Phytochromes and light signal perception by plants--an emerging synthesis

Analogies and Differences in the Photoactivation Mechanism of Bathy and Canonical Bacteriophytochromes Revealed by Multiscale Modeling

Bacteriophytochromes are light-sensing biological machines that switch between two photoreversible states, Pr and Pfr. Their relative stability is opposite in canonical and bathy bacteriophytochromes, but in both cases the switch between them is triggered by the photoisomerization of an embedded bilin chromophore. We applied an integrated multiscale strategy of excited-state QM/MM nonadiabatic dynamics and (QM/)MM molecular dynamics simulations with enhanced sampling techniques to the Agrobacterium fabrum bathy phytochrome and compared the results with those obtained for the canonical phytochrome Deinococcus radiodurans. Contrary to what recently suggested, we found that photoactivation in both phytochromes is triggered by the same hula-twist motion of the bilin chromophore. However, only in the bathy phytochrome, the bilin reaches the final rotated structure already in the first intermediate. This allows a reorientation of the binding pocket in a microsecond time scale, which can propagate through the entire protein causing the spine to tilt.

The PHYB-FOF2-VOZ2 module functions to fine-tune flowering in response to changes in light quality by modulating FLC expression in Arabidopsis

Proper timing of flowering under different environmental conditions is critical for plant propagation. Light quality is a pivotal environmental cue that plays a critical role in flowering regulation. Plants tend to flower late under light with a high red (R)/far-red (FR) light ratio but early under light with a low R/FR light ratio. However, how plants fine-tune flowering in response to changes in light quality is not well understood. Here, we demonstrate that F-box of Flowering 2 (FOF2), an autonomous pathway-related regulator, physically interacts with VASCULAR PLANT ONE-ZINC FINGER 1 and 2 (VOZ1 and VOZ2), which are direct downstream factors of the R/FR light receptor phytochrome B (PHYB). We show that PHYB physically interacts with FOF2, mediates stabilization of the FOF2 protein under FR light and end-of-day FR light, and enhances FOF2 binding to VOZ2, which leads to degradation of VOZ2 by SCFFOF2 E3 ligase. By contrast, PHYB mediates degradation of FOF2 protein under R light and end-of-day R light. Genetic interaction studies demonstrated that FOF2 functions downstream of PHYB to promote FLC expression and inhibit flowering under both high R/FR light and simulated shade conditions, processes that are partially dependent on VOZ proteins. Taken together, our findings suggest a novel mechanism whereby plants fine-tune flowering time through a PHYB-FOF2-VOZ2 module that modulates FLC expression in response to changes in light quality.

Deciphering the dual role of persistent luminescence materials: Toxicity and photoreception effects on rice development

Studies on the toxicity of micro- and nanomaterials in plants have primarily focused on their intrinsic effects. However, there is often oversight when considering the potential perceptual responses that plants may exhibit in response to these materials. In this investigation, we assessed the impact of three commercially available persistent luminescence materials (PLMs) that emit red, green, or blue light under various environmental conditions. We subjected rice (Oryza sativa L.), a short-day plant, to nine distinct treatments, including exposure to particles in isolation, their nocturnal afterglow, or a combination of both. We thoroughly examined rice seedling morphology, photosynthesis patterns, metabolite dynamics, and flowering gene expression to determine the biological responses of plants to these particles. These findings demonstrated that PLMs stably interact with rice, and their emitted afterglow precisely matches the perceptual bandwidth of rice photoreceptors. Notably, the nocturnal afterglow from the red and blue PLMs enhanced the vegetative growth of rice seedlings while inhibiting their reproductive development. The blue PLMs exhibited the most pronounced positive effects, while the red PLMs exhibited inhibitory effects. When exposed to a combination of red and blue PLMs, rice displays enhanced growth and development. The observed alterations in the expression patterns of genes responsible for flowering supported these effects. We concluded that PLMs influence rice growth and development due to their inherent properties and intermittent illumination during dark periods. Both factors collectively shape rice growth and development.

Study on the photosynthetic growth characters in Cimicifuga dahurica (Turcz.) Maxim under different supplemental light environments

Cimicifuga dahurica (C. dahurica) is an important medicinal plant in the northern region of China. The best supplemental light environment helps plant growth, development, and metabolism. In this study, we used two-year-old seedlings as experimental materials. The white light as the control (CK). The different ratios of red (R) and blue (B) combined light were supplemented (T1, 2R: 1B, 255.37 μmol m-2·s-1; T2, 3R: 1B, 279.69 μmol m-2·s-1; T3, 7R: 1B, 211.16 μmol m-2·s-1). The growth characteristics, photosynthetic pigment content, photosynthesis and chlorophyll fluorescence parameters, and primary metabolite content were studied in seedlings. The results showed that: 1) The fresh weight from shoot, root, and total fresh weight were significantly (P < 0.05) increased under T2 and T3 treatment. 2) The contents of chlorophyll a (Chl a), chlorophyll b (Chl b), and total chlorophyll (Chl) were significantly (P < 0.05) increased under T2 treatment, and carotenoid (car) content was reduced. 3) The photochemical quenching (qP), the actual photosynthetic efficiency of PSII (Y(II)), and the photosynthetic electron transfer rate (ETR) from leaves were significantly (P < 0.05) increased under T1 treatment. The Net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO2 concentration (Ci), and transpiration rate (Tr) were significantly (P < 0.05) increased under T2 and T3 treatments. 4) A total of 52 primary metabolites were detected in C. dahurica leaves. Compared with CK, 14, 15, and 18 differential metabolites were screened under T1, T2, and T3 treatments. In addition, D-xylose, D-glucose, glycerol, glycolic acid, and succinic acid were significantly (P < 0.05) accumulated under the T2 treatment, which could regulate the TCA cycle metabolism pathway. The correlation analysis suggested that plant growth was promoted by regulating the change of D-mannose content in galactinol metabolism and amino sugar and nucleotide sugar metabolism. In summary, the growth of C. dahurica was improved under T2 treatment.

Photoreversible Aggregation of the Biliprotein Containing the First and Second GAF Domains of a Cyanobacteriochrome All2699 in Nostoc sp. PCC7120

As plant photoreceptors, phytochromes are capable of detecting red light and far-red light, thereby governing plant growth. All2699 is a photoreceptor found in Nostoc sp. PCC7120 that specifically responds to red light and far-red light. All2699g1g2 is a truncated protein carrying the first and second GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) domains of All2699. In this study, we found that, upon exposure to red light, the protein underwent aggregation, resulting in the formation of protein aggregates. Conversely, under far-red light irradiation, these protein aggregates dissociated. We delved into the factors that impact the aggregation of All2699g1g2, focusing on the protein structure. Our findings showed that the GAF2 domain contains a low-complexity (LC) loop region, which plays a crucial role in mediating protein aggregation. Specifically, phenylalanine at position 239 within the LC loop region was identified as a key site for the aggregation process. Furthermore, our research revealed that various factors, including irradiation time, temperature, concentration, NaCl concentration, and pH value, can impact the aggregation of All2699g1g2. The aggregation led to variations in Pfr concentration depending on temperature, NaCl concentration, and pH value. In contrast, ΔLC did not aggregate and therefore lacked responses to these factors. Consequently, the LC loop region of All2699g1g2 extended and enhanced sensory properties.

