Signaling mechanisms of plant cryptochromes in Arabidopsis thaliana

Identification and Expression Characteristics of the Cryptochrome Gene Family in Chimonobambusa sichuanensis

Cryptochrome is an important class of blue-light receptors involved in various physiological activities such as photomorphogenesis and abiotic stress regulation in plants. In order to investigate the molecular mechanism of blue-light-induced color change in Chimonobambusa sichuanensis, we screened and cloned the gene encoding the blue-light receptor Cryptochrome. In order to investigate the molecular mechanism of blue-light-induced color change in Chimonobambusa sichuanensis, we screened and cloned the gene encoding the blue-light receptor Cryptochrome in Ch.sichuanensis, and analyzed the expression characteristics of the Cryptochrome gene in Ch.sichuanensis under different light intensities, light quality, and temperatures by qRT-PCR. Through homologous cloning, a total of four CsCRY genes were obtained in the Ch.sichuanensis genome, namely, CsCRY1a, CsCRY1b, CsCRY2, and CsCRY3. Structural domain analyses of the encoded proteins of the four genes revealed that all CsCRYs proteins had the typical photoreceptor structural domain, PRK (protein kinase C-related kinase). Phylogenetic tree analyses revealed that the four genes CsCRY1a, CsCRY1b, CsCRY2, and CsCRY3 could be categorized into three subfamilies, with CsCRY1a and CsCRY1b clustered in subfamily I, CsCRY2 classified in subfamily II, and CsCRY3 belonging to subfamily III. All CsCRYs proteins lacked signal peptides and the instability index was higher than 40, among which the isoelectric points of CsCRY1a, CsCRY1b, and CsCRY2 were around five. qRT-PCR analysis revealed that the expression of all four CsCRYs genes was up-regulated at 75 µmol·m-2·s-1 blue-light illumination for 4 h. In addition, under treatments of different light quality, the expression of CsCRY2 genes was significantly higher under blue light than under red light and a mixture of red light and blue light with a light intensity of 1:1; the expression of CsCRY1a and CsCSY1b was significantly higher in the mixed light of red and blue light than in the single light treatment, while under different temperature gradients, CsCRYs genes were highly expressed under low-temperature stress at -5 °C and 0 °C. This study provides a basis for further research on blue-light-induced color change in Ch.sichuanensis and expands the scope of Cryptochrome gene research.

Dissecting sequence-structure-function-diversity in plant cryptochromes

Ubiquitous to every stratum of life, cryptochromes regulate numerous light dependent functions in terrestrial plants. These include light-dependent transcription, circadian rhythm, inhibition of hypocotyl elongation, programmed cell death, promotion of floral initiation, mediation of gravitropic response, responding to biotic and abiotic stress etc. There have been quite a few seminal reviews including on plant cryptochromes, focusing mostly on the detailed functional aspects. This review primarily focuses on understanding the link connecting sequence-structure hierarchy behind the functional diversity in plant cryptochromes. With available sequence information and 3D structure data, we hereby explore the molecular origin of functional diversity in both the subtypes i.e., CRY1 and CRY2. First, we discuss the structural details and functional distinctiveness of all subtypes of plant cryptochromes. Next we draw a comparison not just between two cryptochromes but also other Cryptochrome/Photolyase Family (CPF) members e.g. CRY-DASH/CRY3 and CPD/6-4 photolyases of plant origin. Further, by constructing a phylogenetic profile from multiple sequence alignment we investigate how a crucial activity like DNA repair is restricted to some members of CPF and not all. It is a well-known fact that the function of a protein is heavily if not solely guided by the structure-sequence relationship. Therefore, the resultant hypothesis as drawn from this comparative and collective study could predict functions of many under-studied plant cryptochromes when compared with their well-studied counterparts like Arabidopsis cryptochromes. An extensive sequence-structure-function analysis complemented with evolutionary studies and bibliographic survey is useful towards understanding the immensely diverse CPF.

TaFAR9 and TaFAR10 synergistically regulate fertility conversion of photo-thermo-sensitive genic male sterility lines in wheat by modulating ROS homeostasis

Photo-thermo-sensitive genic male sterility (PTGMS), which exhibits varying fertility levels under different environmental conditions, is a crucial method for heterosis utilization in wheat. However, the mechanisms underlying fertility conversion remain unclear. In the study, three BS type PTGMS lines were analyzed to study fertility conversion characteristics. The results indicated that the fertility conversion occurred during meiosis and was accompanied by an increase in reactive oxygen species (ROS) under a sterile environment. TaFAR9 encoding a novel fatty acyl CoA reductase was identified using transcriptome sequencing. Expression analysis suggested that TaFAR9 was localized in the endoplasmic reticulum (ER), with high expression levels in anthers. Furthermore, the down-regulation of TaFAR9 expression displayed characteristics of male sterility, accompanied by the accumulation of ROS. Cytological analysis revealed abnormal development in the anther and pollen walls of TaFAR9-silenced lines. Additionally, TaFAR9 and TaFAR10 were confirmed to physically interact using molecular docking simulation, yeast two-hybrid, luciferase complementation, and bimolecular fluorescence complementation assays. The reduced expression of TaFAR10 also exhibited male sterility and ROS burst. Moreover, the co-silencing of TaFAR9 and TaFAR10 produced sterility phenotypes that were similar to those observed when silencing TaFAR9 or TaFAR10 individually. Transcriptome analysis suggested that the ROS burst in BSMV: TaFAR9/10 anthers can result in cellular metabolic disorders. These findings indicate that TaFAR9 and TaFAR10 may form heterodimers that synergistically regulate fertility conversion in PTGMS lines by modulating ROS metabolism. And this study offers a fresh insight into the regulatory processes involved in fertility conversion in PTGMS lines.

Application of Red and Blue LED Light on Cultivation and Postharvest of Tomatoes (Solanum lycopersicum L.)

Currently, light-emitting diode (LED) technology has produced a more energy-efficient and versatile technology as an artificial lighting system that can be applied in the agricultural sector. Artificial lighting technology has been proven to be effective in increasing the production of agricultural products, especially horticultural commodities. As one of the primary horticulture commodities, tomatoes are the most common crop produced in controlled environments with LED artificial lighting. The focus of this study is to describe the application of LED lights in tomato cultivation and postharvest. We provide an amalgamation of the recent research achievements on the impact of LED lighting on photosynthesis, vegetative growth, flowering, production, and postharvest of tomatoes. Red-blue (RB) lighting induces photosynthesis; increases the content of chlorophyll a, chlorophyll b, and carotenoids in tomato leaves; regulates vegetative growth in tomatoes; and increases the production of tomatoes. In postharvest tomatoes, blue LED lighting treatment can slowly change the color of the tomato skin to red, maintain hardness, and increase shelf life. Future research may be carried out on the effect of LED artificial lighting on tomatoes' phytochemical, antioxidant and other crucial nutritional content. Different LED wavelengths can be explored to enhance various bioactive compounds and health-promoting components.

Adaptation of STIM1 structure-function relationships for optogenetic control of calcium signaling

In cellular contexts, the oscillation of calcium ions (Ca2+) is intricately linked to various physiological processes, such as cell proliferation, metabolism, and survival. Stromal interaction molecule 1 (STIM1) proteins form a crucial regulatory component in the store-operated calcium entry process. The structural attributes of STIM1 are vital for its functionality, encompassing distinct domains situated in the endoplasmic reticulum lumen and the cytoplasm. The intraluminal domain enables the timely detection of diminishing Ca2+ concentrations, prompting structural modifications that activate the cytoplasmic domain. This activated cytoplasmic domain undergoes conformational alterations and engages with membrane components, opening a channel that facilitates the influx of Ca2+ from the extracellular environment. Given its multiple domains and interaction mechanisms, STIM1 plays a foundational role in cellular biology. This review focuses on the design of optogenetic tools inspired by the structure and function of STIM1. These tools offer a groundbreaking approach for studying and manipulating intracellular Ca2+ signaling with precise spatiotemporal control. We further explore the practical applications of these tools, spanning fundamental scientific research, clinical studies, and their potential for translational research.

