (CONSTITUTIVELY PHOTOMORPHOGENIC1). Secondary and tertiary structure analysis showed that PeUVR8 shares high similarity with the AtUVR8 protein from Arabidopsis thaliana. Using heterologous expression in Arabidopsis, we showed that PeUVR8 overexpression rescued the uvr8 mutant phenotype. In addition, PeUVR8 overexpression in wild-type background seedlings grown under UV-B light inhibited hypocotyl elongation and enhanced anthocyanin accumulation. Furthermore, we examined the interaction between PeUVR8 and AtCOP1 using a bimolecular fluorescence complementation (BiFC) assay. Our data provide evidence that PeUVR8 plays important roles in the control of photomorphogenesis in planta.

Epidermal UV-A absorbance and whole-leaf flavonoid composition in pea respond more to solar blue light than to solar UV radiation

Plants synthesize phenolic compounds in response to certain environmental signals or stresses. One large group of phenolics, flavonoids, is considered particularly responsive to ultraviolet (UV) radiation. However, here we demonstrate that solar blue light stimulates flavonoid biosynthesis in the absence of UV-A and UV-B radiation. We grew pea plants (Pisum sativum cv. Meteor) outdoors, in Finland during the summer, under five types of filters differing in their spectral transmittance. These filters were used to (1) attenuate UV-B; (2) attenuate UV-B and UV-A < 370 nm; (3) attenuate UV-B and UV-A; (4) attenuate UV-B, UV-A and blue light; and (5) as a control not attenuating these wavebands. Attenuation of blue light significantly reduced the flavonoid content in leaf adaxial epidermis and reduced the whole-leaf concentrations of quercetin derivatives relative to kaempferol derivatives. In contrast, UV-B responses were not significant. These results show that pea plants regulate epidermal UV-A absorbance and accumulation of individual flavonoids by perceiving complex radiation signals that extend into the visible region of the solar spectrum. Furthermore, solar blue light instead of solar UV-B radiation can be the main regulator of phenolic compound accumulation in plants that germinate and develop outdoors.

GIP1 protein is a novel cofactor that regulates DNA-binding affinity of redox-regulated members of bZIP transcription factors involved in the early stages of Arabidopsis development

In response to environmental light signals, gene expression adjustments play an important role in regulation of photomorphogenesis. LHCB2.4 is among the genes responsive to light signals, and its expression is regulated by redox-regulated members of G-group bZIP transcription factors. The biochemical interrelations of GBF1-interacting protein 1 (GIP1) and the G-group bZIP transcription factors have been investigated. GIP1, previously shown to enhance DNA-binding activities of maize GBF1 and Arabidopsis GBF3, is a plant specific protein that reduces DNA-binding activity of AtbZIP16, AtbZIP68, and AtGBF1 under non-reducing conditions through direct physical interaction shown by the yeast two-hybrid and pull-down assays. Fluorescence microscopy studies using cyan fluorescent protein (CFP)-fusion protein indicate that GIP1 is exclusively localized in the nucleus. Under non- reducing conditions, GIP1 exhibits predominantly high molecular weight forms, whereas it predominates in low molecular weight monomers under reducing conditions. While reduced GIP1 induced formation of DNA-protein complexes of G-group bZIPs, oxidized GIP1 decreased the amount of those complexes and instead induced its chaperone function suggesting functional switching from redox to chaperone activity. Finally analysis of transgenic plants overexpressing GIP1 revealed that GIP1 is a negative co-regulator in red and blue light mediated hypocotyl elongation. By regulating the repression effect by bZIP16 and the activation effect by bZIP68 and GBF1 on LHCB2.4 expression, GIP1 functions to promote hypocotyl elongation during the early stages of Arabidopsis seedling development.