Conformational Effects on the Absorption Spectra of Phytochromes

Bacteriophytochrome is a photoreceptor protein that contains the biliverdin (BV) chromophore as its active component. The spectra of BV upon mutation remain remarkably unchanged, as far as spectral positions are concerned. This points toward the minimal effect of electrostatic effects on the electronic structure of the chromophore. However, the relative intensities of the Q and Soret bands of the chromophore change dramatically upon mutation. In this work, we delve into the molecular origin of this unusual intensity modulation. Using extensive classical MD and QM/MM calculations, we show that due to mutation, the conformational population of the chromophore changes significantly. The noncovalent interactions, especially the stacking interactions, lead to extra stabilization of the cyclic form in the D207H mutated species as opposed to the open form in the wild-type BV. Thus, unlike the commonly observed direct electrostatic effect on the spectral shift, in the case of BV the difference observed is in varying intensities, and this in turn is driven by a conformational shift due to enhanced stacking interaction.

The mechanism of low blue light-induced leaf senescence mediated by GmCRY1s in soybean

Leaf senescence is a crucial trait that has a significant impact on crop quality and yield. Previous studies have demonstrated that light is a key factor in modulating the senescence process. However, the precise mechanism by which plants sense light and control senescence remains largely unknown, particularly in crop species. In this study, we reveal that the reduction in blue light under shading conditions can efficiently induce leaf senescence in soybean. The blue light receptors GmCRY1s rather than GmCRY2s, primarily regulate leaf senescence in response to blue light signals. Our results show that GmCRY1s interact with DELLA proteins under light-activated conditions, stabilizing them and consequently suppressing the transcription of GmWRKY100 to delay senescence. Conversely, LBL reduces the interaction between GmCRY1s and the DELLA proteins, leading to their degradation and premature senescence of leaves. Our findings suggest a GmCRY1s-GmDELLAs-GmWRKY100 regulatory cascade that is involved in mediating LBL-induced leaf senescence in soybean, providing insight into the mechanism of how light signals regulate leaf senescence. Additionally, we generate GmWRKY100 knockout soybeans that show delayed leaf senescence and improved yield under natural field conditions, indicating potential applications in enhancing soybean production by manipulating the leaf senescence trait.

The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype

Through developmental plasticity, an individual organism integrates influences from its immediate environment with those due to the environment of its parents. While both effects on phenotypes are well documented, their relative impact has been little studied in natural systems, especially at the level of gene expression. We examined this issue in four genotypes of the annual plant Persicaria maculosa by varying two key resources-light and soil moisture-in both generations. Transcriptomic analyses showed that the relative effects of parent and offspring environment on gene expression (i.e. the number of differentially expressed transcripts, DETs) varied both for the two types of resource stress and among genotypes. For light, immediate environment induced more DETs than parental environment for all genotypes, although the precise proportion of parental versus immediate DETs varied among genotypes. By contrast, the relative effect of soil moisture varied dramatically among genotypes, from 8-fold more DETs due to parental than immediate conditions to 10-fold fewer. These findings provide evidence at the transcriptomic level that the relative impacts of parental and immediate environment on the developing organism may depend on the environmental factor and vary strongly among genotypes, providing potential for the interplay of these developmental influences to evolve.

Supplementary White, UV-A, and Far-Red Radiation Differentially Regulates Growth and Nutritional Qualities of Greenhouse Lettuce

Light is a crucial environmental signal and a form of photosynthetic energy for plant growth, development, and nutrient formation. To explore the effects of light quality on the growth and nutritional qualities of greenhouse-grown lettuce (Lactuca sativa L.), lettuce was cultivated under supplementary white (W) light-emitting diodes (LEDs); white plus ultraviolet A LEDs (W+UV); white plus far-red LEDs (W+FR); and the combination of white, far-red, and UV-A LEDs (W+FR+UV) for 25 days, with lettuce grown under natural sunlight used as the control. The results indicate that the leaf length and leaf width values for lettuce grown under the W+FR+UV treatment were significantly higher than those of lettuce grown under other supplementary light treatments. The highest values of shoot fresh weight, shoot dry weight, root fresh weight, and root dry weight were recorded under the W+FR treatment (4.0, 6.0, 8.0, and 12.4 times higher than those under the control treatment, respectively). Lettuce grown under the W+FR treatment exhibited the highest total chlorophyll content (39.1%, 24.6%, and 16.2% higher than that under the W, W+UV, and W+FR+UV treatments, respectively). The carotenoid content of lettuce grown under the W+FR treatment was the highest among all treatments. However, the root activity of greenhouse-grown lettuce was the highest under the W+FR+UV treatment. Soluble sugar content, cellulose content, and starch content in the lettuce responded differently to the light treatments and were highest under the W+UV treatment. In summary, supplementary light promoted growth and nutrient accumulation in lettuce. Specifically, white plus far-red light promoted lettuce growth, and white plus UV increased some specific compounds in greenhouse-grown lettuce. Our findings provide valuable references for the application of light-supplementation strategies to greenhouse lettuce production.

Phosphors Ba2 LaTaO6 :Mn4+ and its alkali metal charge compensation for plant growth illumination

A series of Mn4+ -doped and Mn4+ ,K+ -co-doped Ba2 LaTaO6 (BLT) double-perovskite phosphors was synthesized using a high-temperature solid-state reaction. The phase purity and luminescence properties were also studied. The optimum doping concentration of Mn4+ and K+ was obtained by investigating the photoluminescence excitation spectra and photoluminescence emission spectra. The comparison of BLT:Mn4+ phosphors with and without K+ ions shows that the photoluminescence intensity of K+ -doped phosphors was greatly enhanced. This is because there was a charge difference when Mn4+ ions were doped with Ta5+ ions in BLT. Mn4+ -K+ ion pairs were formed after doping K+ ions, which hinders the nonradiative energy transfer between Mn4+ ions. Therefore, the luminescence intensity, quantum yield, and thermal stability of phosphors were enhanced. The electroluminescence spectra of BLT:Mn4+ and BLT:Mn4+ ,K+ were measured. The spectra showed that the light emitted from the phosphors corresponded well with chlorophyll a and phytochrome PR . The results show that the BLT:Mn4+ ,K+ phosphors had good luminescence properties and application prospects and are ideal materials for plant-illuminated red phosphors.

Shading contributes to Sphagnum decline in response to warming

Experimental warming of an ombrotrophic bog in northern Minnesota has caused a rapid decline in the productivity and areal cover of Sphagnum mosses, affecting whole-ecosystem carbon balance and biogeochemistry. Direct effects of elevated temperature and the attendant drying are most likely the primary cause of the effects on Sphagnum, but there may also be responses to the increased shading from shrubs, which increased with increasing temperature. To evaluate the independent effects of reduction in light availability and deposition of shrub litter on Sphagnum productivity, small plots with shrubs removed were laid out adjacent to the warming experiment on hummocks and hollows in three blocks and with five levels of shading. Four plots were covered with neutral density shade cloth to simulate shading from shrubs of 30%-90% reduction in light; one plot was left open. Growth of Sphagnum angustifolium/fallax and S. divinum declined linearly with increasing shade in hollows, but there was no response to shade on hummocks, where higher irradiance in the open plots may have been inhibitory. Shading caused etiolation of Sphagnum-they were thin and spindly under the deepest shade. A dense mat of shrub litter, corresponding to the amount of shrub litter produced in response to warming, did not inhibit Sphagnum growth or cause increases in potentially toxic base cations. CO2 exchange and chlorophyll-a fluorescence of S. angustifolium/fallax from the 30% and 90% shade cloth plots were measured in the laboratory. Light response curves indicate that maximal light saturated photosynthesis was 42% greater for S. angustifolium/fallax grown under 30% shade cloth relative to plants grown under 90% shade cloth. The response of Sphagnum growth in response to increasing shade is consistent with the hypothesis that increased shade resulting from shrub expansion in response to experimental warming contributed to reduced Sphagnum growth.

