Patterns of expression and normalized levels of the five Arabidopsis phytochromes

Near-infrared imaging of phytochrome-derived autofluorescence in plant nuclei

Capturing images of the nuclear dynamics within live cells is an essential technique for comprehending the intricate biological processes inherent to plant cell nuclei. While various methods exist for imaging nuclei, including combining fluorescent proteins and dyes with microscopy, there is a dearth of commercially available dyes for live-cell imaging. In Arabidopsis thaliana, we discovered that nuclei emit autofluorescence in the near-infrared (NIR) range of the spectrum and devised a non-invasive technique for the visualization of live cell nuclei using this inherent NIR autofluorescence. Our studies demonstrated the capability of the NIR imaging technique to visualize the dynamic behavior of nuclei within primary roots, root hairs, and pollen tubes, which are tissues that harbor a limited number of other organelles displaying autofluorescence. We further demonstrated the applicability of NIR autofluorescence imaging in various other tissues by incorporating fluorescence lifetime imaging techniques. Nuclear autofluorescence was also detected across a wide range of plant species, enabling analyses without the need for transformation. The nuclear autofluorescence in the NIR wavelength range was not observed in animal or yeast cells. Genetic analysis revealed that this autofluorescence was caused by the phytochrome protein. Our studies demonstrated that nuclear autofluorescence imaging can be effectively employed not only in model plants but also for studying nuclei in non-model plant species.

PHYTOCHROME A controls the DNA damage response and cell death tolerance within the Arabidopsis root meristem

The DNA damage response avoids mutations into dividing cells. Here, we analysed the role of photoreceptors on the restriction of root growth imposed by genotoxic agents and its relationship with cell viability and performance of meristems. Comparison of root growth of Arabidopsis WT, phyA-211, phyB-9, and phyA-211phyB-9 double mutants unveiled a critical role for phytochrome A (PhyA) in protecting roots from genotoxic stress, regeneration and cell replenishment in the meristematic zone. PhyA was located on primary root tips, where it influences genes related to the repair of DNA, including ERF115 and RAD51. Interestingly, phyA-211 mutants treated with zeocin failed to induce the expression of the repressor of cell cycle MYB3R3, which correlated with expression of the mitotic cyclin CycB1, suggesting that PhyA is required for safeguarding the DNA integrity during cell division. Moreover, the growth of the primary roots of PhyA downstream component HY5 and root growth analyses in darkness suggest that cell viability and DNA damage responses within root meristems may act independently from light and photomorphogenesis. These data support novel roles for PhyA as a key player for stem cell niche maintenance and DNA damage responses, which are critical for proper root growth.

Liquid-liquid phase separation of TZP promotes PPK-mediated phosphorylation of the phytochrome A photoreceptor

Phytochrome A (phyA) is the plant far-red (FR) light photoreceptor and plays an essential role in regulating photomorphogenic development in FR-rich conditions, such as canopy shade. It has long been observed that phyA is a phosphoprotein in vivo; however, the protein kinases that could phosphorylate phyA remain largely unknown. Here we show that a small protein kinase family, consisting of four members named PHOTOREGULATORY PROTEIN KINASES (PPKs) (also known as MUT9-LIKE KINASES), directly phosphorylate phyA in vitro and in vivo. In addition, TANDEM ZINC-FINGER/PLUS3 (TZP), a recently characterized phyA-interacting protein required for in vivo phosphorylation of phyA, is also directly phosphorylated by PPKs. We reveal that TZP contains two intrinsically disordered regions in its amino-terminal domain that undergo liquid-liquid phase separation (LLPS) upon light exposure. The LLPS of TZP promotes colocalization and interaction between PPKs and phyA, thus facilitating PPK-mediated phosphorylation of phyA in FR light. Our study identifies PPKs as a class of protein kinases mediating the phosphorylation of phyA and demonstrates that the LLPS of TZP contributes significantly to more production of the phosphorylated phyA form in FR light.

Plant thermosensors

Plants dynamically regulate their genes expression and physiological outputs to adapt to changing temperatures. The underlying molecular mechanisms have been extensively studied in diverse plants and in multiple dimensions. However, the question of exactly how temperature is detected at molecular level to transform the physical information into recognizable intracellular signals remains continues to be one of the undetermined occurrences in plant science. Recent studies have provided the physical and biochemical mechanistic breakthrough of how temperature changes can influence molecular thermodynamically stability, thus changing molecular structures, activities, interaction and signaling transduction. In this review, we focus on the thermosensing mechanisms of recognized and potential plant thermosensors, to describe the multi-level thermal input system in plants. We also consider the attributes of a thermosensor on the basis of thermal-triggered changes in function, structure, and physical parameters. This study thus provides a reference for discovering more plant thermosensors and elucidating plant thermal adaptive mechanisms.

Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5

Light plays a central role in plant growth and development, providing an energy source and governing various aspects of plant morphology. Previous study showed that many polyadenylated full-length RNA molecules within the nucleus contain unspliced introns (post-transcriptionally spliced introns, PTS introns), which may play a role in rapidly responding to changes in environmental signals. However, the mechanism underlying post-transcriptional regulation during initial light exposure of young, etiolated seedlings remains elusive. In this study, we used FLEP-seq2, a Nanopore-based sequencing technique, to analyze nuclear RNAs in Arabidopsis (Arabidopsis thaliana) seedlings under different light conditions and found numerous light-responsive PTS introns. We also used single-nucleus RNA sequencing (snRNA-seq) to profile transcripts in single nucleus and investigate the distribution of light-responsive PTS introns across distinct cell types. We established that light-induced PTS introns are predominant in mesophyll cells during seedling de-etiolation following exposure of etiolated seedlings to light. We further demonstrated the involvement of the splicing-related factor A. thaliana PROTEIN ARGININE METHYLTRANSFERASE 5 (AtPRMT5), working in concert with the E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a critical repressor of light signaling pathways. We showed that these two proteins orchestrate light-induced PTS events in mesophyll cells and facilitate chloroplast development, photosynthesis, and morphogenesis in response to ever-changing light conditions. These findings provide crucial insights into the intricate mechanisms underlying plant acclimation to light at the cell-type level.

Root-specific photoreception directs early root development by HY5-regulated ROS balance

Root development is tightly controlled by light, and the response is thought to depend on signal transmission from the shoot. Here, we show that the root apical meristem perceives light independently from aboveground organs to activate the light-regulated transcription factor ELONGATED HYPOCOTYL5 (HY5). The ROS balance between H2O2 and superoxide anion in the root is disturbed under darkness with increased H2O2. We demonstrate that root-derived HY5 directly activates PER6 expression to eliminate H2O2. Moreover, HY5 directly represses UPBEAT1, a known inhibitor of peroxidases, to release the expression of PERs, partially contributing to the light control of ROS balance in the root. Our results reveal an unexpected ability in roots with specific photoreception and provide a mechanistic framework for the HY5-mediated interaction between light and ROS signaling in early root development.