A structural decryption of cryptochromes

Cryptochromes (CRYs), which are signaling proteins related to DNA photolyases, play pivotal roles in sensory responses throughout biology, including growth and development, metabolic regulation, circadian rhythm entrainment and geomagnetic field sensing. This review explores the evolutionary relationships and functional diversity of cryptochromes from the perspective of their molecular structures. In general, CRY biological activities derive from their core structural architecture, which is based on a Photolyase Homology Region (PHR) and a more variable and functionally specific Cryptochrome C-terminal Extension (CCE). The α/β and α-helical domains within the PHR bind FAD, modulate redox reactive residues, accommodate antenna cofactors, recognize small molecules and provide conformationally responsive interaction surfaces for a range of partners. CCEs add structural complexity and divergence, and in doing so, influence photoreceptor reactivity and tailor function. Primary and secondary pockets within the PHR bind myriad moieties and collaborate with the CCEs to tune recognition properties and propagate chemical changes to downstream partners. For some CRYs, changes in homo and hetero-oligomerization couple to light-induced conformational changes, for others, changes in posttranslational modifications couple to cascades of protein interactions with partners and effectors. The structural exploration of cryptochromes underscores how a broad family of signaling proteins with close relationship to light-dependent enzymes achieves a wide range of activities through conservation of key structural and chemical properties upon which function-specific features are elaborated.

The wavelength dependence of oxygen-evolving complex inactivation in Zosteramarina

Zostera marina, a critical keystone marine angiosperm species in coastal seagrass meadows, possesses a photosensitive oxygen evolving complex (OEC). In harsh environments, the photoinactivation of the Z. marina OEC may lead to population declines. However, the factors underlying this photosensitivity remain unclear. Therefore, this study was undertaken to elucidate the elements contributing to Z. marina OEC photosensitivity. Our results demonstrated a gradual decrease in photosystem II performance towards shorter wavelengths, especially blue light and ultraviolet radiation. This phenomenon was characterized by a reduction in Fv/Fm and the rate of O2 evolution, as well as increased fluorescence at 0.3 ms on the OJIP curve. Furthermore, exposure to shorter light wavelengths and longer exposure durations significantly reduced the relative abundance of the OEC peripheral proteins, indicating OEC inactivation. Analyses of light-screening substances revealed that carotenoids, which increased most notably under 420 nm light, might primarily serve as thermal dissipators instead of efficient light filters. In contrast, anthocyanins reacted least to short-wavelength light, in terms of changes to both their content and the expression of genes related to their biosynthesis. Additionally, the levels of aromatically acylated anthocyanins remained consistent across blue-, white-, and red-light treatments. These findings suggest that OEC photoinactivation in Z. marina may be linked to inadequate protection against short-wavelength light, a consequence of insufficient synthesis and aromatic acylation modification of anthocyanins.

Comparative transcriptomic analysis revealed important processes underlying the static magnetic field effects on Arabidopsis

Static magnetic field (SMF) plays important roles in various biological processes of many organisms including plants, though the molecular mechanism remains largely unclear. Here in this study, we evaluated different magnetic setups to test their effects on growth and development on Arabidopsis (Arabidopsis thaliana), and discovered that plant growth was significantly enhanced by inhomogeneous SMF generated by a regular triangular prism magnet perpendicular to the direction of gravity. Comparative transcriptomic analysis revealed that auxin synthesis and signal transduction genes were upregulated by SMF exposure. SMF also facilitated plants to maintain the iron homeostasis. The expression of iron metabolism-related genes was downregulated by SMF, however, the iron content in plant tissues remains relatively unchanged. Furthermore, SMF exposure also helped the plants to reduce ROS level and synergistically maintain the oxidant balance by enhanced activity of antioxidant enzymes and accumulation of nicotinamide. Taken together, our data suggested that SMF is involved in regulating the growth and development of Arabidopsis thaliana through maintaining iron homeostasis and balancing oxidative stress, which could be beneficial for plant survival and growth. The work presented here would extend our understanding of the mechanism and the regulatory network of how magnetic field affects the plant growth, which would provide insights into the development of novel plant synthetic biology technologies to engineer stress-resistant and high-yielding crops.

Molecular mechanisms underlying the signal perception and transduction during seed germination

QuerySeed germination is a vital step in the life cycle of a plant, playing a significant role in seedling establishment and crop yield potential. It is also an important factor in the conservation of plant germplasm resources. This complex process is influenced by a myriad of factors, including environmental conditions, the genetic makeup of the seed, and endogenous hormones. The perception of these environmental signals triggers a cascade of intricate signal transduction events that determine whether a seed germinates or remains dormant. Despite considerable progress in uncovering the molecular mechanisms governing these processes, many questions remain unanswered. In this review, we summarize the current progress in the molecular mechanisms underlying the perception of environmental signals and consequent signal transduction during seed germination, and discuss questions that need to be addressed to better understand the process of seed germination and develop novel strategies for germplasm improvement.

Effect of cryptochrome 1 deficiency and spectral composition of light on photosynthetic processes in A. thaliana under high-intensity light exposure

The role of cryptochrome 1 in photosynthetic processes and pro-/antioxidant balance in the Arabidopsis thaliana plants was studied. Wild type (WT) and hy4 mutant deficient in cryptochrome 1 grown for 20 d under red (RL, 660 nm) and blue (BL, 460 nm) light at an RL:BL = 4:1 ratio were kept for 3 d in different lights: RL:BL = 4:1, RL:BL:GL = 4:1:0.3 (GL - green light, 550 nm), and BL, then were exposed to high irradiance (4 h). Activity of PSII and the rate of photosynthesis in WT and hy4 decreased under the high irradiance in all spectral variants but under BL stronger decrease in the activity was found in the hy4 mutant than in WT. We assumed that lowered resistance of photosynthetic apparatus in the hy4 mutant may be associated with the low activity of the main antioxidant enzymes and reduced content of low-molecular-mass antioxidants in the mutant compared to the WT.

Arabidopsis transcription factor TCP13 promotes shade avoidance syndrome-like responses by directly targeting a subset of shade-responsive gene promoters

TCP13 belongs to a subgroup of TCP transcription factors implicated in the shade avoidance syndrome (SAS), but its exact role remains unclear. Here, we show that TCP13 promotes the SAS-like response by enhancing hypocotyl elongation and suppressing flavonoid biosynthesis as a part of the incoherent feed-forward loop in light signaling. Shade is known to promote the SAS by activating PHYTOCHROME-INTERACTING FACTOR (PIF)-auxin signaling in plants, but we found no evidence in a transcriptome analysis that TCP13 activates PIF-auxin signaling. Instead, TCP13 mimics shade by activating the expression of a subset of shade-inducible and cell elongation-promoting SAUR genes including SAUR19, by direct targeting of their promoters. We also found that TCP13 and PIF4, a molecular proxy for shade, repress the expression of flavonoid biosynthetic genes by directly targeting both shared and distinct sets of biosynthetic gene promoters. Together, our results indicate that TCP13 promotes the SAS-like response by directly targeting a subset of shade-responsive genes without activating the PIF-auxin signaling pathway.

