Phytochrome-interacting factors PIF4 and PIF5 negatively regulate anthocyanin biosynthesis under red light in Arabidopsis seedlings

Effects of Supplemental Lighting on Flavonoid and Anthocyanin Biosynthesis in Strawberry Flesh Revealed via Metabolome and Transcriptome Co-Analysis

The spectral composition of light influences the biosynthesis of flavonoids in many plants. However, the detailed composition of flavonoids and anthocyanins and the molecular basis for their biosynthesis in strawberry fruits under two light-quality treatments, red light supplemented with blue light (RB) and ultraviolet B (UVB) irradiation, remain unclear. In this study, the content of flavonoids and anthocyanins was significantly increased in strawberry fruits under RB light and UVB, respectively. The content of flavonoids and anthocyanins in strawberry fruits under UVB light was dramatically higher than that in strawberry fruits irradiated with RB light, and a total of 518 metabolites were detected by means of LC-MS/MS analysis. Among them, 18 phenolic acids, 23 flavonoids, and 8 anthocyanins were differentially accumulated in the strawberry fruits irradiated with red/blue (RB) light compared to 30 phenolic acids, 46 flavonoids, and 9 anthocyanins in fruits irradiated with UVB. The major genes associated with the biosynthesis of flavonoids and anthocyanins, including structural genes and transcription factors (TFs), were differentially expressed in the strawberry fruits under RB and UVB irradiation, as determined through RNA-seq data analysis. A correlation test of transcriptome and metabolite profiling showed that the expression patterns of most genes in the biosynthesis pathway of flavonoids and anthocyanins were closely correlated with the differential accumulation of flavonoids and anthocyanins. Two TFs, bZIP (FvH4_2g36400) and AP2 (FvH4_1g21210), induced by RB and UVB irradiation, respectively, exhibited similar expression patterns to most structural genes, which were closely correlated with six and eight flavonoids, respectively. These results indicated that these two TFs regulated the biosynthesis of flavonoids and anthocyanins in strawberry fruit under RB light and UVB, respectively. These results provide a systematic and comprehensive understanding of the accumulation of flavonoids and anthocyanins and the molecular basis for their biosynthesis in strawberry fruits under RB light and UVB.

The growth, nutrient uptake and fruit quality in four strawberry cultivars under different Spectra of LED supplemental light

An experiment was conducted in a greenhouse to determine the effects of different supplemental light spectra on the growth, nutrient uptake, and fruit quality of four strawberry cultivars. The plants were grown under natural light and treated with blue (460 nm), red (660 nm), and red/blue (3:1) lights. Results showed that the "Parous" and "Camarosa" had higher fresh and dry mass of leaves, roots, and crowns compared to the "Sabrina" and "Albion". The use of artificial LED lights improved the vegetative growth of strawberry plants. All three supplemental light spectra significantly increased the early fruit yield of cultivars except for "Parous". The red/blue supplemental light spectrum also increased the fruit mass and length of the "Albion". Supplemental light increased the total chlorophyll in "Camarosa" and "Albion", as well as the total soluble solids in fruits. The "Albion" had the highest concentration of fruit anthocyanin, while the "Sabrina" had the lowest. The use of supplemental light spectra significantly increased the fruit anthocyanin concentration in all cultivars. Without supplemental light, the "Camarosa" had the lowest concentration of K and Mg, which increased to the highest concentration with the use of supplemental light spectra. All three spectra increased Fe concentration to the highest value in the "Sabrina", while only the red/blue light spectrum was effective on the "Camarosa". In conclusion, the use of supplemental light can increase the yield and fruit quality of strawberries by elevating nutrients, chlorophyll, and anthocyanin concentrations in plants.

Combined effect of an agro-industrial compost and light spectra composition on yield and phytochemical profile in mizuna and pak choi microgreens

This work aimed to evaluate the growth of two species of microgreens (mizuna and pak choi), using agro-industrial compost as growing media in two different mixes versus one hundred percent peat, under two different LED illumination spectra (LED 1 and LED 2) in a 14 h photoperiod. The experiment was carried-out for two times. Biomass yield, glucosinolates, and phenolic compounds, and nitrate (NO3-) content were analysed in leaf tissues. In both species, the highest fresh and dry biomass production was in compost:peat (50:50%) and LED 2 (Blue/Red/Far Red). In general, compost had a greater influence on nitrate content than light, but in the microgreen pak choi, the anthocyanin content was inhibited by the compost treatment. In the other hand both LED illumination had a positive effect on mizuna for glucosinolates and anthocyanins, and LED 2 also showed a positive effect on pak choi for anthocyanin. Therefore, the use of agri-food compost: peat (50:50%) with LED 2 (blue/red) lighting treatment to obtain microgreens in indoor crops is a plausible technology that provides nutritionally and phytochemically rich crops.