Cooperative transcriptional regulation by ATAF1 and HY5 promotes light-induced cotyledon opening in Arabidopsis thaliana

The opening of the embryonic leaves (cotyledons) as seedlings emerge from the dark soil into the light is crucial to ensure the survival of the plant. Seedlings that sprout in the dark elongate rapidly to reach light but keep their cotyledons closed. During de-etiolation, the transition from dark to light growth, elongation slows and the cotyledons open. Here, we report that the transcription factor ACTIVATING FACTOR1 (ATAF1) participates in de-etiolation and facilitates light-induced cotyledon opening. The transition from dark to light rapidly induced ATAF1 expression and ATAF1 accumulation in cotyledons. Seedlings lacking or overexpressing ATAF1 exhibited reduced or enhanced cotyledon opening, respectively, and transcriptomic analysis indicated that ATAF1 repressed the expression of genes associated with growth and cotyledon closure. The activation of the photoreceptor phytochrome A (phyA) by far-red light induced its association with the ATAF1 promoter and stimulation of ATAF1 expression. The transcription factor ELONGATED HYPOCOTYL5 (HY5), which is also activated in response far-red light, cooperated with phyA to induce ATAF1 expression. ATAF1 and HY5 interacted with one another and cooperatively repressed the expression of growth-promoting and cotyledon closure genes. Together, our study reveals a mechanism through which far-red light promotes cotyledon opening.

Boosting underwater germination in Echinochloa colona seeds: the impact of high amplitude alternating temperatures and potassium nitrate osmopriming

Underwater germination could risk seedling survival, suggesting the need for control through seed perception of environmental cues. These cues include diurnally alternating temperatures tied to drained soils or shallow water tables. We examined high-amplitude alternating temperatures impact on underwater germination. Besides, the conditions experimented by seeds in the soil (e.g. hydration/dehydration phases) change their germinability so we tested if osmopriming could affect underwater germination. We worked with Echinochloa colona seedlots from extensive crop fields, exposing seeds to sequential submergence and drained treatments in combination with cues that promote germination. While a 10°C difference between maximum and minimum daily temperatures maximised germination in drained conditions, higher amplitudes (>15°C) alternating temperatures promoted E. colona underwater germination under hypoxic water (pO2 <4.1kPa). KNO3 osmopriming in drained conditions promoted later underwater germination even under hypoxic water; however, PEG 6000 osmopriming induced seeds to enter secondary dormancy inhibiting underwater germination. KNO3 improved E. colona underwater germination under air-equilibrated floodwater (pO2 : 16.5-17.4kPa) yet not under hypoxic conditions. This suggests that germination can proceed in flooded nitrate-fertile soils as long as it remains aerobic. Hypoxic submergence did not inhibit the induction of hypersensitivity to light in E. colona seeds. This research expands our understanding of wetland seed germination ecophysiology, shedding light on the inducible nature of underwater germination in hydrophyte weeds.

Impact of varying light spectral compositions on photosynthesis, morphology, chloroplast ultrastructure, and expression of light-responsive genes in Marchantia polymorpha

Marchantia polymorpha is a convenient model for studying light of different spectral compositions on various physiological and biochemical processes because its photoreceptor system is vastly simplified. The influence of red light (RL, 660 nm), far-red light (FRL, 730 nm), blue light (BL, 450 nm), and green light (GL, 525 nm) compared to white light (high-pressure sodium light (HPSL), white LEDs (WL 450 + 580 nm) and white fluorescent light (WFL) on photosynthetic and transpiration rates, photosystem II (PSII) activity, photomorphogenesis, and the expression of light and hormonal signaling genes was studied. The ultrastructure of the chloroplasts in different tissues of the gametophyte M. polymorpha was examined. FRL led to the formation of agranal chloroplasts (in the epidermis and the chlorenchyma) with a high starch content (in the parenchyma), which led to a reduced intensity of photosynthesis. BL increased the transcription of genes for the biosynthesis of secondary metabolites - chalcone synthase (CHS), cellulose synthase (CELL), and L-ascorbate peroxidase (APOX3), which is consistent with the increased activity of low-molecular weight antioxidants. FRL increased the expression of phytochrome apoprotein (PHY) and cytokinin oxidase (CYTox) genes, but the expression of the phytochrome interacting factor (PIF) gene decreased, which was accompanied by a significant change in gametophyte morphology. Analysis of crosstalk gene expression, and changes in morphology and photosynthetic activity was carried out.

Reconstitution of phytochrome A-mediated light modulation of the ABA signaling pathways in yeast

Abscisic acid (ABA), a classical plant hormone, plays an essential role in plant adaptation to environmental stresses. The ABA signaling mechanisms have been extensively investigated, and it was shown that the PYR1 (PYRABACTIN RESISTANCE1)/PYL (PYR1-LIKE)/RCAR (REGULATORY COMPONENT OF ABA RECEPTOR) ABA receptors, the PP2C coreceptors, and the SnRK2 protein kinases constitute the core ABA signaling module responsible for ABA perception and initiation of downstream responses. We recently showed that ABA signaling is modulated by light signals, but the underlying molecular mechanisms remain largely obscure. In this study, we established a system in yeast cells that was not only successful in reconstituting a complete ABA signaling pathway, from hormone perception to ABA-responsive gene expression, but also suitable for functionally characterizing the regulatory roles of additional factors of ABA signaling. Using this system, we analyzed the roles of several light signaling components, including the red and far-red light photoreceptors phytochrome A (phyA) and phyB, and the photomorphogenic central repressor COP1, in the regulation of ABA signaling. Our results showed that both phyA and phyB negatively regulated ABA signaling, whereas COP1 positively regulated ABA signaling in yeast cells. Further analyses showed that photoactivated phyA interacted with the ABA coreceptors ABI1 and ABI2 to decrease their interactions with the ABA receptor PYR1. Together, data from our reconstituted yeast ABA signaling system provide evidence that photoactivated photoreceptors attenuate ABA signaling by directly interacting with the key components of the core ABA signaling module, thus conferring enhanced ABA tolerance to light-grown plants.

Temperature perception by plants

Plants constantly face fluctuating ambient temperatures and must adapt to survive under stressful conditions. Temperature affects many aspects of plant growth and development through a complex network of transcriptional responses. Although temperature sensing is a crucial primary step in initiating transcriptional responses via Ca2+ and/or reactive oxygen species signaling, an understanding of how plants perceive temperature has remained elusive. However, recent studies have yielded breakthroughs in our understanding of temperature sensors and thermosensation mechanisms. We review recent findings on potential temperature sensors and emerging thermosensation mechanisms, including biomolecular condensate formation through phase separation in plants. We also compare the temperature perception mechanisms of plants with those of other organisms to provide insights into understanding temperature sensing by plants.