Onion cryptochrome 1 (AcCRY1) regulates photomorphogenesis and photoperiod flowering in Arabidopsis and exploration of its functional mechanisms under blue light

Cryptochromes (CRYs), as blue-light photoreceptors, play a crucial role in regulating flowering time and hypocotyl and cotyledon development. Their physiological functions have been extensively studied in various plant species. However, research on onions remains limited. In this study, we identified AcCRY1 and conducted preliminary investigations into its function. Our results demonstrate that AcCRY1 possesses a conserved domain typical of cryptochromes with high homology to those found in monocots. Furthermore, we examined the expression level of AcCRY1 in onion. The green tissues is significantly higher compared to non-green tissues, and it exhibits a significant response to blue-light induction. AcCRY1 demonstrates cytoplasmic localization under blue-light conditions, while it localizes in the nucleus during darkness, indicating a strong dependence on blue-light for its subcellular distribution. In comparison to cry1, overexpression of AcCRY1 leads to a significant shorten in seedling hypocotyl length, notable expansion of cotyledons, and acceleration of flowering time. The yeast two-hybrid experiment demonstrated the in vitro interaction between AcCRY1, AcCOP1, and AcSPA1. Additionally, BIFC analysis confirmed their interaction in Onion epidermis. Notably, under blue-light conditions, a significantly enhanced binding activity was observed compared to dark conditions. These findings establish a functional foundation for the regulatory role of AcCRY1 in important physiological processes of onion and provide initial insights into the underlying molecular mechanisms.

Synthetic Biology Approaches to Posttranslational Regulation in Plants

To date synthetic biology approaches involving creation of functional genetic modules are used in a wide range of organisms. In plants, such approaches are used both for research in the field of functional genomics and to increase the yield of agricultural crops. Of particular interest are methods that allow controlling genetic apparatus of the plants at post-translational level, which allow reducing non-targeted effects from interference with the plant genome. This review discusses recent advances in the plant synthetic biology for regulation of the plant metabolism at posttranslational level and highlights their future directions.

Magic Blue Light: A Versatile Mediator of Plant Elongation

Blue light plays an important role in regulating plant elongation. However, due to the limitations of older lighting technologies, the responses of plants to pure blue light have not been fully studied, and some of our understandings of the functions of blue light in the literature need to be revisited. This review consolidates and analyzes the diverse findings from previous studies on blue-light-mediated plant elongation. By synthesizing the contrasting results, we uncover the underlying mechanisms and explanations proposed in recent research. Moreover, we delve into the exploration of blue light-emitting diodes (LEDs) as a tool for manipulating plant elongation in controlled-environment plant production, highlighting the latest advancements in this area. Finally, we acknowledge the challenges faced and outline future directions for research in this promising field. This review provides valuable insights into the pivotal role of blue light in plant growth and offers a foundation for further investigations to optimize plant elongation using blue light technology.

Nitric Oxide Regulates Seed Germination by Integrating Multiple Signalling Pathways

Seed germination is of great significance for plant development and crop yield. Recently, nitric oxide (NO) has been shown to not only serve as an important nitrogen source during seed development but also to participate in a variety of stress responses in plants to high salt, drought, and high temperature. In addition, NO can affect the process of seed germination by integrating multiple signaling pathways. However, due to the instability of NO gas activity, the network mechanism for its fine regulation of seed germination remains unclear. Therefore, this review aims to summarize the complex anabolic processes of NO in plants, to analyze the interaction mechanisms between NO-triggered signaling pathways and different plant hormones such as abscisic acid (ABA) and gibberellic acid (GA), ethylene (ET) and reactive oxygen species (ROS) signaling molecules, and to discuss the physiological responses and molecular mechanisms of seeds during the involvement of NO in abiotic stress, so as to provide a reference for solving the problems of seed dormancy release and improving plant stress tolerance.

Impact of additional green light and deficit in cryptochrome 1 on photosynthetic activity and pro-/antioxidant balance in Arabidopsis thaliana

The light spectral composition acting through a set of photoreceptors, such as cryptochromes and phytochromes, plays an important role in maintaining sustainable photosynthesis. An impact of cryptochrome 1 deficiency and additions of green light (GL) against the background of red (RL) and blue (BL) (different ratios of RL:BL:GL) on the activity of the photosynthetic apparatus, the content of photosynthetic pigments, pro-/antioxidant balance, and expression of some genes in the leaves of 23-d-old Arabidopsis thaliana hy4 mutant plants was studied. The deficiency of cryptochrome 1 at RL/BL ratio of 4:1 led to a decrease in the rate of photosynthesis, photosystem II activity, and activity of ascorbate peroxidase and total peroxidase but to an increase in the content of products reacting with thiobarbituric acid. However, in the presence of additional GL, this difference for photosynthetic parameters either decreased or was absent, likely due to a GL-induced decrease in the content of active cryptochrome.

Tuning the Wavelength: Manipulation of Light Signaling to Control Plant Defense

The growth-defense trade-off in plants is a phenomenon whereby plants must balance the allocation of their resources between developmental growth and defense against attack by pests and pathogens. Consequently, there are a series of points where growth signaling can negatively regulate defenses and where defense signaling can inhibit growth. Light perception by various photoreceptors has a major role in the control of growth and thus many points where it can influence defense. Plant pathogens secrete effector proteins to manipulate defense signaling in their hosts. Evidence is emerging that some of these effectors target light signaling pathways. Several effectors from different kingdoms of life have converged on key chloroplast processes to take advantage of regulatory crosstalk. Moreover, plant pathogens also perceive and react to light in complex ways to regulate their own growth, development, and virulence. Recent work has shown that varying light wavelengths may provide a novel way of controlling or preventing disease outbreaks in plants.

N6-methyladenosine mRNA methylation is important for the light response in soybean

N6-methyladenosine (m⁶A) modification of messenger RNA (mRNA) is the most prevalent and abundant modification in eukaryotic mRNA and posttranscriptionally modulates the transcriptome at almost all stages of mRNA metabolism. In plants, m⁶A is crucial for embryonic-phase growth, flowering time control, microspore generation and fruit maturation. However, the role of m⁶A in plant responses to light, the most important environmental stimulus, remains unexplored. Here, we profile the m⁶A transcriptome of Williams 82, a soybean cultivar, and reveal that m⁶A is highly conserved and plays an important role in the response to light stimuli in soybean. Similar to the case in Arabidopsis, m⁶A in soybean is enriched not only around the stop codon and within the 3'UTR but also around the start codon. Moreover, genes with methylation occurring in the 3'UTR have higher expression levels and are more prone to alternative splicing. The core genes in the light signaling pathway, GmSPA1a, GmPRR5e and GmBIC2b, undergo changes in methylation modification and transcription levels in response to light. KEGG pathway analysis revealed that differentially expressed genes with differential m⁶A peaks were involved in the "photosynthesis" and "circadian rhythm" pathways. Our results highlight the important role played by epitranscriptomic mRNA methylation in the light response in soybean and provide a solid basis for determining the functional role of light on RNA m⁶A modification in this plant.