Blue Light Enhances Health-Promoting Sulforaphane Accumulation in Broccoli (Brassica oleracea var. italica) Sprouts through Inhibiting Salicylic Acid Synthesis

As a vegetable with high nutritional value, broccoli (Brassica oleracea var. italica) is rich in vitamins, antioxidants and anti-cancer compounds. Glucosinolates (GLs) are one of the important functional components widely found in cruciferous vegetables, and their hydrolysate sulforaphane (SFN) plays a key function in the anti-cancer process. Herein, we revealed that blue light significantly induced the SFN content in broccoli sprouts, and salicylic acid (SA) was involved in this process. We investigated the molecular mechanisms of SFN accumulation with blue light treatment in broccoli sprouts and the relationship between SFN and SA. The results showed that the SFN accumulation in broccoli sprouts was significantly increased under blue light illumination, and the expression of SFN synthesis-related genes was particularly up-regulated by SA under blue light. Moreover, blue light considerably decreased the SA content compared with white light, and this decrease was more suppressed by paclobutrazol (Pac, an inhibitor of SA synthesis). In addition, the transcript level of SFN synthesis-related genes and the activity of myrosinase (MYR) paralleled the trend of SFN accumulation under blue light treatment. Overall, we concluded that SA participates in the SFN accumulation in broccoli sprouts under blue light.

Functions of Plant Phytochrome Signaling Pathways in Adaptation to Diverse Stresses

Phytochromes are receptors for red light (R)/far-red light (FR), which are not only involved in regulating the growth and development of plants but also in mediated resistance to various stresses. Studies have revealed that phytochrome signaling pathways play a crucial role in enabling plants to cope with abiotic stresses such as high/low temperatures, drought, high-intensity light, and salinity. Phytochromes and their components in light signaling pathways can also respond to biotic stresses caused by insect pests and microbial pathogens, thereby inducing plant resistance against them. Given that, this paper reviews recent advances in understanding the mechanisms of action of phytochromes in plant resistance to adversity and discusses the importance of modulating the genes involved in phytochrome signaling pathways to coordinate plant growth, development, and stress responses.

Flowering and fruit-set in cassava under extended red-light photoperiod supplemented with plant-growth regulators and pruning

BACKGROUND

Cassava (Manihot esculenta Crantz) is staple food and major source of calories for over 500 million people in sub-Saharan Africa. The crop is also a source of income for smallholder farmers, and has increasing potential for industrial utilization. However, breeding efforts to match the increasing demand of cassava are impeded by its inability to flower, delayed or unsynchronized flowering, low proportion of female flowers and high fruit abortions. To overcome these sexual reproductive bottlenecks, this study investigated the effectiveness of using red lights to extend the photoperiod (RLE), as a gateway to enhancing flowering and fruit set under field conditions.

MATERIALS AND METHODS

Panels of cassava genotypes, with non- or late and early flowering response, 10 in each case, were subjected to RLE from dusk to dawn. RLE was further evaluated at low (LL), medium (ML) and high (HL) red light intensities, at ~  ≤ 0.5; 1.0 and 1.5PFD (Photon Flux Density) in µmol m^-2 s^-1 respectively. Additionally, the effect of a cytokinin and anti-ethylene as plant growth regulators (PGR) and pruning under RLE treatment were examined.

RESULTS

RLE stimulated earlier flower initiation in all genotypes, by up to 2 months in the late-flowering genotypes. Height and number of nodes at first branching, particularly in the late-flowering genotypes were also reduced, by over 50%. Number and proportion of pistillate flowers more than doubled, while number of fruits and seeds also increased. Number of branching levels during the crop season also increased by about three. Earlier flowering in many genotypes was most elicited at LL to ML intensities. Additive effects on flower numbers were detected between RLE, PGR and pruning applications. PGR and pruning treatments further increased number and proportion of pistillate flowers and fruits. Plants subjected to PGR and pruning, developed bisexual flowers and exhibited feminization of staminate flowers. Pruning at first branching resulted in higher pistillate flower induction than at second branching.

CONCLUSIONS

These results indicate that RLE improves flowering in cassava, and its effectiveness is enhanced when PGR and pruning are applied. Thus, deployment of these technologies in breeding programs could significantly enhance cassava hybridizations and thus cassava breeding efficiency and impact.

Integrative Analysis of Transcriptome, Proteome, and Phosphoproteome Reveals Potential Roles of Photosynthesis Antenna Proteins in Response to Brassinosteroids Signaling in Maize

Brassinosteroids are a recently discovered group of substances that promote plant growth and productivity. Photosynthesis, which is vital for plant growth and high productivity, is strongly influenced by brassinosteroid signaling. However, the molecular mechanism underlying the photosynthetic response to brassinosteroid signaling in maize remains obscure. Here, we performed integrated transcriptome, proteome, and phosphoproteomic analyses to identify the key photosynthesis pathway that responds to brassinosteroid signaling. Transcriptome analysis suggested that photosynthesis antenna proteins and carotenoid biosynthesis, plant hormone signal transduction, and MAPK signaling in CK VS EBR and CK VS Brz were significantly enriched in the list of differentially expressed genes upon brassinosteroids treatment. Consistently, proteome and phosphoproteomic analyses indicated that photosynthesis antenna and photosynthesis proteins were significantly enriched in the list of differentially expressed proteins. Thus, transcriptome, proteome, and phosphoproteome analyses showed that major genes and proteins related to photosynthesis antenna proteins were upregulated by brassinosteroids treatment in a dose-dependent manner. Meanwhile, 42 and 186 transcription factor (TF) responses to brassinosteroid signals in maize leaves were identified in the CK VS EBR and CK VS Brz groups, respectively. Our study provides valuable information for a better understanding of the molecular mechanism underlying the photosynthetic response to brassinosteroid signaling in maize.

Sr/Ba substitution induced higher thermal stability far red-emitting Ba1-ySryLaLiWO6:Mn4+ phosphors for plant growth applications

A series of red-emitting BaLaLiWO₆:Mn⁴⁺ (BLLW:Mn⁴⁺) phosphors were successfully synthesized by a high-temperature solid-state reaction method. The crystal structure and luminescence properties of the obtained samples were systematically investigated. The emission spectra exhibited a deep red emission band peaking at 716 nm with a full width at half-maximum (FWHM) of 44 nm under 340 nm excitation. The optimal Mn⁴⁺ molar concentration was about 1.2%. In addition, the luminescence mechanism was analyzed using a Tanabe Sugano energy level diagram. With the substitution of Sr for Ba, there was a red shift in the emission spectrum and a blue shift in the excitation spectrum. The emission intensity of BLLW:1.2%Mn⁴⁺ at 150 °C was about 22% of the initial value at room temperature. In contrast, the emission intensity of SrLaLiWO₆:1.2%Mn⁴⁺ still maintained 79% of the initial emission intensity at room temperature at 150 °C. This was due to the fact that with the substitution of Sr for Ba, the W-O bond length gradually decreases, which gradually enhanced the crystal field strength of Mn⁴⁺.

Breeding crops for drought-affected environments and improved climate resilience

Breeding climate-resilient crops with improved levels of abiotic and biotic stress resistance as a response to climate change presents both opportunities and challenges. Applying the framework of the "breeder's equation," which is used to predict the response to selection for a breeding program cycle, we review methodologies and strategies that have been used to successfully breed crops with improved levels of drought resistance, where the target population of environments (TPEs) is a spatially and temporally heterogeneous mixture of drought-affected and favorable (water-sufficient) environments. Long-term improvement of temperate maize for the US corn belt is used as a case study and compared with progress for other crops and geographies. Integration of trait information across scales, from genomes to ecosystems, is needed to accurately predict yield outcomes for genotypes within the current and future TPEs. This will require transdisciplinary teams to explore, identify, and exploit novel opportunities to accelerate breeding program outcomes; both improved germplasm resources and improved products (cultivars, hybrids, clones, and populations) that outperform and replace the products in use by farmers, in combination with modified agronomic management strategies suited to their local environments.