SlPHL1 positively modulates acid phosphatase in response to phosphate starvation by directly activating the genes SlPAP10b and SlPAP15 in tomato

Increased acid phosphatase (APase) activity is a prominent feature of tomato (Solanum lycopersicum) responses to inorganic phosphate (Pi) restriction. SlPHL1, a phosphate starvation response (PHR) transcription factor, has been identified as a positive regulator of low Pi (LP)-induced APase activity in tomato. However, the molecular mechanism underlying this regulation remains to be elucidated. Here, SlPHL1 was found to positively regulate the LP-induced expression of five potential purple acid phosphatase (PAP) genes, namely SlPAP7, SlPAP10b, SlPAP12, SlPAP15, and SlPAP17b. Furthermore, we provide evidence that SlPHL1 can stimulate transcription of these five genes by binding directly to the PHR1 binding sequence (P1BS) located on their promoters. The P1BS mutation notably weakened SlPHL1 binding to the promoters of SlPAP7, SlPAP12, and SlPAP17b but almost completely abolished SlPHL1 binding to the promoters of SlPAP10b and SlPAP15. As a result, the transcriptional activation of SlPHL1 on SlPAP10b and SlPAP15 was substantially diminished. In addition, not only did transient overexpression of either SlPAP10b or SlPAP15 in tobacco leaves increase APase activity, but overexpression of SlPAP15 in Arabidopsis and tomato also increased APase activity and promoted plant growth. Subsequently, two SPX proteins, SlSPX1 and SlSPX4, were shown to physically interact with SlPHL1. Moreover, SlSPX1 inhibited the transcriptional activation of SlPHL1 on SlPAP10b and SlPAP15 and negatively regulated the activity of APase. Taken together, these results demonstrate that SlPHL1-mediated LP signaling promotes APase activity by activating the transcription of SlPAP10b and SlPAP15, which may provide valuable insights into the mechanisms of tomato response to Pi-limited stress.

CstMYB1R1, a REVEILLE-8-like transcription factor, regulates diurnal clock-specific anthocyanin biosynthesis and response to abiotic stress in Crocus sativus L

KEY MESSAGE

CstMYB1R1 acts as a positive regulator of Crocus anthocyanin biosynthesis and abiotic stress tolerance which was experimentally demonstrated through molecular analysis and over-expression studies in Crocus and Nicotiana. Regulatory mechanics of flavonoid/anthocyanin biosynthesis in Crocus floral tissues along the diurnal clock has not been studied to date. MYB proteins represent the most dominant, functionally diverse and versatile type of plant transcription factors which regulate key metabolic and physiological processes in planta. Transcriptome analysis revealed that MYB family is the most dominant transcription factor family in C. sativus. Considering this, a MYB-related REVEILLE-8 type transcription factor, CstMYB1R1, was explored for its possible role in regulating Crocus flavonoid and anthocyanin biosynthetic pathway. CstMYB1R1 was highly expressed in Crocus floral tissues, particularly tepals and its expression was shown to peak at dawn and dusk time points. Anthocyanin accumulation also peaked at dawn and dusk and was minimum at night. Moreover, the diurnal expression pattern of CstMYB1R1 was shown to highly correlate with Crocus ANS/LDOX gene expression among the late anthocyanin pathway genes. CstMYB1R1 was shown to be nuclear localized and transcriptionally active. CstMYB1R1 over-expression in Crocus tepals enhanced anthocyanin levels and upregulated transcripts of Crocus flavonoid and anthocyanin biosynthetic pathway genes. Yeast one hybrid (Y1H) and GUS reporter assay confirmed that CstMYB1R1 interacts with the promoter of Crocus LDOX gene to directly regulate its transcription. In addition, the expression of CstMYB1R1 in Nicotiana plants significantly enhanced flavonoid and anthocyanin levels and improved their abiotic stress tolerance. The present study, thus, confirmed positive role of CstMYB1R1 in regulating Crocus anthocyanin biosynthetic pathway in a diurnal clock-specific fashion together with its involvement in the regulation of abiotic stress response.