Transcriptomic and Physiological Analyses Reveal Potential Genes Involved in Photoperiod-Regulated β-Carotene Accumulation Mechanisms in the Endocarp of Cucumber (Cucumis sativus L.) Fruit

The accumulation of carotenoids in plants is a key nutritional quality in many horticultural crops. Although the structural genes encoding the biosynthetic enzymes are well-characterized, little is known regarding photoperiod-mediated carotenoid accumulation in the fruits of some horticultural crops. Herein, we performed physiological and transcriptomic analyses using two cucumber genotypes, SWCC8 (XIS-orange-fleshed and photoperiod-sensitive) and CC3 (white-fleshed and photoperiod-non-sensitive), established under two photoperiod conditions (8L/16D vs. 12L/12D) at four fruit developmental stages. Day-neutral treatments significantly increased fruit β-carotene content by 42.1% compared to short day (SD) treatments in SWCC8 at 40 DAP with no significant changes in CC3. Day-neutral condition elevated sugar levels of fruits compared to short-day treatments. According to GO and KEGG analyses, the predominantly expressed genes were related to photosynthesis, carotenoid biosynthesis, plant hormone signaling, circadian rhythms, and carbohydrates. Consistent with β-carotene accumulation in SWCC8, the day-neutral condition elevated the expression of key carotenoid biosynthesis genes such as PSY1, PDS, ZDS1, LYCB, and CHYB1 during later stages between 30 to 40 days of fruit development. Compared to SWCC8, CC3 showed an expression of DEGs related to carotenoid cleavage and oxidative stresses, signifying reduced β-carotene levels in CC3 cucumber. Further, a WGCNA analysis revealed co-expression between carbohydrate-related genes (pentose-phosphatase synthase, β-glucosidase, and trehalose-6-phosphatase), photoperiod-signaling genes (LHY, APRR7/5, FKF1, PIF3, COP1, GIGANTEA, and CK2) and carotenoid-biosynthetic genes, thus suggesting that a cross-talk mechanism between carbohydrates and light-related genes induces β-carotene accumulation. The results highlighted herein provide a framework for future gene functional analyses and molecular breeding towards enhanced carotenoid accumulation in edible plant organs.

Effects of light spectrum on the morphophysiology and gene expression of lateral branching in Pepino (Solanum muricatum)

In the present study, we determined the morphological and physiological indicators of Pepino to elucidate its lateral branching responses to different light qualities using a full-spectrum lamp (F) as the control and eight different light ratios using blue light (B) and red light (R). In addition, correlation analysis revealed that the gene expression patterns correlated with lateral branching under various light treatments. Compared with the F treatment, the R treatment increased the plant height and inhibited the elongation of lateral branches, in contrast with the B treatment. The number of lateral branches did not change significantly under different light quality treatments. Moreover, correlation analysis showed that the ratio of blue light was significantly positively correlated with the length of lateral branches and significantly negatively correlated with plant height, aboveground dry weight, and other indicators. We conducted transcriptome sequencing of the sites of lateral branching at three periods under different light quality treatments. The gene related to photodynamic response, cryptochrome (CRY), was the most highly expressed under B treatment, negatively regulated lateral branch length, and positively correlated with plant height. Branched 1, a lateral branch regulation gene, was upregulated under R treatment and inhibited branching. Overall, the red light facilitated internode elongation, leaf area expansion, plant dry weight increase, and inhibition of lateral branching. Soluble sugar content increased, and the lateral branches elongated under blue light. Different light qualities regulated lateral branching by mediating different pathways involving strigolactones and CRY. Our findings laid a foundation for further clarifying the response mechanism of Pepino seedlings to light and provided a theoretical reference for elucidating the regulation of different light qualities on the lateral branching of Pepino.

The Gain and Loss of Cryptochrome/Photolyase Family Members during Evolution

The cryptochrome/photolyase (CRY/PL) family represents an ancient group of proteins fulfilling two fundamental functions. While photolyases repair UV-induced DNA damages, cryptochromes mainly influence the circadian clock. In this study, we took advantage of the large number of already sequenced and annotated genes available in databases and systematically searched for the protein sequences of CRY/PL family members in all taxonomic groups primarily focusing on metazoans and limiting the number of species per taxonomic order to five. Using BLASTP searches and subsequent phylogenetic tree and motif analyses, we identified five distinct photolyases (CPDI, CPDII, CPDIII, 6-4 photolyase, and the plant photolyase PPL) and six cryptochrome subfamilies (DASH-CRY, mammalian-type MCRY, Drosophila-type DCRY, cnidarian-specific ACRY, plant-specific PCRY, and the putative magnetoreceptor CRY4. Manually assigning the CRY/PL subfamilies to the species studied, we have noted that over evolutionary history, an initial increase of various CRY/PL subfamilies was followed by a decrease and specialization. Thus, in more primitive organisms (e.g., bacteria, archaea, simple eukaryotes, and in basal metazoans), we find relatively few CRY/PL members. As species become more evolved (e.g., cnidarians, mollusks, echinoderms, etc.), the CRY/PL repertoire also increases, whereas it appears to decrease again in more recent organisms (humans, fruit flies, etc.). Moreover, our study indicates that all cryptochromes, although largely active in the circadian clock, arose independently from different photolyases, explaining their different modes of action.

Environment-mediated mutagenetic interference on genetic stabilization and circadian rhythm in plants

Many mortal organisms on this planet have developed the potential to merge all internal as well as external environmental cues to regulate various processes running inside organisms and in turn make them adaptive to the environment through the circadian clock. This moving rotator controls processes like activation of hormonal, metabolic, or defense pathways, initiation of flowering at an accurate period, and developmental processes in plants to ensure their stability in the environment. All these processes that are under the control of this rotating wheel can be changed either by external environmental factors or by an unpredictable phenomenon called mutation that can be generated by either physical mutagens, chemical mutagens, or by internal genetic interruption during metabolic processes, which alters normal functionality of organisms like innate immune responses, entrainment of the clock, biomass reduction, chlorophyll formation, and hormonal signaling, despite its fewer positive roles in plants like changing plant type, loss of vernalization treatment to make them survivable in different latitudes, and defense responses during stress. In addition, with mutation, overexpression of gene components sometimes supresses mutation effect and promote normal circadian genes abundance in the cell, while sometimes it affects circadian functionality by generating arrhythmicity and shows that not only mutation but overexpression also effects normal functional activities of plant. Therefore, this review mainly summarizes the role of each circadian clock genes in regulating rhythmicity, and shows that how circadian outputs are controlled by mutations as well as overexpression phenomenon.

Regulation of Phenolic Compound Production by Light Varying in Spectral Quality and Total Irradiance

Photosynthetically active radiation (PAR) is an important environmental cue inducing the production of many secondary metabolites involved in plant oxidative stress avoidance and tolerance. To examine the complex role of PAR irradiance and specific spectral components on the accumulation of phenolic compounds (PheCs), we acclimated spring barley (Hordeum vulgare) to different spectral qualities (white, blue, green, red) at three irradiances (100, 200, 400 µmol m⁻² s⁻¹). We confirmed that blue light irradiance is essential for the accumulation of PheCs in secondary barley leaves (in UV-lacking conditions), which underpins the importance of photoreceptor signals (especially cryptochrome). Increasing blue light irradiance most effectively induced the accumulation of B-dihydroxylated flavonoids, probably due to the significantly enhanced expression of the F3′H gene. These changes in PheC metabolism led to a steeper increase in antioxidant activity than epidermal UV-A shielding in leaf extracts containing PheCs. In addition, we examined the possible role of miRNAs in the complex regulation of gene expression related to PheC biosynthesis.

The C-terminus of a diatom plant-like cryptochrome influences the FAD redox state and binding of interaction partners

A plant-like cryptochrome of diatom microalgae, CryP, acts as a photoreceptor involved in transcriptional regulation. It contains FAD and 5,10-methenyltetrahydrofolate as chromophores. Here, we demonstrate that the unstructured C-terminal extension (CTE) of CryP has an influence on the redox state of the flavin. In CryP lacking the CTE, the flavin is in the oxidized state (FADox), whereas it is a neutral radical (FADH•) in the full-length protein. When the CTE of CryP is coupled to another diatom cryptochrome that naturally binds FADox, this chimera also binds FADH•. In full-length CryP, FADH• is the most stable redox state and oxidation to FADox is extremely slow, whereas reduction to FADH2 is reversible in the dark in approximately 1 h. We also identified novel interaction partners of this algal CRY and characterized two of them in depth regarding their binding activities. BolA, a putative transcription factor, binds to monomeric and to dimeric CryP via the CTE, independent of the redox state of the flavin. In contrast, an unknown protein, ID42612, which occurs solely in heterokont algae, binds only to CryP dimers. This binding is independent of the CTE and shows slight differences in strength depending on the flavin's redox state.