Parental methylation mediates how progeny respond to environments of parents and of progeny themselves

BACKGROUND AND AIMS

Environments experienced by both parents and offspring influence progeny traits, but the epigenetic mechanisms that regulate the balance of parental vs. progeny control of progeny phenotypes are not known. We tested whether DNA methylation in parents and/or progeny mediates responses to environmental cues experienced in both generations.

METHODS

Using Arabidopsis thaliana, we manipulated parental and progeny DNA methylation both chemically, via 5-azacytidine, and genetically, via mutants of methyltransferase genes, then measured progeny germination responses to simulated canopy shade in parental and progeny generations.

KEY RESULTS

We first found that germination of offspring responded to parental but not seed demethylation. We further found that parental demethylation reversed the parental effect of canopy in seeds with low (Cvi-1) to intermediate (Col) dormancy, but it obliterated the parental effect in seeds with high dormancy (Cvi-0). Demethylation did so by either suppressing germination of seeds matured under white-light (Cvi-1) or under canopy (Cvi-0), or by increasing the germination of seeds matured under canopy (Col). Disruption of parental methylation also prevented seeds from responding to their own light environment in one genotype (Cvi-0, most dormant), but it enabled seeds to respond to their own environment in another genotype (Cvi-1, least dormant). Using mutant genotypes, we found that both CG and non-CG DNA methylation were involved in parental effects on seed germination.

CONCLUSIONS

Parental methylation state influences seed germination more strongly than does the progeny's own methylation state, and it influences how seeds respond to environments of parents and progeny in a genotype-specific manner.

N6-methyladenosine RNA modification regulates photosynthesis during photodamage in plants

N⁶-methyladenosine (m⁶A) modification of mRNAs affects many biological processes. However, the function of m⁶A in plant photosynthesis remains unknown. Here, we demonstrate that m⁶A modification is crucial for photosynthesis during photodamage caused by high light stress in plants. The m⁶A modification levels of numerous photosynthesis-related transcripts are changed after high light stress. We determine that the Arabidopsis m⁶A writer VIRILIZER (VIR) positively regulates photosynthesis, as its genetic inactivation drastically lowers photosynthetic activity and photosystem protein abundance under high light conditions. The m⁶A levels of numerous photosynthesis-related transcripts decrease in vir mutants, extensively reducing their transcript and translation levels, as revealed by multi-omics analyses. We demonstrate that VIR associates with the transcripts of genes encoding proteins with functions related to photoprotection (such as HHL1, MPH1, and STN8) and their regulatory proteins (such as regulators of transcript stability and translation), promoting their m⁶A modification and maintaining their stability and translation efficiency. This study thus reveals an important mechanism for m⁶A-dependent maintenance of photosynthetic efficiency in plants under high light stress conditions.

Can plants integrate information on above-ground competition in their directional responses below ground?

BACKGROUND AND AIMS

Light competition can induce varying above-ground responses in plants. However, very little is known regarding the effect of above-ground light competition cues on plant responses below ground. Here we asked whether light competition cues that indicate the occurrence and direction of neighbours above ground might affect directional root placemat.

METHODS

In a common-garden experiment, we examined the integrated responses of the annual procumbent plant Portulaca oleracea to light competition cues and soil nutrient distribution. Soil nutrients were distributed either uniformly or in patches, and light competition was simulated using a transparent green filter, which was spatially located either in the same or opposite direction of the soil nutrient patch.

KEY RESULTS

As predicted, root proliferation of P. oleracea increased in the direction of the enriched soil patches but was homogenously distributed under the uniform nutrient distribution. Interestingly, root distribution was also affected by the light competition cue and increased in its direction regardless of the location of the soil patches.

CONCLUSIONS

Our results provide initial support to the idea that below-ground plant responses to competition might also be regulated by above-ground neighbour cues, highlighting the need to further investigate the combined effects of both above- and below-ground competition cues on root behaviour.

Protein control of photochemistry and transient intermediates in phytochromes

Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded chromophore, triggering large conformational changes in the protein. Despite numerous experimental and computational studies, the role of chromophore-protein interactions in controlling the mechanism and timescale of the process remains elusive. Here, we combine nonadiabatic surface hopping trajectories and adiabatic molecular dynamics simulations to reveal the molecular details of such control for the Deinococcus radiodurans bacteriophytochrome. Our simulations reveal that chromophore photoisomerization proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen bond of the chromophore with a close-by histidine. The resulting photoproduct relaxes to an early intermediate stabilized by a tyrosine, and finally evolves into a late intermediate, featuring a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the active state.

Morphological and physiological variation of soybean seedlings in response to shade

Soybean (Glycine max) is a legume species that is widely used in intercropping. Quantitative analyses of plasticity and genetic differences in soybean would improve the selection and breeding of soybean in intercropping. Here, we used data of 20 varieties from one year artificial shading experiment and one year intercropping experiment to characterize the morphological and physiological traits of soybean seedlings grown under shade and full sun light conditions. Our results showed that shade significantly decreased biomass, leaf area, stem diameter, fraction of dry mass in petiole, leaf mass per unit area, chlorophyll a/b ratio, net photosynthetic rate per unit area at PAR of 500 μmol m-2 s-1 and 1,200 μmol m-2 s-1 of soybean seedling, but significantly increased plant height, fraction of dry mass in stem and chlorophyll content. Light × variety interaction was significant for all measured traits, light effect contributed more than variety effect. The biomass of soybean seedlings was positively correlated with leaf area and stem diameter under both shade and full sunlight conditions, but not correlated with plant height and net photosynthetic rate. The top five (62.75% variation explained) most important explanatory variables of plasticity of biomass were that the plasticity of leaf area, leaf area ratio, leaflet area, plant height and chlorophyll content, whose total weight were 1, 0.9, 0.3, 0.2, 0.19, respectively. The plasticity of biomass was positively correlated with plasticity of leaf area and leaflet area but significant negative correlated with plasticity of plant height. The principal component one account for 42.45% variation explain. A cluster analysis further indicated that soybean cultivars were classified into three groups and cultivars; Jiandebaimaodou, Gongdou 2, and Guixia 3 with the maximum plasticity of biomass. These results suggest that for soybean seedlings grown under shade increasing the capacity for light interception by larger leaf area is more vital than light searching (plant height) and light conversion (photosynthetic rate).

Identification of microRNAs That Provide a Low Light Stress Tolerance-Mediated Signaling Pathway during Vegetative Growth in Rice

Low light intensity affects several physiological parameters during the different growth stages in rice. Plants have various regulatory mechanisms to cope with stresses. One of them is the differential and temporal expression of genes, which is governed by post-transcriptional gene expression regulation through endogenous miRNAs. To decipher low light stress-responsive miRNAs in rice, miRNA expression profiling was carried out using next-generation sequencing of low-light-tolerant (Swarnaprabha) and -sensitive (IR8) rice genotypes through Illumina sequencing. Swarnaprabha and IR8 were subjected to 25% low light treatment for one day, three days, and five days at the active tillering stage. More than 43 million raw reads and 9 million clean reads were identified in Swarnaprabha, while more than 41 million raw reads and 8.5 million clean reads were identified in IR8 after NGS. Importantly, 513 new miRNAs in rice were identified, whose targets were mostly regulated by the genes involved in photosynthesis and metabolic pathways. Additionally, 114 known miRNAs were also identified. Five novel (osa-novmiR1, osa-novmiR2, osa-novmiR3, osa-novmiR4, and osa-novmiR5) and three known (osa-miR166c-3p, osa-miR2102-3p, and osa-miR530-3p) miRNAs were selected for their expression validation through miRNA-specific qRT-PCR. The expression analyses of most of the predicted targets of corresponding miRNAs show negative regulation. Hence, miRNAs modulated the expression of genes providing tolerance/susceptibility to low light stress. This information might be useful in the improvement of crop productivity under low light stress.