Cell Wall Metabolism in Response to Abiotic Stress

This review focuses on the responses of the plant cell wall to several abiotic stresses including drought, flooding, heat, cold, salt, heavy metals, light, and air pollutants. The effects of stress on cell wall metabolism are discussed at the physiological (morphogenic), transcriptomic, proteomic and biochemical levels. The analysis of a large set of data shows that the plant response is highly complex. The overall effects of most abiotic stress are often dependent on the plant species, the genotype, the age of the plant, the timing of the stress application, and the intensity of this stress. This shows the difficulty of identifying a common pattern of stress response in cell wall architecture that could enable adaptation and/or resistance to abiotic stress. However, in most cases, two main mechanisms can be highlighted: (i) an increased level in xyloglucan endotransglucosylase/hydrolase (XTH) and expansin proteins, associated with an increase in the degree of rhamnogalacturonan I branching that maintains cell wall plasticity and (ii) an increased cell wall thickening by reinforcement of the secondary wall with hemicellulose and lignin deposition. Taken together, these results show the need to undertake large-scale analyses, using multidisciplinary approaches, to unravel the consequences of stress on the cell wall. This will help identify the key components that could be targeted to improve biomass production under stress conditions.

Dealing with light: the widespread and multitasking cryptochrome/photolyase family in photosynthetic organisms

Light is essential for the life of photosynthetic organisms as it is a source of energy and information from the environment. Light excess or limitation can be a cause of stress however. Photosynthetic organisms exhibit sophisticated mechanisms to adjust their physiology and growth to the local environmental light conditions. The cryptochrome/photolyase family (CPF) is composed of flavoproteins with similar structures that display a variety of light-dependent functions. This family encompasses photolyases, blue-light activated enzymes that repair ultraviolet-light induced DNA damage, and cryptochromes, known for their photoreceptor functions in terrestrial plants. For this review, we searched extensively for CPFs in the available genome databases to trace the distribution and evolution of this protein family in photosynthetic organisms. By merging molecular data with current knowledge from the functional characterization of CPFs from terrestrial and aquatic organisms, we discuss their roles in (i) photoperception, (ii) biological rhythm regulation and (iii) light-induced stress responses. We also explore their possible implication in light-related physiological acclimation and their distribution in phototrophs living in different environments. The outcome of this structure-function analysis reconstructs the complex scenarios in which CPFs have evolved, as highlighted by the novel functions and biochemical properties of the most recently described family members in algae.

Cloning of the cryptochrome-encoding PeCRY1 gene from Populus euphratica and functional analysis in Arabidopsis

Cryptochromes are photolyase-like blue/UV-A light receptors that evolved from photolyases. In plants, cryptochromes regulate various aspects of plant growth and development. Despite of their involvement in the control of important plant traits, however, most studies on cryptochromes have focused on lower plants and herbaceous crops, and no data on cryptochrome function are available for forest trees. In this study, we isolated a cryptochrome gene, PeCRY1, from Euphrates poplar (Populus euphratica), and analyzed its structure and function in detail. The deduced PeCRY1 amino acid sequence contained a conserved N-terminal photolyase-homologous region (PHR) domain as well as a C-terminal DQXVP-acidic-STAES (DAS) domain. Secondary and tertiary structure analysis showed that PeCRY1 shares high similarity with AtCRY1 from Arabidopsis thaliana. PeCRY1 expression was upregulated at the mRNA level by light. Using heterologous expression in Arabidopsis, we showed that PeCRY1 overexpression rescued the cry1 mutant phenotype. In addition, PeCRY1 overexpression inhibited hypocotyl elongation, promoted root growth, and enhanced anthocyanin accumulation in wild-type background seedlings grown under blue light. Furthermore, we examined the interaction between PeCRY1 and AtCOP1 using a bimolecular fluorescence complementation (BiFc) assay. Our data provide evidence for the involvement of PeCRY1 in the control of photomorphogenesis in poplar.