Light and Plant Growth Regulators on In Vitro Proliferation

Plant tissue cultures depend entirely upon artificial light sources for illumination. The illumination should provide light in the appropriate regions of the electromagnetic spectrum for photomorphogenic responses and photosynthetic metabolism. Controlling light quality, irradiances and photoperiod enables the production of plants with desired characteristics. Moreover, significant money savings may be achieved using both more appropriate and less consuming energy lamps. In this review, the attention will be focused on the effects of light characteristics and plant growth regulators on shoot proliferation, the main process in in vitro propagation. The effects of the light spectrum on the balance of endogenous growth regulators will also be presented. For each light spectrum, the effects on proliferation but also on plantlet quality, i.e., shoot length, fresh and dry weight and photosynthesis, have been also analyzed. Even if a huge amount of literature is available on the effects of light on in vitro proliferation, the results are often conflicting. In fact, a lot of exogenous and endogenous factors, but also the lack of a common protocol, make it difficult to choose the most effective light spectrum for each of the large number of species. However, some general issues derived from the analysis of the literature are discussed.

Signaling Mechanisms by Arabidopsis Cryptochromes

Cryptochromes (CRYs) are blue light photoreceptors that regulate growth, development, and metabolism in plants. In Arabidopsis thaliana (Arabidopsis), CRY1 and CRY2 possess partially redundant and overlapping functions. Upon exposure to blue light, the monomeric inactive CRYs undergo phosphorylation and oligomerization, which are crucial to CRY function. Both the N- and C-terminal domains of CRYs participate in light-induced interaction with multiple signaling proteins. These include the COP1/SPA E3 ubiquitin ligase, several transcription factors, hormone signaling intermediates and proteins involved in chromatin-remodeling and RNA N6 adenosine methylation. In this review, we discuss the mechanisms of Arabidopsis CRY signaling in photomorphogenesis and the recent breakthroughs in Arabidopsis CRY research.

Light-Engineering Technology for Enhancing Plant Disease Resistance

Insect vector-borne diseases are a major constraint to a wide variety of crops. Plants integrate environmental light and internal signalings to defend dual stresses both from the vector insects and vector-transmitted pathogens. In this review, we highlight a studies that demonstrate how light regulates plants deploying mechanisms against vector-borne diseases. Four major host defensive pathways involved in the host defense network against multiple biotic stresses are reviewed: innate immunity, phytohormone signaling, RNA interference, and protein degradation. The potential with light-engineering technology with light emitting diodes (LEDs) and genome engineering technology for fine-tuning crop defense and yield are also discussed.

The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are utilized as coenzymes in many biochemical reduction-oxidation reactions owing to the ability of the tricyclic isoalloxazine ring system to employ the oxidized, radical and reduced state. We have analyzed the genome of Arabidopsis thaliana to establish an inventory of genes encoding flavin-dependent enzymes (flavoenzymes) as a basis to explore the range of flavin-dependent biochemical reactions that occur in this model plant. Expectedly, flavoenzymes catalyze many pivotal reactions in primary catabolism, which are connected to the degradation of basic metabolites, such as fatty and amino acids as well as carbohydrates and purines. On the other hand, flavoenzymes play diverse roles in anabolic reactions most notably the biosynthesis of amino acids as well as the biosynthesis of pyrimidines and sterols. Importantly, the role of flavoenzymes goes much beyond these basic reactions and extends into pathways that are equally crucial for plant life, for example the production of natural products. In this context, we outline the participation of flavoenzymes in the biosynthesis and maintenance of cofactors, coenzymes and accessory plant pigments (e. g. carotenoids) as well as phytohormones. Moreover, several multigene families have emerged as important components of plant immunity, for example the family of berberine bridge enzyme-like enzymes, flavin-dependent monooxygenases and NADPH oxidases. Furthermore, the versatility of flavoenzymes is highlighted by their role in reactions leading to tRNA-modifications, chromatin regulation and cellular redox homeostasis. The favorable photochemical properties of the flavin chromophore are exploited by photoreceptors to govern crucial processes of plant adaptation and development. Finally, a sequence- and structure-based approach was undertaken to gain insight into the catalytic role of uncharacterized flavoenzymes indicating their involvement in unknown biochemical reactions and pathways in A. thaliana.

Different response modes and cooperation modulations of blue-light receptors in photomorphogenesis

Cryptochromes photoreceptors, CRY1 and CRY2 in Arabidopsis, mediate blue light responses in plants and metazoa. The signalling interactions underlying photomorphogenesis of cryptochromes action have been extensively studied in experiment, expecting a systematical analysis of the dynamic mechanisms of photosensory signalling network from a global view. In this study, we developed a signalling network model to quantitatively investigate the different response modes and cooperation modulations on photomorphogenesis for CRY1 and CRY2 under blue light. The model shows that the different modes of time-dependent and fluence-rate-dependent phosphorylations for CRY1 and CRY2 are originated from their different phosphorylation rates and degradation rates. Our study indicates that, due to the strong association between blue-light inhibitor of cryptochromes (BIC) and CRY2, BIC negatively modulates CRY2 phosphorylation, which was confirmed by our experiment. The experiment also validated the model prediction that the time-dependent BIC-CRY1 and the fluence-rate-dependent BIC-CRY2 are both bell-shaped under blue light. Importantly, the model proposes that the COP1-SPA abundance can strongly inhibit the phosphorylation response of CRY2, resulting in the positive regulation of CRY2 phosphorylation by CRY1 through COP1-SPA. The model also predicts that the CRY1-HY5 axis, rather than CRY2-HY5 pathway, plays a dominant role in blue-light-dependent photomorphogenesis.

Coordinative regulation of plants growth and development by light and circadian clock

The circadian clock, known as an endogenous timekeeping system, can integrate various cues to regulate plant physiological functions for adapting to the changing environment and thus ensure optimal plant growth. The synchronization of internal clock with external environmental information needs a process termed entrainment, and light is one of the predominant entraining signals for the plant circadian clock. Photoreceptors can detect and transmit light information to the clock core oscillator through transcriptional or post-transcriptional interactions with core-clock components to sustain circadian rhythms and regulate a myriad of downstream responses, including photomorphogenesis and photoperiodic flowering which are key links in the process of growth and development. Here we summarize the current understanding of the molecular network of the circadian clock and how light information is integrated into the circadian system, especially focus on how the circadian clock and light signals coordinately regulate the common downstream outputs. We discuss the functions of the clock and light signals in regulating photoperiodic flowering among various crop species.

Cryptochromes and the Circadian Clock: The Story of a Very Complex Relationship in a Spinning World

Cryptochromes are flavin-containing blue light photoreceptors, present in most kingdoms, including archaea, bacteria, plants, animals and fungi. They are structurally similar to photolyases, a class of flavoproteins involved in light-dependent repair of UV-damaged DNA. Cryptochromes were first discovered in Arabidopsis thaliana in which they control many light-regulated physiological processes like seed germination, de-etiolation, photoperiodic control of the flowering time, cotyledon opening and expansion, anthocyanin accumulation, chloroplast development and root growth. They also regulate the entrainment of plant circadian clock to the phase of light-dark daily cycles. Here, we review the molecular mechanisms by which plant cryptochromes control the synchronisation of the clock with the environmental light. Furthermore, we summarise the circadian clock-mediated changes in cell cycle regulation and chromatin organisation and, finally, we discuss a putative role for plant cryptochromes in the epigenetic regulation of genes.