Bilirubin is produced nonenzymatically in plants to maintain chloroplast redox status

Bilirubin, a potent antioxidant, is a product of heme catabolism in heterotrophs. Heterotrophs mitigate oxidative stress resulting from free heme by catabolism into bilirubin via biliverdin. Although plants also convert heme to biliverdin, they are generally thought to be incapable of producing bilirubin because they lack biliverdin reductase, the enzyme responsible for bilirubin biosynthesis in heterotrophs. Here, we demonstrate that bilirubin is produced in plant chloroplasts. Live-cell imaging using the bilirubin-dependent fluorescent protein UnaG revealed that bilirubin accumulated in chloroplasts. In vitro, bilirubin was produced nonenzymatically through a reaction between biliverdin and reduced form of nicotinamide adenine dinucleotide phosphate at concentrations comparable to those in chloroplasts. In addition, increased bilirubin production led to lower reactive oxygen species levels in chloroplasts. Our data refute the generally accepted pathway of heme degradation in plants and suggest that bilirubin contributes to the maintenance of redox status in chloroplasts.

Influence of a phyA Mutation on Polyamine Metabolism in Arabidopsis Depends on Light Spectral Conditions

The aim of the study was to reveal the influence of phyA mutations on polyamine metabolism in Arabidopsis under different spectral compositions. Polyamine metabolism was also provoked with exogenous spermine. The polyamine metabolism-related gene expression of the wild type and phyA plants responded similarly under white and far-red light conditions but not at blue light. Blue light influences rather the synthesis side, while far red had more pronounced effects on the catabolism and back-conversion of the polyamines. The observed changes under elevated far-red light were less dependent on PhyA than the blue light responses. The polyamine contents were similar under all light conditions in the two genotypes without spermine application, suggesting that a stable polyamine pool is important for normal plant growth conditions even under different spectral conditions. However, after spermine treatment, the blue regime had more similar effects on synthesis/catabolism and back-conversion to the white light than the far-red light conditions. The additive effects of differences observed on the synthesis, back-conversion and catabolism side of metabolism may be responsible for the similar putrescine content pattern under all light conditions, even in the presence of an excess of spermine. Our results demonstrated that both light spectrum and phyA mutation influence polyamine metabolism.

Arabidopsis phytochromes A and B synergistically repress SPA1 under blue light

In Arabidopsis, although studies have demonstrated that phytochrome A (phyA) and phyB are involved in blue light signaling, how blue light-activated phytochromes modulate the activity of the CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)-SUPPRESSOR OF PHYA-105 (SPA1) E3 complex remains largely unknown. Here, we show that phyA responds to early and weak blue light, whereas phyB responds to sustainable and strong blue light. Activation of both phyA and phyB by blue light inhibits SPA1 activity. Specifically, blue light irradiation promoted the nuclear import of both phytochromes to stimulate their binding to SPA1, abolishing SPA1's interaction with LONG HYPOCOTYL 5 (HY5) to release HY5, which promoted seedling photomorphogenesis.

Global Analysis of Dark- and Heat-Regulated Alternative Splicing in Arabidopsis

Alternative splicing (AS) is one of the major post-transcriptional regulation mechanisms that contributes to plant responses to various environmental perturbations. Darkness and heat are two common abiotic factors affecting plant growth, yet the involvement and regulation of AS in the plant responses to these signals remain insufficiently examined. In this study, we subjected Arabidopsis seedlings to 6 h of darkness or heat stress and analyzed their transcriptome through short-read RNA sequencing. We revealed that both treatments altered the transcription and AS of a subset of genes yet with different mechanisms. Dark-regulated AS events were found enriched in photosynthesis and light signaling pathways, while heat-regulated AS events were enriched in responses to abiotic stresses but not in heat-responsive genes, which responded primarily through transcriptional regulation. The AS of splicing-related genes (SRGs) was susceptible to both treatments; while dark treatment mostly regulated the AS of these genes, heat had a strong effect on both their transcription and AS. PCR analysis showed that the AS of the Serine/Arginine-rich family gene SR30 was reversely regulated by dark and heat, and heat induced the upregulation of multiple minor SR30 isoforms with intron retention. Our results suggest that AS participates in plant responses to these two abiotic signals and reveal the regulation of splicing regulators during these processes.

Regulation of Plant Photoresponses by Protein Kinase Activity of Phytochrome A

Extensive research has been conducted for decades to elucidate the molecular and regulatory mechanisms for phytochrome-mediated light signaling in plants. As a result, tens of downstream signaling components that physically interact with phytochromes are identified, among which negative transcription factors for photomorphogenesis, PHYTOCHROME-INTERACTING FACTORs (PIFs), are well known to be regulated by phytochromes. In addition, phytochromes are also shown to inactivate an important E3 ligase complex consisting of CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSORs OF phyA-105 (SPAs). This inactivation induces the accumulation of positive transcription factors for plant photomorphogenesis, such as ELONGATED HYPOCOTYL 5 (HY5). Although many downstream components of phytochrome signaling have been studied thus far, it is not fully elucidated which intrinsic activity of phytochromes is necessary for the regulation of these components. It should be noted that phytochromes are autophosphorylating protein kinases. Recently, the protein kinase activity of phytochrome A (phyA) has shown to be important for its function in plant light signaling using Avena sativa phyA mutants with reduced or increased kinase activity. In this review, we highlight the function of phyA as a protein kinase to explain the regulation of plant photoresponses by phyA.

Light and temperature regulate m6A-RNA modification to regulate growth in plants

N6-methyladenosine is a highly dynamic, abundant mRNA modification which is an excellent potential mechanism for fine tuning gene expression. Plants adapt to their surrounding light and temperature environment using complex gene regulatory networks. The role of m6A in controlling gene expression in response to variable environmental conditions has so far been unexplored. Here, we map the transcriptome-wide m6A landscape under various light and temperature environments. Identified m6A-modifications show a highly specific spatial distribution along transcripts with enrichment occurring in 5'UTR regions and around transcriptional end sites. We show that the position of m6A modifications on transcripts might influence cellular transcript localization and the presence of m6A-modifications is associated with alternative polyadenylation, a process which results in multiple RNA isoforms with varying 3'UTR lengths. RNA with m6A-modifications exhibit a higher preference for shorter 3'UTRs. These shorter 3'UTR regions might directly influence transcript abundance and localization by including or excluding cis-regulatory elements. We propose that environmental stimuli might change the m6A landscape of plants as one possible way of fine tuning gene regulation through alternative polyadenylation and transcript localization.