Shedding light on ethylene metabolism in higher plants

Ethylene metabolism in higher plants is regulated by a wide array of endogenous and environmental factors. During most physiological processes, ethylene levels are mainly determined by a strict control of the rate-limiting biosynthetic steps responsible for the production of 1-aminocyclopropane-1-carboxylic acid (ACC) and its subsequent conversion to ethylene. Responsible for these reactions, the key enzymes ACC synthase and ACC oxidase are encoded by multigene families formed by members that can be differentially regulated at the transcription and post-translational levels by specific developmental and environmental signals. Among the wide variety of environmental cues controlling plant ethylene production, light quality, duration, and intensity have consistently been demonstrated to influence the metabolism of this plant hormone in diverse plant tissues, organs, and species. Although still not completely elucidated, the mechanisms underlying the interaction between light signal transduction and ethylene evolution appears to involve a complex network that includes central transcription factors connecting multiple signaling pathways, which can be reciprocally modulated by ethylene itself, other phytohormones, and specific light wavelengths. Accumulating evidence has indicated particular photoreceptors as essential mediators in light-induced signaling cascades affecting ethylene levels. Therefore, this review specifically focuses on discussing the current knowledge of the potential molecular mechanisms implicated in the light-induced responses affecting ethylene metabolism during the regulation of developmental and metabolic plant responses. Besides presenting the state of the art in this research field, some overlooked mechanisms and future directions to elucidate the exact nature of the light-ethylene interplay in higher plants will also be compiled and discussed.

Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana

Our understanding of gene regulation in plants is constrained by our limited knowledge of plant cis-regulatory DNA and its dynamics. We mapped DNase I hypersensitive sites (DHSs) in A. thaliana seedlings and used genomic footprinting to delineate ∼ 700,000 sites of in vivo transcription factor (TF) occupancy at nucleotide resolution. We show that variation associated with 72 diverse quantitative phenotypes localizes within DHSs. TF footprints encode an extensive cis-regulatory lexicon subject to recent evolutionary pressures, and widespread TF binding within exons may have shaped codon usage patterns. The architecture of A. thaliana TF regulatory networks is strikingly similar to that of animals in spite of diverged regulatory repertoires. We analyzed regulatory landscape dynamics during heat shock and photomorphogenesis, disclosing thousands of environmentally sensitive elements and enabling mapping of key TF regulatory circuits underlying these fundamental responses. Our results provide an extensive resource for the study of A. thaliana gene regulation and functional biology.

The impact of chromatin dynamics on plant light responses and circadian clock function

Research on the functional properties of nucleosome structure and composition dynamics has revealed that chromatin-level regulation is an essential component of light signalling and clock function in plants, two processes that rely extensively on transcriptional controls. In particular, several types of histone post-translational modifications and chromatin-bound factors act sequentially or in combination to establish transcriptional patterns and to fine-tune the transcript abundance of a large repertoire of light-responsive genes and clock components. Cytogenetic approaches have also identified light-induced higher-order chromatin changes that dynamically organize the condensation of chromosomal domains into sub-nuclear foci containing silenced repeat elements. In this review, we report recently identified molecular actors that establish chromatin state dynamics in response to light signals such as photoperiod, intensity, and spectral quality. We also highlight the chromatin-dependent mechanisms that contribute to the 24-h circadian gene expression and its impact on plant physiology and development. The commonalities and contrasts of light- and clock-associated chromatin-based mechanisms are discussed, with particular emphasis on their impact on the selective regulation and rapid modulation of responsive genes.

DNA Microarray Analysis of Plastid Gene Expression in anArabidopsisMutant Deficient in a Plastid Transcription Factor Sigma, SIG2

The plastid genome of higher plants contains more than one hundred genes for photosynthesis, gene expression, and other processes. Plastid transcription is done by two types of RNA polymerase, PEP and NEP. PEP is a eubacteria-type RNA polymerase that is essential for chloroplast development. In Arabidopsis thaliana, six sigma factors (SIG1-6) are encoded by the nuclear genome, and postulated to determine the transcription specificity of PEP. In this study, we constructed a DNA microarray for all of the plastid protein-coding genes, and analyzed the effects of the sig2 lesion on the global plastid gene expression. Of the 79 plastid protein genes, it was found that only the psaJ transcript was decreased in the mutant, whereas transcripts of 47 genes were rather increased. Since many of the up-regulated genes are under the control of NEP, it was suggested that the NEP activity was increased in the sig2-1 mutant.