Functional analysis of a novel cryptochrome gene (GbCRY1) from Ginkgo biloba

Cryptochrome (CRY) is a blue light receptor that is widely distributed in animals, plants, and microorganisms. CRY as a coding gene of cryptochrome that regulates the organism gene expression and plays an important role in organism growth and development. In this study, we identified four photolyase/cryptochrome (PHR/CRY) members from the genome of Ginkgo biloba. Phylogenetic tree analysis showed that the Ginkgo PHR/CRY family members were closely related to Arabidopsis thaliana and Solanum lycopersicum. We isolated a cryptochrome gene, GbCRY1, from G. biloba and analyzed its structure and function. GbCRY1 shared high similarity with AtCRY1 from A. thaliana. GbCRY1 expression level was higher in stems and leaves and lower in roots, male strobili, female strobili. GbCRY1 expression level fluctuated periodically within 24 h, gradually increased in the dark, and decreased under blue light. The newly germinated ginkgo seedlings were cultured under dark, white light, and blue light conditions. The blue light normally induced photomorphogenesis of ginkgo seedlings, which included hypocotyl elongation inhibition, leaf expansion inhibition, and chlorophyll formation. Treating dark-adapted ginkgo leaves with blue light could induce stomatal opening. At the same time, blue light reduced the expression level of GbCRY1 in the process of inducing photomorphogenesis and stoma opening. Our results provide evidence that GbCRY1 expression is affected by space, circadian cycle and light, and also proves that GbCRY1 is related to ginkgo circadian clock, photomorphogenesis and stoma opening process.

Structural insights into photoactivation of plant Cryptochrome-2

Cryptochromes (CRYs) are evolutionarily conserved photoreceptors that mediate various light-induced responses in bacteria, plants, and animals. Plant cryptochromes govern a variety of critical growth and developmental processes including seed germination, flowering time and entrainment of the circadian clock. CRY's photocycle involves reduction of their flavin adenine dinucleotide (FAD)-bound chromophore, which is completely oxidized in the dark and semi to fully reduced in the light signaling-active state. Despite the progress in characterizing cryptochromes, important aspects of their photochemistry, regulation, and light-induced structural changes remain to be addressed. In this study, we determine the crystal structure of the photosensory domain of Arabidopsis CRY2 in a tetrameric active state. Systematic structure-based analyses of photo-activated and inactive plant CRYs elucidate distinct structural elements and critical residues that dynamically partake in photo-induced oligomerization. Our study offers an updated model of CRYs photoactivation mechanism as well as the mode of its regulation by interacting proteins.

Light-Induced Dynamic Change of Phytochrome B and Cryptochrome 1 Stabilizes SINATs in Arabidopsis

Ubiquitin-dependent protein degradation plays an important role in many plant developmental processes. We previously identified a class of SINA RING-type E3 ligases of Arabidopsis thaliana (SINATs), whose protein levels decrease in the dark and increase in red and blue light, but the underlying mechanism is unclear. In this study, we created transgenic lines carrying point mutations in SINAT genes and photoreceptors-NLS or -NES transgenic plants to investigate the regulatory mechanism of SINAT protein stability. We demonstrated that the degradation of SINATs is self-regulated, and SINATs interact with photoreceptors phytochrome B (phyB) and cryptochrome 1 (CRY1) in the cytoplasm, which leads to the degradation of SINATs in the dark. Furthermore, we observed that the red light-induced subcellular localization change of phyB and blue light-induced the dissociation of CRY1 from SINATs and was the major determinant for the light-promoted SINATs accumulation. Our findings provide a novel mechanism of how the stability and degradation of the E3 ligase SINATs are regulated by an association and dissociation mechanism through the red light-induced subcellular movement of phyB and the blue light-induced dissociation of CRY1 from SINATs.

Structural insights into the photoactivation of Arabidopsis CRY2

The blue-light receptor cryptochrome (CRY) in plants undergoes oligomerization to transduce blue-light signals after irradiation, but the corresponding molecular mechanism remains poorly understood. Here, we report the cryogenic electron microscopy structure of a blue-light-activated CRY2 tetramer at a resolution of 3.1 Å, which shows how the CRY2 tetramer assembles. Our study provides insights into blue-light-mediated activation of CRY2 and a theoretical basis for developing regulators of CRYs for optogenetic manipulation.

Light- and hormone-mediated development in non-flowering plants: An overview

Light, hormones and their interaction regulate different aspects of development in non-flowering plants. They might have played a role in the evolution of different plant groups by conferring specific adaptive evolutionary changes. Plants are sessile organisms. Unlike animals, they lack the opportunity to abandon their habitat in unfavorable conditions. They respond to different environmental cues and adapt accordingly to control their growth and developmental pattern. While phytohormones are known to be internal regulators of plant development, light is a major environmental signal that shapes plant processes. It is plausible that light-hormone crosstalk might have played an important role in plant evolution. But how the crosstalk between light and phytohormone signaling pathways might have shaped the plant evolution is unclear. One of the possible reasons is that flowering plants have been studied extensively in context of plant development, which cannot serve the purpose of evolutionary comparisons. In order to elucidate the role of light, hormone and their crosstalk in the evolutionary adaptation in plant kingdom, one needs to understand various light- and hormone-mediated processes in diverse non-flowering plants. This review is an attempt to outline major light- and phytohormone-mediated responses in non-flowering plant groups such as algae, bryophytes, pteridophytes and gymnosperms.

Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response

BACKGROUND

Transcription factors (TFs) are essential regulators of growth and development in eukaryotes. Basic-helix-loop-helix (bHLHs) is one of the most significant TFs families involved in several critical regulatory functions. Cryptochrome-interacting bHLH (CIB) and cryptochromes form an extensive regulatory network to mediate a plethora of pathways. Although bHLHs regulate critical biological processes in plants, the information about pineapple bHLHs remains unexplored.

RESULTS

Here, we identified a total of 121 bHLH proteins in the pineapple genome. The identified genes were renamed based on the ascending order of their gene ID and classified into 18 subgroups by phylogenetic analysis. We found that bHLH genes are expressed in different organs and stages of pineapple development. Furthermore, by the ectopic expression of AcCIB2 in Arabidopsis and complementation of Atcib2 mutant, we verified the involvement of AcCIB2 in photomorphogenesis and abiotic stress response.

CONCLUSIONS

Our findings revealed that AcCIB2 plays an essential role in flowering time regulation and abiotic stress response. The present study provides additional insights into the current knowledge of bHLH genes and suggests their potential role in various biological processes during pineapple development.

Genome-wide identification of WD40 genes reveals a functional diversification of COP1-like genes in Rosaceae

Genome-wide identification of WD40-like genes reveals a duplication of COP1-like genes, one of the key players involved in regulation of flowering time and photomorphogenesis, with strong functional diversification in Rosaceae. WD40 proteins play crucial roles in a broad spectrum of developmental and physiological processes. Here, we conducted a systematic characterization of this family of genes in Rosa chinensis 'Old Blush' (OB), a founder genotype for modern rose domestication. We identified 187 rose WD40 genes and classified them into 5 clusters and 15 subfamilies with 11 of RcWD40s presumably generated via tandem duplication. We found RcWD40 genes were expressed differentially following stages of vegetative and reproductive development. We detected a duplication of CONSTITUTIVE PHOTOMORPHOGENIC1-like genes in rose (RcCOP1 and RcCOP1L) and other Rosaceae plants. Featuring a distinct expression pattern and a different profile of cis-regulatory-elements in the transcriptional regulatory regions, RcCOP1 seemed being evolutionarily conserved while RcCOP1L did not dimerize with RcHY5 and RcSPA4. Our data thus reveals a functional diversification of COP1-like genes in Rosacaeae plants, and provides a valuable resource to explore the potential function and evolution of WD40-like genes in Rosaceae plants.