Plants Utilize Suberin Biopolymers as a Vector for Transmitting Visible Light through Their Roots

Plants conduct light from their aboveground tissues belowground to their root system. This phenomenon may influence root growth and perhaps serve to stimulate natural biological functions of the microorganisms associating with them. Here we show that light transmission in maize roots largely occurs within the endodermis, a region rich in suberin polyester biopolymers. Using cork as a natural resource rich in suberin polymers, we extracted, depolymerized, and examined light transmission in the visible and infrared regions. Suberin co-monomers dissolved in toluene showed no evidence of enhanced light transmission over that of the pure solvent in the visible light region and reduced light transmission in the infrared region. However, when these co-monomers were catalytically repolymerized using Bi(OTf)₃, light transmission through suspended polymers significantly increased 1.3-fold in the visible light region over that in pure toluene, but was reduced in the infrared region.

Phytochrome B enhances seed germination tolerance to high temperature by reducing S-nitrosylation of HFR1

Light and ambient high temperature (HT) have opposite effects on seed germination. Light induces seed germination through activating the photoreceptor phytochrome B (phyB), resulting in the stabilization of the transcription factor HFR1, which in turn sequesters the suppressor PIF1. HT suppresses seed germination and triggers protein S-nitrosylation. Here, we find that HT suppresses seed germination by inducing the S-nitrosylation of HFR1 at C164, resulting in its degradation, the release of PIF1, and the activation of PIF1-targeted SOMNUS (SOM) expression to alter gibberellin (GA) and abscisic acid (ABA) metabolism. Active phyB (phyBY276H ) antagonizes HFR1 S-nitrosylation and degradation by increasing S-nitrosoglutathione reductase (GSNOR) activity. In line with this, substituting cysteine-164 of HFR1 with serine (HFR1C164S ) abolishes the S-nitrosylation of HFR1 and decreases the HT-induced degradation of HFR1. Taken together, our study suggests that HT and phyB antagonistically modulate the S-nitrosylation level of HFR1 to coordinate seed germination, and provides the possibility to enhance seed thermotolerance through gene-editing of HFR1.

Molecular basis of nitrogen starvation-induced leaf senescence

Nitrogen (N), a macronutrient, is often a limiting factor in plant growth, development, and productivity. To adapt to N-deficient environments, plants have developed elaborate N starvation responses. Under N-deficient conditions, older leaves exhibit yellowing, owing to the degradation of proteins and chlorophyll pigments in chloroplasts and subsequent N remobilization from older leaves to younger leaves and developing organs to sustain plant growth and productivity. In recent years, numerous studies have been conducted on N starvation-induced leaf senescence as one of the representative plant responses to N deficiency, revealing that leaf senescence induced by N deficiency is highly complex and intricately regulated at different levels, including transcriptional, post-transcriptional, post-translational and metabolic levels, by multiple genes and proteins. This review summarizes the current knowledge of the molecular mechanisms associated with N starvation-induced leaf senescence.

TIME FOR COFFEE regulates phytochrome A-mediated hypocotyl growth through dawn-phased signaling

To enhance plant fitness under natural conditions, the circadian clock is synchronized and entrained by light via photoreceptors. In turn, the circadian clock exquisitely regulates the abundance and activity of photoreceptors via largely uncharacterized mechanisms. Here we show that the clock regulator TIME FOR COFFEE (TIC) controls the activity of the far-red light photoreceptor phytochrome A (phyA) at multiple levels in Arabidopsis thaliana. Null mutants of TIC displayed dramatically increased sensitivity to light irradiation with respect to hypocotyl growth, especially to far-red light. RNA-sequencing demonstrated that TIC and phyA play largely opposing roles in controlling light-regulated gene expression at dawn. Additionally, TIC physically interacts with the transcriptional repressor TOPLESS (TPL), which was associated with the significantly increased PHYA transcript levels in the tic-2 and tpl-1 mutants. Moreover, TIC interacts with phyA in the nucleus, thereby affecting phyA protein turnover and the formation of phyA nuclear speckles following light irradiation. Genetically, phyA was found to act downstream of TIC in regulating far red light-inhibited growth. Taken together, these findings indicate that TIC acts as a major negative regulator of phyA by integrating transcriptional and post-translational mechanisms at multiple levels.

Effects of different photoperiods on flower opening, flower closing and circadian expression of clock-related genes in Iris domestica and I. dichotoma

The circadian clock can entrain to forced light-dark cycles by adjusting the phases and periods of flower opening and closing in ephemeral flowers. The responses of circadian rhythms to the same light conditions differ from species. However, the differences in internal genetic mechanisms underlying the different responses between species remain unclear. Iris domestica and I. dichotoma have ephemeral flowers and significantly divergent flower opening and closing times. The effects of different photoperiods (continuous darkness, 4L20D, 8L16D, 12L12D, 16L8D, 20L4D and continuous white light) on flower opening and closing, and expression patterns of seven genes (CRYPTOCHROME 1, PHYTOCHROME B, LATE ELONGATED HYPOCOTYL, PSEUDO RESPONSE REGULATOR 95, PHYTOCHROME INTERACTING FACTOR 4-like, SMUX AUXIN UP RNA 64-like and senescence-associated gene 39-like) involved in the circadian regulation of flower opening and closing were compared between I. domestica and I. dichotoma. Flower opening and closing in the two species exhibited circadian rhythms under continuous darkness (DD), but showed arrhythmia in continuous white light (LL). In the two species, keeping robust rhythms, strong synchronicity, rapid progressions of flower opening and closing and reaching full opening stage required a dark period longer than 4 h. In light-dark cycles with dark periods longer than 4 h, flower opening and closing times of the two species delayed with the delay of dawn, and the degree to which flower opening time varies with the time of dawn was greater in I. dichotoma than in I. domestica. The arrhythmia of flower opening and closing under 20L4D and LL would result from the arrhythmic output signals rather than arrhythmia of oscillators and photoreceptors. The different responses of the two species to the change of photoperiods would be caused by the transcriptional differences of genes in the output pathway of circadian clock system rather than in the input pathway or oscillators.

Phytochrome B Positively Regulates Red Light-Mediated ER Stress Response in Arabidopsis

Light plays a crucial role in plant growth and development, and light signaling is integrated with various stress responses to adapt to different environmental changes. During this process, excessive protein synthesis overwhelms the protein-folding ability of the endoplasmic reticulum (ER), causing ER stress. Although crosstalk between light signaling and ER stress response has been reported in plants, the molecular mechanisms underlying this crosstalk are poorly understood. Here, we demonstrate that the photoreceptor phytochrome B (phyB) induces the expression of ER luminal protein chaperones as well as that of unfolded protein response (UPR) genes. The phyB-5 mutant was less sensitive to tunicamycin (TM)-induced ER stress than were the wild-type plants, whereas phyB-overexpressing plants displayed a more sensitive phenotype under white light conditions. ER stress response genes (BiP2 and BiP3), UPR-related bZIP transcription factors (bZIP17, bZIP28, and bZIP60), and programmed cell death (PCD)-associated genes (OXI1, NRP1, and MC8) were upregulated in phyB-overexpressing plants, but not in phyB-5, under ER stress conditions. The ER stress-sensitive phenotype of phyB-5 under red light conditions was eliminated with a reduction in photo-equilibrium by far-red light and darkness. The N-terminal domain of phyB is essential for signal transduction of the ER stress response in the nucleus, which is similar to light signaling. Taken together, our results suggest that phyB integrates light signaling with the UPR to relieve ER stress and maintain proper plant growth.