Acclimation Strategy of Masson Pine (Pinus massoniana) by Limiting Flavonoid and Terpenoid Production under Low Light and Drought

Low light and drought often limit the growth and performance of Masson pines (Pinus massoniana) in the subtropical forest ecosystem of China. We speculated that stress-induced defensive secondary metabolites, such as flavonoids and terpenoids, might influence the growth of Masson pines, considering the existence of tradeoffs between growth and defense. However, the mechanisms of Masson pines responsive to low light and drought at the levels of these two metabolites remain unclear. In the present work, the compositions of flavonoids and terpenoids, as well as their biosynthetic pathways, were revealed through metabolome and transcriptome analyses, respectively, coupled with a study on carbon allocation using a ¹³CO₂-pulse-labeling experiment in two-year-old seedlings under low light (LL), drought (DR), and their combined stress (DL) compared to a control (CK). A total of 35 flavonoids and derivatives (LL vs. CK: 18; DR vs. CK: 20; and DL vs. CK: 18), as well as 29 terpenoids and derivatives (LL vs. CK: 23; DR vs. CK: 13; and DL vs. CK: 7), were differentially identified in the leaves. Surprisingly, most of them were decreased under all three stress regimes. At the transcriptomic level, most or all of the detected DEGs (differentially expressed genes) involved in the biosynthetic pathways of flavonoids and terpenoids were downregulated in phloem and xylem under stress treatments. This indicated that stress treatments limited the production of flavonoids and terpenoids. The reduction in the ¹³C allocation to stems might suggest that it is necessary for maintaining the growth of Masson pine seedlings at the whole-plant level by attenuating energetic resources to the biosynthetic pathways of flavonoids and terpenoids when facing the occurrence of adverse environments. Our results provide new insight into understanding the acclimation strategy of Masson pines or other conifers in adverse environments.

Periodicity and Spectral Composition of Light in the Regulation of Hypocotyl Elongation of Sunflower Seedlings

This study presents the hypocotyl elongation of sunflower seedlings germinated under different light conditions. Elongation was rhythmic under diurnal (LD) photoperiods but uniform (arrhythmic) under free-running conditions of white light (LL) or darkness (DD). On the sixth day after the onset of germination, seedlings were entrained in all diurnal photoperiods. Their hypocotyl elongation was dual, showing different kinetics in daytime and nighttime periods. The daytime elongation peak was around midday and 1-2 h after dusk in the nighttime. Plantlets compensated for the differences in the daytime and nighttime durations and exhibited similar overall elongation rates, centered around the uniform elongation in LL conditions. Thus, plants from diurnal photoperiods and LL could be grouped together as white-light treatments that suppressed hypocotyl elongation. Hypocotyl elongation was significantly higher under DD than under white-light photoperiods. In continuous monochromatic blue, yellow, green, or red light, hypocotyl elongation was also uniform and very high. The treatments with monochromatic light and DD had similar overall elongation rates; thus, they could be grouped together. Compared with white light, monochromatic light promoted hypocotyl elongation. Suppression of hypocotyl elongation and rhythmicity reappeared in some combination with two or more monochromatic light colors. The presence of red light was obligatory for this suppression. Plantlets entrained in diurnal photoperiods readily slipped from rhythmic into uniform elongation if they encountered any kind of free-running conditions. These transitions occurred whenever the anticipated duration of daytime or nighttime was extended more than expected, or when plantlets were exposed to constant monochromatic light. This study revealed significant differences in the development of sunflower plantlets illuminated with monochromatic or white light.

Sustainable Food Production: Innovative Netting Concepts and Their Mode of Action on Fruit Crops

Net application in agriculture has a long history. Nets were usually used for the protection of plants against different hazards (hail, wind, birds, pests, excessive sun radiation) and, lately, from insects (nets with smaller mesh size). In recent years, photoselective netting technology has emerged, which adds desired plant responses caused by light quality changes to their basic protective properties. A combination of anti-insect and photoselective net technology (anti-insect photoselective nets) may present a notable contribution to the sustainable food production concept. Notable positive effects of this eco-friendly approach on agroecosystems are mainly achievable due to its non-pesticide pest protection of cultivated plants and, at the same time, promotion of special beneficial morphological and physiological plant responses. Although netting has been extensively studied over the last decade, there is a pronounced lack of publications and analyses that deal with their mode of action on fruit trees, which is especially true for new netting concepts. A better understanding of such mechanisms can lead to improved development and/or utilization of this technology and enhanced generation of value-added products. This review was based on a revision of the literature regarding netting in agriculture, with emphasis on fruit cultivation, and the following databases were used: Web of Science, ScienceDirect, Scopus, and Google Scholar. Although this study aims to comprehend a majority of fruit species, it narrows down to those usually net-protected and, hence, studied, such as apple, peach or nectarine, kiwifruit, blueberry, etc. Nets mainly differ in their mesh size and color, which are the parameters that mostly determine their capacity for light quantity and quality modification. Such light modifications, directly or indirectly (e.g., change in microclimate), initiate different fruit tree responses (in some cases, mechanisms) through which the final effect is realized on their vegetative and generative traits. For instance, some of them include a shade avoidance mechanism (initiated by changes in red to a far-red ratio, blue light levels, etc.), source–sink relationship, and carbohydrate availability (actualized by changes in photosynthesis efficiency, vegetative and generative growth, etc.), plant stress response (actualized by microclimate changes), etc. In most cases, these responses are interconnected, which contributes to the complexity of this topic and emphasizes the importance of a better understanding of it.

The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization

Photoactivation of bacteriophytochrome involves a cis-trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the chromophore to adopt a more planar configuration, which we assign to the early Lumi-R state. The isomerization process is completed via helix inversion of the biliverdin chromophore to form the late Lumi-R state. The mechanistic insights into the photoisomerization process are essential to understand how bacteriophytochrome has evolved to mediate photoactivation and to engineer this protein for new applications.

Artificial light at night: an underappreciated effect on phenology of deciduous woody plants

Artificial light at night (ALAN), an increasing anthropogenic driver, is widespread and shows rapid expansion with potential adverse impact on the terrestrial ecosystem. However, whether and to what extent does ALAN affect plant phenology, a critical factor influencing the timing of terrestrial ecosystem processes, remains unexplored due to limited ALAN observation. Here, we used the Black Marble ALAN product and phenology observations from USA National Phenology Network to investigate the impact of ALAN on deciduous woody plants phenology in the conterminous United States. We found that (1) ALAN significantly advanced the date of breaking leaf buds by 8.9 ± 6.9 days (mean ± SD) and delayed the coloring of leaves by 6.0 ± 11.9 days on average; (2) the magnitude of phenological changes was significantly correlated with the intensity of ALAN (P < 0.001); and (3) there was an interaction between ALAN and temperature on the coloring of leaves, but not on breaking leaf buds. We further showed that under future climate warming scenarios, ALAN will accelerate the advance in breaking leaf buds but exert a more complex effect on the coloring of leaves. This study suggests intensified ALAN may have far-reaching but underappreciated consequences in disrupting key ecosystem functions and services, which requires an interdisciplinary approach to investigate. Developing lighting strategies that minimize the impact of ALAN on ecosystems, especially those embedded and surrounding major cities, is challenging but must be pursued.