The Arabidopsis thaliana hypocotyl, a model to identify and study control mechanisms of cellular expansion

Developmental biology studies in general benefit from model organisms that are well characterized. Arabidopsis thaliana fulfills this criterion and represents one of the best experimental systems to study developmental processes in higher plants. Light is a crucial factor that drives photosynthesis, but that also regulates plant morphogenesis. As the hypocotyl is completely embryonic of origin, its growth occurs solely by expansion of the cells and this process is strongly dependent on the light conditions. In this review, we provide evidence that the hypocotyl serves as ideal model object to study cell expansion mechanisms and its regulation. We focus on the regulation of hypocotyl development by light and highlight the key modulating proteins in this signaling cascade. Downstream of light-signaling, cellular expansion is greatly dependent on specific cell wall depositions, which is related to cortical microtubular (re)arrangements and on composition and/or extensibility of the cell wall. We discuss possible further experimental approaches to broaden our knowledge on hypocotyl development, which will give an outlook on the probable evolution of the field.

Cryptochrome 1 regulates growth and development in Brassica through alteration in the expression of genes involved in light, phytohormone and stress signalling

The blue light photoreceptors cryptochromes are ubiquitous in higher plants and are vital for regulating plant growth and development. In spite of being involved in controlling agronomically important traits like plant height and flowering time, cryptochromes have not been extensively characterized from agriculturally important crops. Here we show that overexpression of CRY1 from Brassica napus (BnCRY1), an oilseed crop, results in short-statured Brassica transgenics, likely to be less prone to wind and water lodging. The overexpression of BnCRY1 accentuates the inhibition of cell elongation in hypocotyls of transgenic seedlings. The analysis of hypocotyl growth inhibition and anthocyanin accumulation responses in BnCRY1 overexpressors substantiates that regulation of seedling photomorphogenesis by cry1 is dependent on light intensity. This study highlights that the photoactivated cry1 acts through coordinated induction and suppression of specific downstream genes involved in phytohormone synthesis or signalling, and those involved in cell wall modification, during de-etiolation of Brassica seedlings. The microarray-based transcriptome profiling also suggests that the overexpression of BnCRY1 alters abiotic/biotic stress signalling pathways; the transgenic seedlings were apparently oversensitive to abscisic acid (ABA) and mannitol.

Comparative transcriptional profiling of three super-hybrid rice combinations

Utilization of heterosis has significantly increased rice yields. However, its mechanism remains unclear. In this study, comparative transcriptional profiles of three super-hybrid rice combinations, LY2163, LY2186 and LYP9, at the flowering and filling stages, were created using rice whole-genome oligonucleotide microarray. The LY2163, LY2186 and LYP9 hybrids yielded 1193, 1630 and 1046 differentially expressed genes (DGs), accounting for 3.2%, 4.4% and 2.8% of the total number of genes (36,926), respectively, after using the z-test (p < 0.01). Functional category analysis showed that the DGs in each hybrid combination were mainly classified into the carbohydrate metabolism and energy metabolism categories. Further analysis of the metabolic pathways showed that DGs were significantly enriched in the carbon fixation pathway (p < 0.01) for all three combinations. Over 80% of the DGs were located in rice quantitative trait loci (QTLs) of the Gramene database, of which more than 90% were located in the yield related QTLs in all three combinations, which suggested that there was a correlation between DGs and rice heterosis. Pathway Studio analysis showed the presence of DGs in the circadian regulatory network of all three hybrid combinations, which suggested that the circadian clock had a role in rice heterosis. Our results provide information that can help to elucidate the molecular mechanism underlying rice heterosis.