Guard-cell phytochromes impact seedling photomorphogenesis and rosette leaf morphology

Using a previously established transgenic approach to inactivate phytochrome chromophore synthesis in specific organs or tissues, we used a guard cell-specific promoter to induce phytochrome deficiencies in guard cells of Arabidopsis thaliana. Analyses of multiple homozygous lines depleted of phytochromes in stomatal guard cells indicated elongated hypocotyls specifically in red and far-red growth conditions. Furthermore, rosette leaves of adult plants with guard cell-specific phytochrome deficiencies showed enhanced serration compared to the wild-type Col-0 parent. Thus, we demonstrate that guard cell-localized phytochromes impact the inhibition of hypocotyl elongation, as well as leaf margin morphology of adult rosette leaves in A. thaliana.

Light-dependent activation of HY5 promotes mycorrhizal symbiosis in tomato by systemically regulating strigolactone biosynthesis

Light quality affects mutualisms between plant roots and arbuscular mycorrhizal fungi (AMFs), which modify nutrient acquisition in plants. However, the mechanisms by which light systemically modulates root colonization by AMFs and phosphate uptake in roots remain unclear. We used a range of approaches, including grafting techniques, protein immunoblot analysis, electrophoretic mobility shift assay, chromatin immunoprecipitation, and dual-luciferase assays, to unveil the molecular basis of light signal transmission from shoot to root that mediates arbuscule development and phosphate uptake in tomato. The results show that shoot phytochrome B (phyB) triggers shoot-derived mobile ELONGATED HYPOCOTYL5 (HY5) protein accumulation in roots, and HY5 further positively regulates transcription of strigolactone (SL) synthetic genes, thus forming a shoot phyB-dependent systemic signaling pathway that regulates the synthesis and accumulation of SLs in roots. Further experiments with carotenoid cleavage dioxygenase 7 mutants and supplementary red light confirm that SLs are indispensable in the red-light-regulated mycorrhizal symbiosis in roots. Our results reveal a phyB-HY5-SLs systemic signaling cascade that facilitates mycorrhizal symbiosis and phosphate utilization in plants. The findings provide new prospects for the potential application of AMFs and light manipulation to effectively improve nutrient utilization and minimize the use of chemical fertilizers and associated pollution.

Mutual upregulation of HY5 and TZP in mediating phytochrome A signaling

Phytochrome A (phyA) is the far-red (FR) light photoreceptor in plants that is essential for seedling de-etiolation under FR-rich environments, such as canopy shade. TANDEM ZINC-FINGER/PLUS3 (TZP) was recently identified as a key component of phyA signal transduction in Arabidopsis thaliana; however, how TZP is integrated into the phyA signaling networks remains largely obscure. Here, we demonstrate that ELONGATED HYPOCOTYL5 (HY5), a well-characterized transcription factor promoting photomorphogenesis, mediates FR light induction of TZP expression by directly binding to a G-box motif in the TZP promoter. Furthermore, TZP physically interacts with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), an E3 ubiquitin ligase targeting HY5 for 26S proteasome-mediated degradation, and this interaction inhibits COP1 interaction with HY5. Consistent with those results, TZP post-translationally promotes HY5 protein stability in FR light, and in turn, TZP protein itself is destabilized by COP1 in both dark and FR light conditions. Moreover, tzp hy5 double mutants display an additive phenotype relative to their respective single mutants under high FR light intensities, indicating that TZP and HY5 also function in largely independent pathways. Together, our data demonstrate that HY5 and TZP mutually upregulate each other in transmitting the FR light signal, thus providing insights into the complicated but delicate control of phyA signaling networks.

Analysis of Phytochrome-Dependent Seed Germination in Arabidopsis

Light-dependent seed germination guarantees seedling proximity to the soil surface, enabling quick photosynthetic energy supply. While seedling hypocotyl length is mainly used in phytochrome physiological assays to determine the functional impact of photoreceptor point mutations, different intracellular localizations, or the function of signal transduction components, phytochrome-controlled seed germination offers a different, very sensitive tool to test the phytochrome photoreceptor network. Photon fluences as low as 1 nmol m^-2 are sufficient to elicit the phytochrome A (phyA)-dependent very low fluence response (VLFR), whereas higher fluences (> 10 μmol m^-2) are needed to elicit the phyB-controlled and phyB-photoreversible low fluence response (LFR). Taking advantage of the different sensitivities of both phytochromes to different light qualities and quantities, a screening protocol is presented to score germination under different light conditions.

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

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

SUMOylation of different targets fine-tunes phytochrome signaling

Plants monitor their surrounding ambient light environment by specialized photoreceptor proteins. Among them, phytochromes monitor red and far-red light. These molecules perceive photons, undergo a conformational change, and regulate diverse light signaling pathways, resulting in the mediation of key developmental and growth responses throughout the whole life of plants. Posttranslational modifications of the photoreceptors and their signaling partners may modify their function. For example, the regulatory role of phosphorylation has been investigated for decades by using different methodological approaches. In the past few years, a set of studies revealed that ubiquitin-like short protein molecules, called small ubiquitin-like modifiers (SUMOs) are attached reversibly to different members of phytochrome signaling pathways, including phytochrome B, the dominant receptor of red light signaling. Furthermore, SUMO attachment modifies the action of the target proteins, leading to altered light signaling and photomorphogenesis. This review summarizes recent results regarding SUMOylation of various target proteins, the regulation of their SUMOylation level, and the physiological consequences of SUMO attachment. Potential future research directions are also discussed.