INTERMEDIUM-C mediates the shade-induced bud growth arrest in barley

Tiller formation is a key agronomic determinant for grain yield in cereal crops. The modulation of this trait is controlled by transcriptional regulators and plant hormones, tightly regulated by external environmental conditions. While endogenous (genetic) and exogenous (environmental factors) triggers for tiller formation have mostly been investigated separately, it has remained elusive how they are integrated into the developmental program of this trait. The transcription factor gene INTERMEDIUM-C (INT-C), which is the barley ortholog of the maize domestication gene TEOSINTE BRANCHED1 (TB1), has a prominent role in regulating tiller bud outgrowth. Here we show that INT-C is expressed in tiller buds, required for bud growth arrest in response to shade. In contrast to wild-type plants, int-c mutant plants are impaired in their shade response and do not stop tiller production after shading. Gene expression levels of INT-C are up-regulated under light-limiting growth conditions, and down-regulated after decapitation. Transcriptome analysis of wild-type and int-c buds under control and shading conditions identified target genes of INT-C that belong to auxin and gibberellin biosynthesis and signaling pathways. Our study identifies INT-C as an integrator of the shade response into tiller formation, which is prerequisite for implementing shading responses in the breeding of cereal crops.

Improved fluorescent phytochromes for in situ imaging

Modern biology investigations on phytochromes as near-infrared fluorescent pigments pave the way for the development of new biosensors, as well as for optogenetics and in vivo imaging tools. Recently, near-infrared fluorescent proteins (NIR-FPs) engineered from biliverdin-binding bacteriophytochromes and cyanobacteriochromes, and from phycocyanobilin-binding cyanobacterial phytochromes have become promising probes for fluorescence microscopy and in vivo imaging. However, current NIR-FPs typically suffer from low fluorescence quantum yields and short fluorescence lifetimes. Here, we applied the rational approach of combining mutations known to enhance fluorescence in the cyanobacterial phytochrome Cph1 to derive a series of highly fluorescent variants with fluorescence quantum yield exceeding 15%. These variants were characterised by biochemical and spectroscopic methods, including time-resolved fluorescence spectroscopy. We show that these new NIR-FPs exhibit high fluorescence quantum yields and long fluorescence lifetimes, contributing to their bright fluorescence, and provide fluorescence lifetime imaging measurements in E.coli cells.

WRKY2 and WRKY10 regulate the circadian expression of PIF4 during the day through interactions with CCA1/LHY and phyB

WRKY transcription factors are known mostly for their function in plant defense, abiotic stress responses, senescence, seed germination, and development of the pollen, embryo, and seed. Here, we report the regulatory functions of two WRKY proteins in photomorphogenesis and PIF4 expression. PIF4 is a critical signaling hub in light, temperature, and hormonal signaling pathways. Either its expression or its accumulation peaks in the morning and afternoon. WRKY2 and WRKY10 form heterodimers and recognize their target site in the PIF4 promoter near the MYB element that is bound by CCA1 and LHY under red and blue light. WRKY2 and WRKY10 interact directly with CCA1/LHY to enhance their targeting but interact indirectly with SHB1. The two WRKY proteins also interact with phyB, and their interaction enhances the targeting of CCA1 and LHY to the PIF4 promoter. SHB1 associates with the WRKY2 and WRKY10 loci and enhances their expression in parallel with the PIF4 expression peaks. This forward regulatory loop further sustains the accumulation of the two WRKY proteins and the targeting of CCA1/LHY to the PIF4 locus. In summary, interactions of two WRKY proteins with CCA1/LHY and phyB maintain an optimal expression level of PIF4 toward noon and afternoon, which is essential to sketch the circadian pattern of PIF4 expression.

Breeding effects on canopy light attenuation in maize: a retrospective and prospective analysis

The light attenuation process within a plant canopy defines energy capture and vertical distribution of light and nitrogen (N). The vertical light distribution can be quantitatively described with the extinction coefficient (k), which associates the fraction of intercepted photosynthetically active radiation (fPARi) with the leaf area index (LAI). Lower values of k correspond to upright leaves and homogeneous vertical light distribution, increasing radiation use efficiency (RUE). Yield gains in maize (Zea mays L.) were accompanied by increases in optimum plant density and leaf erectness. Thus, the yield-driven breeding programs and management changes, such as reduced row spacing, selected a more erect leaf habit under different maize production systems (e.g., China and the USA). In this study, data from Argentina revealed that k decreased at a rate of 1.1% year-1 since 1989, regardless of plant density and in agreement with Chinese reports (1.0% year-1 since 1981). A reliable assessment of changes in k over time is critical for predicting (i) modifications in resource use efficiency (e.g. radiation, water, and N), improving estimations derived from crop simulation models; (ii) differences in productivity caused by management practices; and (iii) limitations to further exploit this trait with breeding.

WRKY transcription factors and ethylene signaling modify root growth during the shade-avoidance response

Shade-intolerant plants rapidly elongate their stems, branches, and leaf stalks to compete with neighboring vegetation, maximizing sunlight capture for photosynthesis. This rapid growth adaptation, known as the shade-avoidance response (SAR), comes at a cost: reduced biomass, crop yield, and root growth. Significant progress has been made on the mechanistic understanding of hypocotyl elongation during SAR; however, the molecular interpretation of root growth repression is not well understood. Here, we explore the mechanisms by which SAR induced by low red:far-red light restricts primary and lateral root (LR) growth. By analyzing the whole-genome transcriptome, we identified a core set of shade-induced genes in roots of Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum) seedlings grown in the shade. Abiotic and biotic stressors also induce many of these shade-induced genes and are predominantly regulated by WRKY transcription factors. Correspondingly, a majority of WRKY genes were among the shade-induced genes. Functional analysis using transgenics of these shade-induced WRKYs revealed that their role is essentially to restrict primary root and LR growth in the shade; captivatingly, they did not affect hypocotyl elongation. Similarly, we also found that ethylene hormone signaling is necessary for limiting root growth in the shade. We propose that during SAR, shade-induced WRKY26, 45, and 75, and ethylene reprogram gene expression in the root to restrict its growth and development.

Novel red color emitting Ca0.995 Mg2 (SO4 )3 :0.5Eu2+ phosphor under UV, blue and green excitation for plant growth LEDs

In the recent few years, Eu²⁺ and Mn⁴⁺ activated phosphors are widely used as potential color converters for indoor plant cultivation lighting application due to their marvellous luminescence characteristics as well as low cost. In this investigation, we are synthesized novel red color emitting Ca_(2-x) Mg₂ (SO₄ )₃ : xmol% Eu²⁺ (x = 0-1.0 mol%) phosphors via solid-state reaction method in reducing atmosphere. The PL excitation spectra of synthesized phosphors exhibited a broad excitation band with three excitation bands peaking at 349 nm, 494 nm and 554 nm. Under these excitations, emission spectra exhibits broad band in the red color region around 634 nm. The PL emission intensity were measured for different concentration of Eu²⁺ . The maximum Eu²⁺ doping concentration in Ca₂ Mg₂ (SO₄ )₃ host was observed for 0.5 mol%. According to Dexter theory, it was determined that dipole-dipole interaction is responsible for concentration quenching. The luminous red color emission of the sample was confirmed by CIE color coordinate. The results of PL excitation and emission spectrum of prepared phosphors are well-matched with excitation and emission wavelengths of phytochrome P_R . Therefore, as per the entire investigation and obtained results it was concluded that the synthesized Ca_0.995 Mg₂ (SO₄ )₃ :0.5mol%Eu²⁺ phosphor has huge potential for plant cultivation application.