Molecular mechanisms suppressing COP1/SPA E3 ubiquitin ligase activity in blue light

Arabidopsis CONSTITUTIVE PHOTOMORPHOGENIC1/SUPPRESSOR OF PHYA-105 (COP1/SPA) is an E3 ubiquitin ligase complex that prevents photomorphogenesis in darkness by ubiquitinating and subsequently degrading light-responsive transcription factors. Upon light perception, photoreceptors directly interact with the COP1/SPA complex to suppress its activity. In blue light (450-500 nm of visible spectrum), COP1/SPA activity is inhibited by the cryptochrome photoreceptors (CRY1 and CRY2), FKF1 from the ZEITLUPE family as well as phytochrome A. Together, these photoreceptors regulate vital aspects of plant growth and development from seedling stage to the induction of flowering. This review presents and discusses the recent advances in blue light-mediated suppression of COP1/SPA activity.

Structural insights into BIC-mediated inactivation of Arabidopsis cryptochrome 2

Cryptochromes (CRYs) are blue-light receptors in plants that harbor FAD as a cofactor and regulate various physiological responses. Photoactivated CRYs undergo oligomerization, which increases the binding affinity to downstream signaling partners. Despite decades of research on the activation of CRYs, little is known about how they are inactivated. Binding of blue-light inhibitors of cryptochromes (BICs) to CRY2 suppresses its photoactivation, but the underlying mechanism remains unknown. Here, we report crystal structures of CRY2N (CRY2 PHR domain) and the BIC2-CRY2N complex with resolutions of 2.7 and 2.5 Å, respectively. In the BIC2-CRY2N complex, BIC2 exhibits an extremely extended structure that sinuously winds around CRY2N. In this way, BIC2 not only restrains the transfer of electrons and protons from CRY2 to FAD during photoreduction but also interacts with the CRY2 oligomer to return it to the monomer form. Uncovering the mechanism of CRY2 inactivation lays a solid foundation for the investigation of cryptochrome protein function.

Phototropin2 Contributes to the Chloroplast Avoidance Response at the Chloroplast-Plasma Membrane Interface

Blue-light-induced chloroplast movements play an important role in maximizing light utilization for photosynthesis in plants. Under a weak light condition, chloroplasts accumulate to the cell surface to capture light efficiently (chloroplast accumulation response). Conversely, chloroplasts escape from strong light and move to the side wall to reduce photodamage (chloroplast avoidance response). The blue light receptor phototropin (phot) regulates these chloroplast movements and optimizes leaf photosynthesis by controlling other responses in addition to chloroplast movements. Seed plants such as Arabidopsis (Arabidopsis thaliana) have phot1 and phot2. They redundantly mediate phototropism, stomatal opening, leaf flattening, and the chloroplast accumulation response. However, the chloroplast avoidance response is induced by strong blue light and regulated primarily by phot2. Phots are localized mainly on the plasma membrane. However, a substantial amount of phot2 resides on the chloroplast outer envelope. Therefore, differentially localized phot2 might have different functions. To determine the functions of plasma membrane- and chloroplast envelope-localized phot2, we tethered it to these structures with their respective targeting signals. Plasma membrane-localized phot2 regulated phototropism, leaf flattening, stomatal opening, and chloroplast movements. Chloroplast envelope-localized phot2 failed to mediate phototropism, leaf flattening, and the chloroplast accumulation response but partially regulated the chloroplast avoidance response and stomatal opening. Based on the present and previous findings, we propose that phot2 localized at the interface between the plasma membrane and the chloroplasts is required for the chloroplast avoidance response and possibly for stomatal opening as well.

Light Perception: A Matter of Time

Optimizing the perception of external cues and regulating physiology accordingly help plants to cope with the constantly changing environmental conditions to which they are exposed. An array of photoreceptors and intricate signaling pathways allow plants to convey the surrounding light information and synchronize an endogenous timekeeping system known as the circadian clock. This biological clock integrates multiple cues to modulate a myriad of downstream responses, timing them to occur at the best moment of the day and the year. Notably, the mechanism underlying entrainment of the light-mediated clock is not clear. This review addresses known interactions between the light-signaling and circadian-clock networks, focusing on the role of light in clock entrainment and known molecular players in this process.

Cryptochrome 2 competes with COP1 substrates to repress COP1 ubiquitin ligase activity during Arabidopsis photomorphogenesis

In plants, the cryptochrome photoreceptors suppress the activity of the COP1/SPA ubiquitin ligase to initiate photomorphogenesis in blue light. Both CRY1 and CRY2 interact with the COP1/SPA complex in a blue light-dependent manner. The mechanisms underlying the inhibition of COP1 activity through direct interactions with photoactivated CRYs are not fully understood. Here we tested the hypothesis that CRY2 inhibits COP1 by displacing the degradation substrates from COP1. To this end, we analyzed the role of a conserved valine-proline (VP) motif in the C-terminal domain of CRY2 (CCT2), which resembles the core COP1-WD40-binding sequences present in the substrates of COP1. We show that the VP motif in CRY2 is essential for the interaction of CRY2 with COP1 in yeast two-hybrid assays and in planta Mutations in the VP motif of CRY2 abolished the CRY2 activity in photomorphogenesis, indicating the importance of VP. The interaction between COP1 and its VP-containing substrate PAP2 was prevented in the presence of coexpressed CRY2, but not in the presence of CRY2 carrying a VP mutation. Thus, since both PAP2 and CRY2 engage VP motifs to bind to COP1, these results demonstrate that CRY2 outcompetes PAP2 for binding to COP1. We further found that the previously unknown interaction between SPA1-WD and CCT2 occurs via the VP motif in CRY2, suggesting structural similarities in the VP-binding pockets of COP1-WD40 and SPA1-WD40 domains. A VP motif present in CRY1 is also essential for binding to COP1. Thus, CRY1 and CRY2 might share this mechanism of COP1 inactivation.

Hypocotyl elongation is regulated by supplemental blue and red light in cucumber seedling

Light is fundamental for plants in growth and development, with regulating by integration of photoreceptors, hormones, and transcription factors. In this study, the cucumber seedlings were supplemented with different ratios of red and blue light (1R1B, 2R1B, 1R2B and weak daylight as control), with triggering change of phenotype, and gene expression profiles of CsPHYs and CsCRYs, CsGAs/BRs, and CsPIFs in hypocotyls. The cucumber seedling growth was significantly improved by supplemental light quality as compared with CK, and the seedlings in 2R1B were the stoutest, with obviously shortening hypocotyls, and higher dry weight and seedlings index at two-leaf stage. The gene expression of photoreceptor and hormone, including CsPHYA, CsPHYB, CsCRY1, CsGA20ox1, CsGA20ox2, CsGA3ox1, was significantly up-regulated in hypocotyl under different supplemental light conditions. The cucumber seedlings silenced by pTRV2-PIF4 had an obvious shortened hypocotyl. The expression level of CsCRY1, CsGA20ox1 and CsGA3ox1 was markedly down-regulation, whereas CsPHYA and CsPHYB expression increased observably and CsGA20ox2 expression was not dramatically difference in pTRV2-PIF4-infected seedlings. Thus, cucumber seedlings hypocotyl elongation was regulated by different supplemental light through crosstalk of photoreceptor, GAs, PIFs, and increasing ratio of red light could promote suppression of hypocotyl elongation.