Protein Kinase Activity of Phytochrome A Positively Correlates With Photoresponses in Arabidopsis

Plant phytochromes are known as autophosphorylating serine/threonine protein kinases. However, the functional importance of their kinase activity is not fully elucidated. Previously, the kinase activity is shown to be necessary for the function of Avena sativa phytochrome A (AsphyA) using transgenic plants with mutants displaying reduced kinase activity, such as K411L and T418D. In this study, we isolated and analyzed two AsphyA mutants, K411R and T418V, that showed increased kinase activity. Transgenic phyA-201 plants with these mutants showed hypersensitive responses to far-red (FR) light, such as shorter hypocotyls and more expanded cotyledons than those of control plant (i.e., transgenic phyA-201 plant with wild-type AsphyA). Contrary to the mutants with reduced kinase activity, these mutants accelerated FR-induced phosphorylation and subsequent degradation of phytochrome-interacting factor 3 (PIF3) in Arabidopsis. Moreover, elongated hypocotyl 5 (HY5), a critical positive regulator of photoresponses in plants, accumulated in higher amounts in the transgenic plants under FR light than in the control plant. In addition, PIF1 degradation was accelerated in the transgenic plants. Consequently, the transgenic plants exhibit higher germination frequencies than the control plant. Collectively, our results demonstrate that the AsphyA mutants with increased kinase activity are hyperactive in plants, supporting a positive relationship between the kinase activity of phytochromes and photoresponses in plants.

Differing biophysical properties underpin the unique signaling potentials within the plant phytochrome photoreceptor families

Many aspects of photoperception by plants and microorganisms are initiated by the phytochrome (Phy) family of photoreceptors that detect light through interconversion between red light- (Pr) and far-red light-absorbing (Pfr) states. Plants synthesize a small family of Phy isoforms (PhyA to PhyE) that collectively regulate photomorphogenesis and temperature perception through redundant and unique actions. While the selective roles of these isoforms have been partially attributed to their differing abundances, expression patterns, affinities for downstream partners, and turnover rates, we show here from analysis of recombinant Arabidopsis chromoproteins that the Phy isoforms also display distinct biophysical properties. Included are a hypsochromic shift in the Pr absorption for PhyC and varying rates of Pfr to Pr thermal reversion, part of which can be attributed to the core photosensory module in each. Most strikingly, PhyB combines strong temperature dependence of thermal reversion with an order-of-magnitude faster rate to likely serve as the main physiological thermosensor, whereby thermal reversion competes with photoconversion. In addition, comparisons of Pfr occupancies for PhyA and PhyB under a range of red- and white-light fluence rates imply that low-light environments are effectively sensed by PhyA, while high-light environments, such as full sun, are effectively sensed by PhyB. Parallel analyses of the Phy isoforms from potato and maize showed that the unique features within the Arabidopsis family are conserved, thus indicating that the distinct biophysical properties among plant Phy isoforms emerged early in Phy evolution, likely to enable full interrogation of their light and temperature environments.

Improving the Predictive Value of Phytochrome Photoequilibrium: Consideration of Spectral Distortion Within a Leaf

The ratio of active phytochrome (Pfr) to total phytochrome (Pr + Pfr), called phytochrome photo-equilibrium (PPE; also called phytochrome photostationary state, PSS) has been used to explain shade avoidance responses in both natural and controlled environments. PPE is commonly estimated using measurements of the spectral photon distribution (SPD) above the canopy and photoconversion coefficients. This approach has effectively predicted morphological responses when only red and far-red (FR) photon fluxes have varied, but controlled environment research often utilizes unique ratios of wavelengths so a more rigorous evaluation of the predictive ability of PPE on morphology is warranted. Estimations of PPE have rarely incorporated the optical effects of spectral distortion within a leaf caused by pigment absorbance and photon scattering. We studied stem elongation rate in the model plant cucumber under diverse spectral backgrounds over a range of one to 45% FR (total photon flux density, 400-750 nm, of 400 μmol m^-2 s^-1) and found that PPE was not predictive when blue and green varied. Preferential absorption of red and blue photons by chlorophyll results in an SPD that is relatively enriched in green and FR at the phytochrome molecule within a cell. This can be described by spectral distortion functions for specific layers of a leaf. Multiplying the photoconversion coefficients by these distortion functions yields photoconversion weighting factors that predict phytochrome conversion at the site of photon perception within leaf tissue. Incorporating spectral distortion improved the predictive value of PPE when phytochrome was assumed to be homogeneously distributed within the whole leaf. In a supporting study, the herbicide norflurazon was used to remove chlorophyll in seedlings. Using distortion functions unique to either green or white cotyledons, we came to the same conclusions as with whole plants in the longer-term study. Leaves of most species have similar spectral absorbance so this approach for predicting PPE should be broadly applicable. We provide a table of the photoconversion weighting factors. Our analysis indicates that the simple, intuitive ratio of FR (700-750 nm) to total photon flux (far-red fraction) is also a reliable predictor of morphological responses like stem length.

The phyB-dependent induction of HY5 promotes iron uptake by systemically activating FER expression

Iron (Fe) deficiency affects global crop productivity and human health. However, the role of light signaling in plant Fe uptake remains uncharacterized. Here, we find that light-induced Fe uptake in tomato (Solanum lycopersicum L.) is largely dependent on phytochrome B (phyB). Light induces the phyB-dependent accumulation of ELONGATED HYPOCOTYL 5 (HY5) protein both in the leaves and roots. HY5 movement from shoots to roots activates the expression of FER transcription factor, leading to the accumulation of transcripts involved in Fe uptake. Mutation in FER abolishes the light quality-induced changes in Fe uptake. The low Fe uptake observed in phyB, hy5, and fer mutants is accompanied by lower photosynthetic electron transport rates. Exposure to red light at night increases Fe accumulation in wild-type fruit but has little effects on fruit of phyB mutants. Taken together, these results demonstrate that Fe uptake is systemically regulated by light in a phyB-HY5-FER-dependent manner. These findings provide new insights how the manipulation of light quality could be used to improve Fe uptake and hence the nutritional quality of crops.

Light signalling shapes plant-plant interactions in dense canopies

Plants growing at high densities interact via a multitude of pathways. Here, we provide an overview of mechanisms and functional consequences of plant architectural responses initiated by light cues that occur in dense vegetation. We will review the current state of knowledge about shade avoidance, as well as its possible applications. On an individual level, plants perceive neighbour-associated changes in light quality and quantity mainly with phytochromes for red and far-red light and cryptochromes and phototropins for blue light. Downstream of these photoreceptors, elaborate signalling and integration takes place with the PHYTOCHROME INTERACTING FACTORS, several hormones and other regulators. This signalling leads to the shade avoidance responses, consisting of hyponasty, stem and petiole elongation, apical dominance and life cycle adjustments. Architectural changes of the individual plant have consequences for the plant community, affecting canopy structure, species composition and population fitness. In this context, we highlight the ecological, evolutionary and agricultural importance of shade avoidance.