CstPIF4 Integrates Temperature and Circadian Signals and Interacts with CstMYB16 to Repress Anthocyanins in Crocus

Crocus sativus has emerged as an important crop because it is the only commercial source of saffron that contains unique apocarotenoids. Saffron is composed of dried stigmas of Crocus flower and constitutes the most priced spice of the world. Crocus floral organs are dominated by different classes of metabolites. While stigmas are characterized by the presence of apocarotenoids, tepals are rich in flavonoids and anthocyanins. Therefore, an intricate regulatory network might play a role in allowing different compounds to dominate in different organs. Work so far done on Crocus is focussed on apocarotenoid metabolism and its regulation. There are no reports describing the regulation of flavonoids and anthocyanins in Crocus tepals. In this context, we identified an R2R3 transcription factor, CstMYB16, which resembles subgroup 4 (SG4) repressors of Arabidopsis. CstMYB16 is nuclear localized and acts as a repressor. Overexpression of CstMYB16 in Crocus downregulated anthocyanin biosynthesis. The C2/EAR motif was responsible for the repressor activity of CstMYB16. CstMYB16 binds to the promoter of the anthocyanin biosynthetic pathway gene (LDOX) and reduces its expression. CstMYB16 also physically interacts with CstPIF4, which in turn is regulated by temperature and circadian clock. Thus, CstPIF4 integrates these signals and forms a repressor complex with CstMYB16, which is involved in the negative regulation of anthocyanin biosynthesis in Crocus. Independent of CstPIF4, CstMYB16 also represses CstPAP1 expression, which is a component of the MYB-bHLH-WD40 (MBW) complex and positively controls anthocyanin biosynthesis. This is the first report on identifying and describing regulators of anthocyanin biosynthesis in Crocus.

The red/far-red light photoreceptor FvePhyB regulates tissue elongation and anthocyanin accumulation in woodland strawberry

Light is an important environmental signal that influences plant growth and development. Among the photoreceptors, phytochromes can sense red/far-red light to coordinate various biological processes. However, their functions in strawberry are not yet known. In this study, we identified an EMS mutant, named P8, in woodland strawberry (Fragaria vesca) that showed greatly increased plant height and reduced anthocyanin content. Mapping-by-sequencing revealed that the causal mutation in FvePhyB leads to premature termination of translation. The light treatment assay revealed that FvePhyB is a bona fide red/far-red light photoreceptor, as it specifically inhibits hypocotyl length under red light. Transcriptome analysis showed that the FvePhyB mutation affects the expression levels of genes involved in hormone synthesis and signaling and anthocyanin biosynthesis in petioles and fruits. The srl mutant with a longer internode is caused by a mutation in the DELLA gene FveRGA1 (Repressor of GA1) in the gibberellin pathway. We found that the P8 srl double mutant has much longer internodes than srl, suggesting a synergistic role of FvePhyB and FveRGA1 in this process. Taken together, these results demonstrate the important role of FvePhyB in regulating plant architecture and anthocyanin content in woodland strawberry.

Light regulation of the biosynthesis of phenolics, terpenoids, and alkaloids in plants

Biosynthesis of specialized metabolites (SM), including phenolics, terpenoids, and alkaloids, is stimulated by many environmental factors including light. In recent years, significant progress has been made in understanding the regulatory mechanisms involved in light-stimulated SM biosynthesis at the transcriptional, posttranscriptional, and posttranslational levels of regulation. While several excellent recent reviews have primarily focused on the impacts of general environmental factors, including light, on biosynthesis of an individual class of SM, here we highlight the regulation of three major SM biosynthesis pathways by light-responsive gene expression, microRNA regulation, and posttranslational modification of regulatory proteins. In addition, we present our future perspectives on this topic.