Pivotal Roles of Cryptochromes 1a and 2 in Tomato Development and Physiology

Cryptochromes are flavin-containing blue/UVA light photoreceptors that regulate various plant light-induced physiological processes. In Arabidopsis (Arabidopsis thaliana), cryptochromes mediate de-etiolation, photoperiodic control of flowering, entrainment of the circadian clock, cotyledon opening and expansion, anthocyanin accumulation, and root growth. In tomato (Solanum lycopersicum), cryptochromes are encoded by a multigene family, comprising CRY1a, CRY1b, CRY2, and CRY3 We have previously reported the phenotypes of tomato cry1a mutants and CRY2 overexpressing plants. Here, we report the isolation by targeting induced local lesions in genomes, of a tomato cry2 knock-out mutant, its introgression in the indeterminate Moneymaker background, and the phenotypes of cry1a/cry2 single and double mutants. The cry1a/cry2 mutant showed phenotypes similar to its Arabidopsis counterpart (long hypocotyls in white and blue light), but also several additional features such as increased seed weight and internode length, enhanced hypocotyl length in red light, inhibited primary root growth under different light conditions, anticipation of flowering under long-day conditions, and alteration of the phase of circadian leaf movements. Both cry1a and cry2 control the levels of photosynthetic pigments in leaves, but cry2 has a predominant role in fruit pigmentation. Metabolites of the sterol, tocopherol, quinone, and sugar classes are differentially accumulated in cry1a and cry2 leaves and fruits. These results demonstrate a pivotal role of cryptochromes in controlling tomato development and physiology. The manipulation of these photoreceptors represents a powerful tool to influence important agronomic traits such as flowering time and fruit quality.

Candidate Variants for Additive and Interactive Effects on Bioenergy Traits in Switchgrass (Panicum virgatum L.) Identified by Genome-Wide Association Analyses

Switchgrass ( L.) is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving simple additive marker effects and also interactions with genetic backgrounds (e.g., ecotypes) or synergies with other markers. We analyzed plant height, C content, N content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotypes. We performed association analyses based on exome capture sequencing and tested 439,170 markers for marginal effects, 83,290 markers for marker × ecotype interactions, and up to 311,445 marker pairs for pairwise interactions. Analyses of pairwise interactions focused on subsets of marker pairs preselected on the basis of marginal marker effects, gene ontology annotation, and pairwise marker associations. Our tests identified 12 significant effects. Homology and gene expression information corroborated seven effects and indicated plausible causal pathways: flowering time and lignin synthesis for plant height; plant growth and senescence for C content and mineral concentration. Four pairwise interactions were detected, including three interactions preselected on the basis of pairwise marker correlations. Furthermore, a marker × ecotype interaction and a pairwise interaction were confirmed in an independent switchgrass panel. Our analyses identified reliable candidate variants for important bioenergy traits. Moreover, they exemplified the importance of interactive effects for depicting genetic bases and illustrated the usefulness of preselecting marker pairs for identifying pairwise marker interactions in association studies.

ClCRY2 facilitates floral transition in Chrysanthemum lavandulifolium by affecting the transcription of circadian clock-related genes under short-day photoperiods

Plants sense photoperiod signals to confirm the optimal flowering time. Previous studies have shown that Cryptochrome2 (CRY2) functions to promote floral transition in the long-day plant (LDP) Arabidopsis; however, the function and molecular mechanism by which CRY2 regulates floral transition in short-day plants (SDPs) is still unclear. In this study, we identified a CRY2 homologous gene, ClCRY2, from Chrysanthemum lavandulifolium, a typical SDP. The morphological changes in the C. lavandulifolium shoot apex and ClFTs expression analysis under SD conditions showed that adult C. lavandulifolium completed the developmental transition from vegetative growth to reproductive growth after eight SDs. Meanwhile, ClCRY2 mRNA exhibited an increasing trend from 0 to 8 d of SD treatment. ClCRY2 overexpression in wild-type (WT) Arabidopsis and C. lavandulifolium resulted in early flowering. The transcript levels of the CONSTANS-like (COL) genes ClCOL1, ClCOL4, and ClCOL5, and FLOWERING LOCUS T (FT) homologous gene ClFT1 were upregulated in ClCRY2 overexpression (ClCRY2-OE) C. lavandulifolium under SD conditions. The transcript levels of some circadian clock-related genes, including PSEUDO-REPONSE REGULATOR 5 (PRR5), ZEITLUPE (ZTL), FLAVIN-BINDING KELCH REPEAT F-BOX 1 (FKF1), and GIGANTEA (GI-1 and GI-2), were upregulated in ClCRY2-OE C. lavandulifolium, while the expression levels of other circadian clock-related genes, such as EARLY FLOWERING 3 (ELF3), ELF4, LATE ELONGATED HYPOCOTYL (LHY), PRR73, and REVEILLE8 (RVE8), were downregulated in ClCRY2-OE C. lavandulifolium under SD conditions. Taken together, the results suggest that ClCRY2 promotes floral transition by fine-tuning the expression of circadian clock-related gene, ClCOLs and ClFT1 in C. lavandulifolium under SD conditions.

Comparative RNA-Seq analysis on the regulation of cucumber sex differentiation under different ratios of blue and red light

Cucumber (Cucumis sativus L.) is a typical monoecism vegetable with individual male and female flowers, which has been used as a plant model for sex determination. It is well known that light is one of the most important environmental stimuli, which control the timing of the transition from vegetative growth to reproductive development. However, whether light controls sex determination remains elusive. To unravel this problem, we performed high-throughput RNA-Seq analyses, which compared the transcriptomes of shoot apices between R2B1(Red light:Blue light = 2:1)-treated and R4B1(Red light:Blue light = 4:1)-treated cucumber seedlings. Results showed that the higher proportion of blue light in the R2B1 treatment significantly induced the formation of female flowers and accelerated female flowering time in this whole study. The genes related to flowering time, such as flowering locus T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1), were up-regulated after R2B1 treatment. Furthermore, the transcriptome analysis showed that up-regulation and down-regulation of specific DEGs (the differentially expressed genes) were primarily the result of plant hormone signal transduction after treatments. The specific DEGs related with auxin formed the highest percentage of DEGs in the plant hormone signal transduction. In addition, the expression levels of transcription factors also changed after R2B1 treatment. Thus, sex differentiation affected by light quality might be induced by plant hormone signal transduction and transcription factors. These results provide a theoretical basis for further investigation of the regulatory mechanism of female flower formation under different light qualities in cucumber seedlings.

Phytochrome and Phytohormones: Working in Tandem for Plant Growth and Development

Being sessile organisms, plants need to continually adapt and modulate their rate of growth and development in accordance with the changing environmental conditions, a phenomenon referred to as plasticity. Plasticity in plants is a highly complex process that involves a well-coordinated interaction between different signaling pathways, the spatiotemporal involvement of phytohormones and cues from the environment. Though research studies are being carried out over the years to understand how plants perceive the signals from changing environmental conditions and activate plasticity, such remain a mystery to be resolved. Among all environmental cues, the light seems to be the stand out factor influencing plant growth and development. During the course of evolution, plants have developed well-equipped signaling system that enables regulation of both quantitative and qualitative differences in the amount of perceived light. Light influences essential developmental switches in plants ranging from germination or transition to flowering, photomorphogenesis, as well as switches in response to shade avoidances and architectural changes occurring during phototropism. Abscisic acid (ABA) is controlling seed germination and is regulated by light. Furthermore, circadian clock adds another level of regulation to plant growth by integrating light signals with different hormonal pathways. MYB96 has been identified as a regulator of circadian gating of ABA-mediated responses in plants by binding to the TIMING OF CAB EXPRESSION 1(TOC1) promoter. This review will present a representative regulatory model, highlight the successes achieved in employing novel strategies to dissect the levels of interaction and provide perspective for future research on phytochrome-phytohormones relationships toward facilitating plant growth, development, and function under abiotic-biotic stresses.