Light-Mediated Regulation of Leaf Senescence

Light is the primary regulator of various biological processes during the plant life cycle. Although plants utilize photosynthetically active radiation to generate chemical energy, they possess several photoreceptors that perceive light of specific wavelengths and then induce wavelength-specific responses. Light is also one of the key determinants of the initiation of leaf senescence, the last stage of leaf development. As the leaf photosynthetic activity decreases during the senescence phase, chloroplasts generate a variety of light-mediated retrograde signals to alter the expression of nuclear genes. On the other hand, phytochrome B (phyB)-mediated red-light signaling inhibits the initiation of leaf senescence by repressing the phytochrome interacting factor (PIF)-mediated transcriptional regulatory network involved in leaf senescence. In recent years, significant progress has been made in the field of leaf senescence to elucidate the role of light in the regulation of nuclear gene expression at the molecular level during the senescence phase. This review presents a summary of the current knowledge of the molecular mechanisms underlying light-mediated regulation of leaf senescence.

Carotenoid Biosynthesis and Plastid Development in Plants: The Role of Light

Light is an important cue that stimulates both plastid development and biosynthesis of carotenoids in plants. During photomorphogenesis or de-etiolation, photoreceptors are activated and molecular factors for carotenoid and chlorophyll biosynthesis are induced thereof. In fruits, light is absorbed by chloroplasts in the early stages of ripening, which allows a gradual synthesis of carotenoids in the peel and pulp with the onset of chromoplasts' development. In roots, only a fraction of light reaches this tissue, which is not required for carotenoid synthesis, but it is essential for root development. When exposed to light, roots start greening due to chloroplast development. However, the colored taproot of carrot grown underground presents a high carotenoid accumulation together with chromoplast development, similar to citrus fruits during ripening. Interestingly, total carotenoid levels decrease in carrots roots when illuminated and develop chloroplasts, similar to normal roots exposed to light. The recent findings of the effect of light quality upon the induction of molecular factors involved in carotenoid synthesis in leaves, fruit, and roots are discussed, aiming to propose consensus mechanisms in order to contribute to the understanding of carotenoid synthesis regulation by light in plants.

Molecular pathways regulating elongation of aerial plant organs: a focus on light, the circadian clock, and temperature

Organs such as hypocotyls and petioles rapidly elongate in response to shade and temperature cues, contributing to adaptive responses that improve plant fitness. Growth plasticity in these organs is achieved through a complex network of molecular signals. Besides conveying information from the environment, this signaling network also transduces internal signals, such as those associated with the circadian clock. A number of studies performed in Arabidopsis hypocotyls, and to a lesser degree in petioles, have been informative for understanding the signaling networks that regulate elongation of aerial plant organs. In particular, substantial progress has been made towards understanding the molecular mechanisms that regulate responses to light, the circadian clock, and temperature. Signals derived from these three stimuli converge on the BAP module, a set of three different types of transcription factors that interdependently promote gene transcription and growth. Additional key positive regulators of growth that are also affected by environmental cues include the CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSOR OF PHYA-105 (SPA) E3 ubiquitin ligase proteins. In this review we summarize the key signaling pathways that regulate the growth of hypocotyls and petioles, focusing specifically on molecular mechanisms important for transducing signals derived from light, the circadian clock, and temperature. While it is clear that similarities abound between the signaling networks at play in these two organs, there are also important differences between the mechanisms regulating growth in hypocotyls and petioles.

Arabidopsis ROOT PHOTOTROPISM2 Is a Light-Dependent Dynamic Modulator of Phototropin1

The Arabidopsis (Arabidopsis thaliana) blue light photoreceptor phototropin1 (phot1) is a blue light-activated Ser/Thr protein kinase that mediates various light responses, including phototropism. The function of phot1 in hypocotyl phototropism is dependent on the light induction of ROOT PHOTOTROPISM2 (RPT2) proteins within a broad range of blue light intensities. It is not yet known however how RPT2 contributes to the photosensory adaptation of phot1 to high intensity blue light and the phototropic responses under bright light conditions. We show that RPT2 suppresses the activity of phot1 and demonstrate that RPT2 binds to the PHOT1 light, oxygen or voltage sensing1 (LOV1) domain that is required for its high photosensitivity. Our biochemical analyses revealed that RPT2 inhibits autophosphorylation of phot1, suggesting that it suppresses the photosensitivity and/or kinase activity of phot1 through the inhibition of LOV1 function. We found that RPT2 proteins are degraded via a ubiquitin-proteasome pathway when phot1 is inactive and are stabilized under blue light in a phot1-dependent manner. We propose that RPT2 is a molecular rheostat that maintains a moderate activation level of phot1 under any light intensity conditions.

Coordinated Shoot and Root Responses to Light Signaling in Arabidopsis

Light is one of the most important environmental signals and regulates many biological processes in plants. Studies on light-regulated development have mainly focused on aspects of shoot growth, such as de-etiolation, cotyledon opening, inhibition of hypocotyl elongation, flowering, and anthocyanin accumulation. However, recent studies have demonstrated that light is also involved in regulating root growth and development in Arabidopsis. In this review, we summarize the progress in understanding how shoots and roots coordinate their responses to light through different light-signaling components and pathways, including the COP1 (CONSTITUTIVELY PHOTOMORPHOGENIC 1), HY5 (ELONGATED HYPOCOTYL 5), and MYB73/MYB77 (MYB DOMAIN PROTEIN 73/77) pathways.

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.

Thermal Reversion of Plant Phytochromes

Phytochromes are red/far-red reversible photoreceptors essential for plant growth and development. Phytochrome signaling is mediated by the physiologically active far-red-absorbing Pfr form that can be inactivated to the red-absorbing Pr ground state by light-dependent photoconversion or by light-independent thermal reversion, also termed dark reversion. Although the term "dark reversion" is justified by historical reasons and frequently used in the literature, "thermal reversion" more appropriately describes the process of light-independent but temperature-regulated Pfr relaxation that not only occurs in darkness but also in light and is used throughout the review. Thermal reversion is a critical parameter for the light sensitivity of phytochrome-mediated responses and has been studied for decades, often resulting in contradictory findings. Thermal reversion is an intrinsic property of the phytochrome molecules but can be modulated by intra- and intermolecular interactions, as well as biochemical modifications, such as phosphorylation. In this review, we outline the research history of phytochrome thermal reversion, highlighting important predictions that have been made before knowing the molecular basis. We further summarize and discuss recent findings about the molecular mechanisms regulating phytochrome thermal reversion and its functional roles in light and temperature sensing in plants.

Nuclear-encoded sigma factor 6 (SIG6) is involved in the block of greening response in Arabidopsis thaliana

PREMISE

Light is critical in the ability of plants to accumulate chlorophyll. When exposed to far-red (FR) light and then grown in white light in the absence of sucrose, wild-type seedlings fail to green in a response known as the FR block of greening (BOG). This response is controlled by phytochrome A through repression of protochlorophyllide reductase-encoding (POR) genes by FR light coupled with irreversible plastid damage. Sigma (SIG) factors are nuclear-encoded proteins that contribute to plant greening and plastid development through regulating gene transcription in chloroplasts and impacting retrograde signaling from the plastid to nucleus. SIGs are regulated by phytochromes, and the expression of some SIG factors is reduced in phytochrome mutant lines, including phyA. Given the association of phyA with the FR BOG and its regulation of SIG factors, we investigated the potential regulatory role of SIG factors in the FR BOG response.