Combined Transcriptomic and Metabolomic Approach Revealed a Relationship between Light Control, Photoprotective Pigments, and Lipid Biosynthesis in Olives

Olive possesses excellent nutritional and economic values for its main healthy products. Among them, a high content of antioxidant compounds, balanced during the ripening process, are produced under genetic and environmental control, resulting in high variability among cultivars. The genes involved in these complex pathways are mainly known, but despite many studies which indicated the key role of light quality and quantity for the synthesis of many metabolites in plants, limited information on these topics is available in olive. We carried out a targeted gene expression profiling in three olive cultivars, Cellina di Nardò, Ruveia, and Salella, which were selected for their contrasting oleic acid and phenolic content. The -omics combined approach revealed a direct correlation between a higher expression of the main flavonoid genes and the high content of these metabolites in 'Cellina di Nardò'. Furthermore, it confirmed the key role of FAD2-2 in the linoleic acid biosynthesis. More interestingly, in all the comparisons, a co-regulation of genes involved in photoperception and circadian clock machinery suggests a key role of light in orchestrating the regulation of these pathways in olive. Therefore, the identified genes in our analyses might represent a useful tool to support olive breeding, although further investigations are needed.

Photobiotechnology for abiotic stress resilient crops: Recent advances and prospects

Massive crop failures worldwide are caused by abiotic stress. In plants, adverse environmental conditions cause extensive damage to the overall physiology and agronomic yield at various levels. Phytochromes are photosensory phosphoproteins that absorb red (R)/far red (FR) light and play critical roles in different physiological and biochemical responses to light. Considering the role of phytochrome in essential plant developmental processes, genetically manipulating its expression offers a promising approach to crop improvement. Through modulated phytochrome-mediated signalling pathways, plants can become more resistant to environmental stresses by increasing photosynthetic efficiency, antioxidant activity, and expression of genes associated with stress resistance. Plant growth and development in adverse environments can be improved by understanding the roles of phytochromes in stress tolerance characteristics. A comprehensive overview of recent findings regarding the role of phytochromes in modulating abiotic stress by discussing biochemical and molecular aspects of these mechanisms of photoreceptors is offered in this review.

PIF1, a phytochrome-interacting factor negatively regulates drought tolerance and carotenoids biosynthesis in tobacco

The phytochrome-interacting factors (PIFs) function crucially in multiple physiological processes, but the biological functions of some PIFs remain elusive in some species. Here, a PIF transcription factor NtPIF1 was cloned and characterized in tobacco (Nicotiana tabacum L.). The transcript of NtPIF1 was significantly induced by drought stress treatments, and it localized in the nuclear. Knockout of NtPIF1 by CRISPR/Cas9 system led to the improved drought tolerance of tobacco with increased osmotic adjustment, antioxidant activity, photosynthetic efficiency and decreased water loss rate. On the contrary, NtPIF1-overexpression plants displays drought-sensitive phenotypes. In addition, NtPIF1 reduced the biosynthesis of abscisic acid (ABA) and its upstream carotenoids by regulating the expression of genes involved in ABA and carotenoids biosynthetic pathway upon drought stress. Electrophoretic mobility shift and dual-luciferase assays illustrated that, NtPIF1 directly bind to the E-box elements within the promoters of NtNCED3, NtABI5, NtZDS and Ntβ-LCY to repress their transcription. Overall, these data suggested that NtPIF1 negatively regulate tobacco adaptive response to drought stress and carotenoids biosynthesis; moreover, NtPIF1 has the potential to develop drought-tolerant tobacco plants using CRISPR/Cas9 system.

Effect of light quality on polyphenol biosynthesis in three varieties of mung bean sprouts with different color seed coats

We investigated the mechanism of the effect of different light qualities on the synthesis and regulation of mung bean sprouts. Light quality acts as a signal molecule, strongly enhancing polyphenol biosynthesis in sprouts. Mung bean (Vigna radiata) sprouts are a popular sprouting vegetable all over the world and are an excellent source of polyphenols with high antioxidant activity. This study investigated the effects of light qualities on the kinetic changes and metabolic regulation mechanism of light signal-mediating polyphenols in three mung bean sprout cultivars. Experimental results showed that three light qualities significantly enhanced the contents of caffeic acid, rutin, vitexin, genistin and delphinidin 3-glucoside. Interestingly, ferulic acid and vitexin responded selectively to blue light and red light, severally. Most genes involved in polyphenol biosynthesis were activated under different light quality conditions, resulting in an overaccumulation of phenylpropanoids. Pearson correlation analysis showed that PAL, F3H, F3'H and F3'5'H expression correlated highly with rutin, whereas ANS expression paralleled anthocyanin biosynthesis. Moreover, MYB111, MYB3, MYB4, MYB1 and MYC2 were critical regulators of polyphenol biosynthesis in mung bean sprouts. These changes were likely due to the changes in the expression of the photoreceptor genes CRY-D, PHOT2, PHYE and light response genes (PIF3 and HY5). Our results provide insights into polyphenol biosynthesis in sprouts and microgreens.