Hydrogen sulfide improves tall fescue photosynthesis response to low-light stress by regulating chlorophyll and carotenoid metabolisms

Hydrogen sulfide (H₂S), as a gaseous messenger molecule, plays critical roles in signal transduction and biological modulation. In the present study, the roles of H₂S in regulating chlorophyll (Chl) and carotenoid (Car) contents to improve photosynthesis in tall fescue were investigated under low-light (LL) stress. Compared to control conditions, LL stress significantly reduced total biomass, net photosynthetic rate (P_n), maximal quantum yield of photosystem II (PSII) photochemistry (F_v/F_m), and the contents of Chl and Car. Under exogenous sodium hydrosulfide (NaHS, H₂S donor) application, these parameters were enhanced, ultimately increasing photosynthesis. Moreover, exogenous H₂S up-regulated the expression of chlorophyll biosynthesis genes while down-regulated chlorophyll degradation genes, resulting in increases in chlorophyll precursors. Components of carotenoids and expression of genes encoding biosynthesis and degradation enzymes varied similarly. Additionally, application exogenous H₂S up-regulated expression of FaDES1 and FaDCD. Thus, it enhanced L-cysteine desulfhydrase 1 (DES1, EC 4.4.1.1) and D-cysteine desulfhydrase (DCD, EC 4.4.1.15) activities leading to elevated endogenous H₂S. However, these responses were reversed by treatment with hypotaurine (HT, H₂S scavenger). These results suggested that H₂S is involved in regulating photosynthesis to improve LL tolerance via modulating Chl and Car metabolisms in tall fescue.

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.

Artificial light pollution inhibits plant phenology advance induced by climate warming

Natural photic regime has been drastically altered by the artificial night sky luminance. Despite evidence of sufficient light brightness inducing plant physiology and affecting phenology, generalization regarding effects of light pollution on plant phenology across species and locations is less clear. Meanwhile, the relative contributions and joint effects of artificial light pollution and climate change or other anthropic stressors still remain unknown. To fill this knowledge gap, we utilized in situ plant phenological observations of seven tree species during 1991-2015 in Europe, night-time light dataset and gridded temperature dataset to investigate the impacts of the artificial light pollution on spatial-temporal shifts of plant phenological phases under climatic warming. We found 70% of the observation sites were exposed to increased light pollution during 1992-2015. Among them, plant phenological phases substantially delayed at 12-39% observation sites of leaf-out, and 6-53% of flowering. We also found plant species appeared to be more sensitive to artificial light pollution, and phenology advancement was hindered more prominently and even delay phenomenon exhibited when the color level showed stronger sky brightness. Linear mixed models indicate that although temperature plays a dominant role in shifts of plant phenological phases at the spatial scale, the inhibitory effect of artificial light pollution is evident considering the interactions. To our knowledge, this study is the first to quantitatively establish the relationship between artificial light pollution and plant phenology across species and locations. Meanwhile, these findings provide a new insight into the ecological responses of plant phenology to the potential but poorly understood environmental stressors under this warmer world and call for light pollution to be accorded the equal status as other global change phenomena.

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

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

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

Plant Communication

Communication occurs when a sender emits a cue perceived by a receiver that changes the receiver's behavior. Plants perceive information regarding light, water, other nutrients, touch, herbivores, pathogens, mycorrhizae, and nitrogen-fixing bacteria. Plants also emit cues perceived by other plants, beneficial microbes, herbivores, enemies of herbivores, pollinators, and seed dispersers. Individuals responding to light cues experienced increased fitness. Evidence for benefits of responding to cues involving herbivores and pathogens is more limited. The benefits of emitting cues are also less clear, particularly for plant–plant communication. Reliance on multiple or dosage-dependent cues can reduce inappropriate responses, and plants often remember past cues. Plants have multiple needs and prioritize conflicting cues such that the risk of abiotic stress is treated as greater than that of shading, which is in turn treated as greater than that of consumption. Plants can distinguish self from nonself and kin from strangers. They can identify the species of competitor or consumer and respond appropriately. Cues involving mutualists often contain highly specific information.

Germination of small tropical seeds has distinct light quality and temperature requirements, depending on microhabitat

The coexistence of plant species in tropical rainforests is related to specific abiotic resources, varying according to the occurrence microhabitat of each species. Light quality is the main abiotic factor influencing germination of small seeds; however, studies often do not discriminate its effect from that of light irradiance. This study compared specific requirements for seed germination of ten small-seeded species, with restricted occurrence in only one of three contrasting microhabitats: forest understorey, edge of clearings and open areas. Laboratory experiments were carried out to test temperature regime (constant or fluctuating), light quality (R:FR) and light irradiance (PAR), which reproduce high and low conditions commonly found in the microhabitats. Seed germination of all species occurred between 20 and 30 °C, only seeds of open area species were able to germinate at 35 °C and no species required alternating temperatures to germinate. Irrespective of species and microhabitat, a decrease in the R:FR reduced the germination percentage; however, there were differences in the capacity to germinate at low R:FR. The values of R:FR_50% were higher for open area and edge species (0.441-0.345) than for understorey species (0.181-0.109), with few exceptions. For all species and most of the tests, germination was not influenced by PAR. Light quality is the most important light signal for germination of small seeds; irradiance has little effect. Our results suggest two distinct patterns of germination for small-seeded species: open area and edge species are light-demanding and require high R:FR to germinate, while understorey species are shade-tolerant and germinate at low R:FR. These differences are responsible for distinct microhabitat occurrence and help to explain the coexistence of species in tropical forests.

Leaf density and chemical composition explain variation in leaf mass area with spectral composition among 11 widespread forbs in a common garden

Leaf mass per area (LMA) is a key leaf functional trait correlated with plant strategies dictating morphology, physiology, and biochemistry. Although sunlight is generally accepted as a dominant factor driving LMA, the contribution of each spectral region of sunlight in shaping LMA is poorly understood. In the present study, we grew 11 widespread forb species in a common garden and dissected the traits underpinning differences in LMA, such as its morphological components (leaf density [LD] and leaf thickness [LT]), macroelement, and metabolite composition under five spectral-attenuation treatments: (1) transmitting c. 95% of the whole solar spectrum (> 280 nm), (2) attenuating ultraviolet-B radiation (UV-B), (3) attenuating both UV-A and UV-B radiation, (4) attenuating UV radiation and blue light, (5) attenuating UV radiation, blue, and green light. We found that LMA, LD, and chemical traits varied significantly across species depending on spectral treatments. LMA was significantly increased by UV-B radiation and green light, while LD was increased by UV-A but decreased by blue light. LMA positively correlated with LD across treatments but was only weakly related to LT, suggesting that LD was a better determinate of LMA for this specific treatment. Regarding leaf elemental and metabolite composition, carbon, nitrogen, and total phenolics were all positively correlated with LMA, whereas lignin, non-structural carbohydrates, and soluble sugars had negative relationships with LMA. These trends imply a tradeoff between biomass allocation to structural and metabolically functional components. In conclusion, sunlight can spectrally drive LMA mainly through modifying functional and structural support.

Constitutive Photomorphogenic 1 Enhances ER Stress Tolerance in Arabidopsis

Interaction between light signaling and stress response has been recently reported in plants. Here, we investigated the role of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a key regulator of light signaling, in endoplasmic reticulum (ER) stress response in Arabidopsis. The cop1-4 mutant Arabidopsis plants were highly sensitive to ER stress induced by treatment with tunicarmycin (Tm). Interestingly, the abundance of nuclear-localized COP1 increased under ER stress conditions. Complementation of cop1-4 mutant plants with the wild-type or variant types of COP1 revealed that the nuclear localization and dimerization of COP1 are essential for its function in plant ER stress response. Moreover, the protein amount of ELONGATED HYPOCOTYL 5 (HY5), which inhibits bZIP28 to activate the unfolded protein response (UPR), decreased under ER stress conditions in a COP1-dependent manner. Accordingly, the binding of bZIP28 to the BIP3 promoter was reduced in cop1-4 plants and increased in hy5 plants compared with the wild type. Furthermore, introduction of the hy5 mutant locus into the cop1-4 mutant background rescued its ER stress-sensitive phenotype. Altogether, our results suggest that COP1, a negative regulator of light signaling, positively controls ER stress response by partially degrading HY5 in the nucleus.