METHODS

We examined FR BOG responses in sig mutants, phytochrome-deficient lines, and mutant lines for several phy-associated factors. We quantified chlorophyll levels and examined expression of key BOG-associated genes.

RESULTS

Among six sig mutants, only the sig6 mutant significantly accumulated chlorophyll after FR BOG treatment, similar to the phyA mutant. SIG6 appears to control protochlorophyllide accumulation by contributing to the regulation of tetrapyrrole biosynthesis associated with glutamyl-tRNA reductase (HEMA1) function, select phytochrome-interacting factor genes (PIF4 and PIF6), and PENTA1, which regulates PORA mRNA translation after FR exposure.

CONCLUSIONS

Regulation of SIG6 plays a significant role in plant responses to FR exposure during the BOG response.

Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants

Phytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.

Light regulates hydrogen sulfide signalling during skoto- and photo-morphogenesis in foxtail millet

Signal transduction mediated by photoreceptors regulates many physiological processes during plant growth and development including seed germination, flowering and photosynthesis, which are also regulated by hydrogen sulfide (H2S). However, studies of the connection between the vital environmental factors - light and the significant endogenous gasotransmitter - H2S, is lacking. Here, the seedlings of foxtail millet were used to reveal the mechanism of light regulation in H2S generation. Results showed that seedling hypocotyl elongation was promoted by H2S, but inhibited by HA under dark or white light condition. H2S contents in hypocotyl increased at first under red, blue or white light then decreased, and the duration of increase under white light was longer than under red or blue light. The activity of cysteine desulfhydrases, which catalyse H2S generation, was increased by red light but decreased by blue and white light. The expressions of cysteine desulfhydrases coding genes LCD1 and LCD2 were promoted by red or white light, but inhibited by blue light. In contrast, DES gene was promoted by white light but inhibited by red or blue light. In addition, the activities of LCDs were regulated by the phosphorylation mediated by photoreceptors PHYB and CRY1/CRY2. Finally, there are two pathways of light regulating H2S production, including a rapid process that involves the modification of phosphorylation on LCDs protein mediated by photoreceptors directly or indirectly, as well as a slower process that involves in regulating the expressions of LCDs and DES genes. This discovery has potential value for the application of H2S in agricultural production protecting the crops from unsuited light condition.

Comparative transcription analysis of photosensitive and non-photosensitive eggplants to identify genes involved in dark regulated anthocyanin synthesis

BACKGROUND

Light is a key environmental factor in regulation of anthocyanin biosynthesis. Through a large number of bagging screenings, we obtained non-photosensitive eggplants that still have decent amount of anthocyanin synthesized after bagging. In the present study, transcriptome was made to explore the molecular mechanism of dark-regulated anthocyanin synthesis in non-photosensitive eggplant.

RESULTS

The transcriptome of the pericarp at 0 h, 0.5 h, 4 h, and 8 h after bag removal were sequenced and analyzed. Comparison of the sequencing data with those of photosensitive eggplant for the same time period showed that anthocyanin synthesis genes had different expression trends. Based on the expression trends of the structural genes, it was discovered that 22 transcription factors and 4 light signal transduction elements may be involved in the anthocyanin synthesis in two types of eggplants. Through transcription factor target gene prediction and yeast one-hybrid assay, SmBIM1, SmAP2, SmHD, SmMYB94, SmMYB19, SmTT8, SmYABBY, SmTTG2, and SmMYC2 were identified to be directly or indirectly bound to the promoter of the structural gene SmCHS. These results indicate that the identified 9 genes participated in the anthocyanin synthesis in eggplant peel and formed a network of interactions among themselves.

CONCLUSIONS

Based on the comparative transcription, the identified 22 transcription factors and 4 light signal transduction elements may act as the key factors in dark regulated anthocyanin synthesis in non-photosensitive eggplant. The results provided a step stone for further analysis of the molecular mechanism of dark-regulated anthocyanin synthesis in non-photosensitive eggplant.

Red And far-red regulation of filament movement correlates with the expression of phytochrome and FHY1 genes in Spirogyra varians (Zygnematales, Streptophyta)1

Spirogyra filaments show unique photomovement that differs in response to blue, red, and far-red light. Phototropins involved in the blue-light movement have been characterized together with downstream signaling components, but the photoreceptors and mechanical effectors of red- and far-red light movement are not yet characterized. The filaments of Spirogyra varians slowly bent and aggregated to form a tangled mass in red light. In far-red light, the filaments unbent, stretched rapidly, and separated from each other. Mannitol and/or sorbitol treatment significantly inhibited this far-red light movement suggesting that turgor pressure is the driving force of this movement. The bending and aggregating movements of filaments in red light were not affected by osmotic change. Three phytochrome homologues isolated from S. varians showed unique phylogenetic characteristics. Two canonical phytochromes, named SvPHY1 and SvPHY2, and a noncanonical phytochrome named SvPHYX2. SvPHY1 is the first PHY1 family phytochrome reported in zygnematalean algae. The gene involved in the transport of phytochromes into the nucleus was characterized, and its expression in response to red and far-red light was measured using quantitative PCR. Our results suggest that the phytochromes and the genes involved in the transport system into the nucleus are well conserved in S. varians.

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.

Phytochrome A Regulates Carbon Flux in Dark Grown Tomato Seedlings

Phytochromes comprise a small family of photoreceptors with which plants gather environmental information that they use to make developmental decisions, from germination to photomorphogenesis to fruit development. Most phytochromes are activated by red light and de-activated by far-red light, but phytochrome A (phyA) is responsive to both and plays an important role during the well-studied transition of seedlings from dark to light growth. The role of phytochromes during skotomorphogenesis (dark development) prior to reaching light, however, has received considerably less attention although previous studies have suggested that phytochrome must play a role even in the dark. We profiled proteomic and transcriptomic seedling responses in tomato during the transition from dark to light growth and found that phyA participates in the regulation of carbon flux through major primary metabolic pathways, such as glycolysis, beta-oxidation, and the tricarboxylic acid (TCA) cycle. Additionally, phyA is involved in the attenuation of root growth soon after reaching light, possibly via control of sucrose allocation throughout the seedling by fine-tuning the expression levels of several sucrose transporters of the SWEET gene family even before the seedling reaches the light. Presumably, by participating in the control of major metabolic pathways, phyA sets the stage for photomorphogenesis for the dark grown seedling in anticipation of light.