Novel Roles of SPATULA in the Control of Stomata and Trichome Number, and Anthocyanin Biosynthesis

The bHLH transcription factor SPATULA (SPT) has been identified as a regulator during different stages of Arabidopsis development, including the control of leaf size. However, the mechanism via which it performs this function has not been elucidated. To better understand the role of SPT during leaf development, we used a transcriptomic approach to identify putative target genes. We found putative SPT target genes related to leaf development, and to stomata and trichome formation. Furthermore, genes related to anthocyanin biosynthesis. In this work, we demonstrate that SPT is a negative regulator of stomata number and a positive regulator of trichome number. In addition, SPT is required for sucrose-mediated anthocyanin biosynthesis.

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.

Biosynthetic regulatory network of flavonoid metabolites in stems and leaves of Salvia miltiorrhiza

Flavonoid secondary metabolites can treat and prevent many diseases, but systematic studies on regulation of the biosynthesis of such metabolites in aboveground parts of Salvia miltiorrhiza are lacking. In this study, metabonomic and transcriptomic analyses of different S. miltiorrhiza phenotypes were conducted to explore pathways of synthesis, catalysis, accumulation, and transport of the main flavonoid secondary metabolites regulating pigment accumulation. Tissue localization and quantitative analysis of flavonoid secondary metabolites were conducted by laser scanning confocal microscopy (LSCM). A total 3090 differentially expressed genes were obtained from 114,431 full-length unigenes in purple and green phenotypes, and 108 functional genes were involved in flavonoid biosynthesis. Five key phenylpropane structural genes (PAL, 4CL, ANS, 3AT, HCT) were highly differentially expressed, and four transcription factor genes (MYB, WRKY, bHLH, bZiP) were identified. In addition, six GST genes, nine ABC transporters, 22 MATE genes, and three SNARE genes were detected with key roles in flavonoid transport. According to LSCM, flavonoids were mainly distributed in epidermis, cortex, and collenchyma. Thus, comprehensive and systematic analyses were used to determine biosynthesis, accumulation, and transport of flavonoids in stems and leaves of different S. miltiorrhiza phenotypes. The findings will provide a reference for flavonoid production and cultivar selection.

Transcription factor CmbHLH16 regulates petal anthocyanin homeostasis under different lights in Chrysanthemum

Light is essential to plant survival and elicits a wide range of plant developmental and physiological responses under different light conditions. A low red-to-far red (R/FR) light ratio induces shade-avoidance responses, including decreased anthocyanin accumulation, whereas a high R/FR light ratio promotes anthocyanin biosynthesis. However, the detailed molecular mechanism underpinning how different R/FR light ratios regulate anthocyanin homeostasis remains elusive, especially in non-model species. Here, we demonstrate that a low R/FR light ratio induced the expression of CmMYB4, which suppressed the anthocyanin activator complex CmMYB6-CmbHLH2, leading to the reduction of anthocyanin accumulation in Chrysanthemum (Chrysanthemum morifolium) petals. Specifically, CmMYB4 recruited the corepressor CmTPL (TOPLESS) to directly bind the CmbHLH2 promoter and suppressed its transcription by impairing histone H3 acetylation. Moreover, the low R/FR light ratio inhibited the PHYTOCHROME INTERACTING FACTOR family transcription factor CmbHLH16, which can competitively bind to CmMYB4 and destabilize the CmMYB4-CmTPL protein complex. Under the high R/FR light ratio, CmbHLH16 was upregulated, which impeded the formation of the CmMYB4-CmTPL complex and released the suppression of CmbHLH2, thus promoting anthocyanin accumulation in Chrysanthemum petals. Our findings reveal a mechanism by which different R/FR light ratios fine-tune anthocyanin homeostasis in flower petals.