NaLaMgWO6:Mn4+/Pr3+/Bi3+ bifunctional phosphors for optical thermometer and plant growth illumination matching phytochrome PR and PFR

Phytochromes P_R and P_FR distributed in different organs of plant can effectively absorb red and far-red light, respectively. Therefore, plant growth can be controlled by changing the ratio of red light to far-red light. The emission of Pr³⁺ (transition from ³P₀→³F_2,3) and Mn⁴⁺(transition from ²E_g→⁴A_2g) is located at the red and far-red range which matches with the absorption band of P_R and P_FR, respectively. Herein, NaLaMgWO₆:Mn⁴⁺/Pr³⁺/Bi³⁺ phosphors with improving luminescence properties via Bi³⁺ doping have been successfully prepared by the sol-gel method. With the variation of temperature, the photoluminescence (PL) of Pr³⁺/Mn⁴⁺ (corresponding to P_FR/P_R) of titled phosphors can be tuned, which is very useful for controlling the plant growth. Moreover, based on the fluorescence intensity ratios (FIR) of the two activator Mn⁴⁺ and Pr³⁺, the maximum relative sensitivity was approximately 3.39%/K at 298 K. All the results indicated that the titled phosphor is a bifunctional material for plant growth illumination with high matching phytochrome (P_R and P_FR) and temperature sensing with high sensitivity.

Cyclophilins and Their Functions in Abiotic Stress and Plant-Microbe Interactions

Plants have developed a variety of mechanisms and regulatory pathways to change their gene expression profiles in response to abiotic stress conditions and plant–microbe interactions. The plant–microbe interaction can be pathogenic or beneficial. Stress conditions, both abiotic and pathogenic, negatively affect the growth, development, yield and quality of plants, which is very important for crops. In contrast, the plant–microbe interaction could be growth-promoting. One of the proteins involved in plant response to stress conditions and plant–microbe interactions is cyclophilin. Cyclophilins (CyPs), together with FK506-binding proteins (FKBPs) and parvulins, belong to a big family of proteins with peptidyl-prolyl cis-trans isomerase activity (Enzyme Commission (EC) number 5.2.1.8). Genes coding for proteins with the CyP domain are widely expressed in all organisms examined, including bacteria, fungi, animals, and plants. Their different forms can be found in the cytoplasm, endoplasmic reticulum, nucleus, chloroplast, mitochondrion and in the phloem space. They are involved in numerous processes, such as protein folding, cellular signaling, mRNA processing, protein degradation and apoptosis. In the past few years, many new functions, and molecular mechanisms for cyclophilins have been discovered. In this review, we aim to summarize recent advances in cyclophilin research to improve our understanding of their biological functions in plant defense and symbiotic plant–microbe interactions.

Response of Lignin Metabolism to Light Quality in Wheat Population

The low red/far-red (R/FR) light proportion at the base of the high-density wheat population leads to poor stem quality and increases lodging risk. We used Shannong 23 and Shannong 16 as the test materials. By setting three-light quality treatments: normal light (CK), red light (RL), and far-red light (FRL), we irradiated the base internodes of the stem with RL and FRL for 7h. Our results showed that RL irradiation enhanced stem quality, as revealed by increased breaking strength, stem diameter, wall thickness and, dry weight per unit length, and the total amount of lignin and related gene expression increased, at the same time. The composition of lignin subunits was related to the lodging resistance of wheat. The proportion of S+G subunits and H subunits played a key role in wheat lodging resistance. RL could increase the content of S subunits and G subunits and the proportion of S+G subunits, reduce the proportion of H subunits. We described here, to the best of our knowledge, the systematic study of the mechanism involved in the regulation of stem breaking strength by light quality, particularly the effect of light quality on lignin biosynthesis and its relationship with lodging resistance in wheat.

Functional convergence of growth responses to shade and warmth in Arabidopsis

Shade and warmth promote the growth of the stem, but the degree of mechanistic convergence and functional association between these responses is not clear. We analysed the quantitative impact of mutations and natural genetic variation on the hypocotyl growth responses of Arabidopsis thaliana to shade and warmth, the relationship between the abundance of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and growth stimulation by shade or warmth, the effects of both cues on the transcriptome and the consequences of warm temperature on carbon balance. Growth responses to shade and warmth showed strong genetic linkage and similar dependence on PIF4 levels. Temperature increased growth and phototropism even within a range where damage by extreme high temperatures is unlikely to occur in nature. Both cues enhanced the expression of growth-related genes and reduced the expression of photosynthetic genes. However, only warmth enhanced the expression of genes involved in responses to heat. Warm temperatures substantially increased the amount of light required to compensate for the daily carbon dioxide balance. We propose that the main ecological function of hypocotyl growth responses to warmth is to increase the access of shaded photosynthetic organs to light, which implies functional convergence with shade avoidance.

Influence of Arctic light conditions on crop production and quality

The natural light conditions above the Arctic Circle are unique in terms of annual variation creating special growth conditions for crop production. These include low solar elevations, very long daily photosynthetic light periods, midnight sun/absence of dark nights, and altered spectral distribution depending on solar elevation. All these factors are known to affect the growth and the metabolism of plants, although their influence on northern crop plants has not yet been reviewed. The ongoing global warming is especially affecting the temperature × light interactions in the Arctic, and understanding the impact on crop production and plant metabolism will be important for an Arctic contribution to global food production. Arctic light conditions have a strong influence on the timing of plant development, which together with temperature limits the number of cultivars suitable for Arctic agriculture. This review compiles information from the reports about the effects of light conditions at high latitudes on growth, biomass production, flowering and quality of the crop plants and discusses the gained knowledge and the key gaps to be addressed.

Photons from NIR LEDs can delay flowering in short-day soybean and Cannabis: Implications for phytochrome activity

Photons during the dark period delay flowering in short-day plants (SDP). Red photons applied at night convert phytochromes to the active far-red absorbing form (Pfr), leading to inhibition of flowering. Far-red photons (greater than 700 nm) re-induce flowering when applied after a pulse of red photons during the dark period. However, far-red photons at sufficiently high intensity and duration delay flowering in sensitive species. Mechanistically, this response occurs because phytochrome-red (Pr) absorbance is not zero beyond 700 nm. We applied nighttime photons from near infrared (NIR) LEDs (peak 850 nm) over a 12 h dark period. Flowering was delayed in Glycine max and Cannabis sativa (two photosensitive species) by 3 and 12 days, respectively, as the flux of photons from NIR LEDs was increased up to 83 and 116 μmol m-2 s-1. This suggests that long wavelength photons from NIR LEDs can activate phytochromes (convert Pr to Pfr) and thus alter plant development.

Anything New under the Sun? An Update on Modulation of Bioactive Compounds by Different Wavelengths in Agricultural Plants

Plants continuously rely on light as an energy source and as the driver of many processes in their lifetimes. The ability to perceive different light radiations involves several photoreceptors, which in turn activate complex signalling cascades that ultimately lead to a rearrangement in plant metabolism as an adaptation strategy towards specific light conditions. This review, after a brief summary of the structure and mode of action of the different photoreceptors, introduces the main classes of secondary metabolites and specifically focuses on the influence played by the different wavelengths on the content of these compounds in agricultural plants, because of their recognised roles as nutraceuticals.