Determining the Effects of Light on the Fruit Peel Quality of Photosensitive and Nonphotosensitive Eggplant

With the development of facility agriculture, low-light stress is a prominent problem and a popular research topic currently. In this study, transcriptome analysis was used to analyze the genes in the fruit peel of photosensitive and nonphotosensitive eggplant and to explore the mechanism of changes in fruit color, texture, hormone content, aroma, and taste of these two different types of eggplant. We identified 51, 65, 66, and 66 genes involved in synthesizing anthocyanins, texture, hormone content, and aroma and flavor, respectively, in the two different types of eggplant based on the variation in gene expression trends in the fruit peel. These results provide a basis for further analysis of the molecular mechanism underlying the regulatory processes in eggplant fruits under low-light stress.

Anthocyanins as Key Phytochemicals Acting for the Prevention of Metabolic Diseases: An Overview

Anthocyanins are water-soluble pigments present in fruits and vegetables, which render them an extensive range of colors. They have a wide distribution in the human diet, are innocuous, and, based on numerous studies, have supposed preventive and therapeutical benefits against chronic affections such as inflammatory, neurological, cardiovascular, digestive disorders, diabetes, and cancer, mostly due to their antioxidant action. Despite their great potential as pharmaceutical applications, they have a rather limited use because of their rather low stability to environmental variations. Their absorption was noticed to occur best in the stomach and small intestine, but the pH fluctuation of the digestive system impacts their rapid degradation. Urine excretion and tissue distribution also occur at low rates. The aim of this review is to highlight the chemical characteristics of anthocyanins and emphasize their weaknesses regarding bioavailability. It also targets to deliver an update on the recent advances in the involvement of anthocyanins in different pathologies with a focus on in vivo, in vitro, animal, and human clinical trials.

RNA-Seq Analysis Identifies Transcription Factors Involved in Anthocyanin Biosynthesis of 'Red Zaosu' Pear Peel and Functional Study of PpPIF8

Red-skinned pears are favored by people for their attractive appearance and abundance of anthocyanins. However, the molecular basis of anthocyanin biosynthesis in red pears remains elusive. Here, a comprehensive transcriptome analysis was conducted to explore the potential regulatory mechanism of anthocyanin biosynthesis in 'Red Zaosu' pear (Pyrus pyrifolia × Pyrus communis). Gene co-expression analysis and transcription factor mining identified 263 transcription factors, which accounted for 6.59% of the total number of transcription factors in the pear genome in two gene modules that are highly correlated with anthocyanin biosynthesis. Clustering, gene network modeling with STRING-DB, and local motif enrichment analysis (CentriMo) analysis suggested that PpPIF8 may play a role in anthocyanin biosynthesis. Furthermore, eight PIFs were identified in the pear genome, of which only PpPIF8 was rapidly induced by light. Functional studies showed that PpPIF8 localizes in the nucleus and is preferentially expressed in the tissue of higher levels of anthocyanin. The overexpression of PpPIF8 in pear peel and pear calli promotes anthocyanin biosynthesis and upregulates the expression of anthocyanin biosynthesis genes. Yeast-one hybrid and transgenic analyses indicated that PpPIF8 binds to the PpCHS promoter to induce PpCHS expression. The positive effect of PpPIF8 on anthocyanin biosynthesis is different from previously identified negative regulators of PyPIF5 and MdPIF7 in pear and apple. Taken together, our data not only provide a comprehensive view of transcription events during the coloration of pear peel, but also resolved the regulatory role of PpPIF8 in the anthocyanin biosynthesis pathway.

Transcriptome Analysis Reveals Differences in Anthocyanin Accumulation in Cotton (Gossypium hirsutum L.) Induced by Red and Blue Light

Many factors, including illumination, affect anthocyanin biosynthesis and accumulation in plants. light quality is the key factor affecting the process of photoinduced anthocyanin biosynthesis and accumulation. We observed that the red color of the Upland cotton accession Huiyuan with the R1 mutation turned to normal green color under light-emitting diodes (LEDs), which inspired us to investigate the effect of red and blue lights on the biosynthesis and accumulation of anthocyanins. We found that both red and blue lights elevated accumulation of anthocyanins. Comparative transcriptomic analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and GSEA, revealed that genes differentially expressed under different light conditions were enriched with the pathways of circadian rhythm, phenylpropanoid biosynthesis, anthocyanin biosynthesis, and flavone and flavonol biosynthesis. Not surprisingly, all the major structural genes related to biosynthesis of anthocyanins, including the key regulatory MYB transcription factor (GhPAP1D) and anthocyanin transporter (GhGSTF12), were induced by red or blue light treatment. However, LARs and MATEs related to biosynthesis of proanthocyanidins were more significantly up-regulated by red light radiation than by blue light radiation. Vice versa, the accumulation of anthocyanins under red light was not as high as that under blue light. In addition, we demonstrated a potential role of GhHY5, a key regulator in plant circadian rhythms, in regulation of anthocyanin accumulation, which could be achieved via interaction with GhPAP1D. Together, these results indicate different effect of red and blue lights on biosynthesis and accumulation of anthocyanins and a potential module including GhHY5 and GhPAP1D in regulation of anthocyanin accumulation in cotton. These results also suggest that the substrates responsible the synthesis of anthocyanins under blue light is diverted to biosynthesis of proanthocyanidin under red light.

Phytochrome interacting factor MdPIF7 modulates anthocyanin biosynthesis and hypocotyl growth in apple

Light affects many physiological and developmental processes of plants by regulating the expression and activity of light-responsive proteins. Among them, phytochrome interacting factors (PIFs) play pivotal roles in the regulation of anthocyanin accumulation and hypocotyl growth. However, the molecular mechanism is not well understood, especially in woody plants, such as apple (Malus × domestica). In this study, we identified a light-responsive PIF protein, MdPIF7, in apple and investigated the molecular mechanism of its regulation of anthocyanin biosynthesis and hypocotyl growth. We found that overexpression of MdPIF7 decreased anthocyanin accumulation in transgenic apple materials and promoted hypocotyl elongation in ectopically expressed Arabidopsis (Arabidopsis thaliana). Further investigation showed that MdPIF7 functioned by interacting with B-box 23 (MdBBX23), a positive regulator of anthocyanin biosynthesis in apple and hypocotyl growth inhibition in ectopically expressed Arabidopsis, and attenuating the transcriptional activation of MdBBX23 on LONG HYPOCOTYL 5 (MdHY5). In addition, MdPIF7 interacted with basic region leucine zipper 44 (MdbZIP44) and ethylene response factor 38 (MdERF38), two positive regulators of anthocyanin biosynthesis, and it negatively regulated MdbZIP44- and MdERF38-promoted anthocyanin accumulation by interfering with the interaction between MdbZIP44/MdERF38 and MdMYB1. Taken together, our results reveal that MdPIF7 regulates anthocyanin biosynthesis in apple and hypocotyl growth in ectopically expressed Arabidopsis through MdPIF7-MdBBX23-MdHY5 and MdPIF7-MdbZIP44/MdERF38-MdMYB1 modules. Our findings enrich the functional studies of PIF proteins and provide insights into the molecular mechanism of PIF-mediated anthocyanin biosynthesis and hypocotyl growth.

Comparative Transcriptome Analysis between Two Potato Cultivars in Tuber Induction to Reveal Associated Genes with Anthocyanin Accumulation

Anthocyanins are generally accumulated within a few layers, including the epidermal cells of leaves and stems in plants. Solanum tuberosum cv. ‘Jayoung’ (hereafter, JY) is known to accumulate anthocyanin both in inner tissues and skins. We discovered that anthocyanin accumulation in the inner tissues of JY was almost diminished (more than 95% was decreased) in tuber induction condition. To investigate the transcriptomic mechanism of anthocyanin accumulation in JY flesh, which can be modulated by growth condition, we performed mRNA sequencing with white-colored flesh tissue of Solanum tuberosum cv. ‘Atlantic’ (hereafter, ‘Daeseo’, DS) grown under canonical growth conditions, a JY flesh sample grown under canonical growth conditions, and a JY flesh sample grown under tuber induction conditions. We could identify 36 common DEGs (differentially expressed genes) in JY flesh from canonical growth conditions that showed JY-specifically increased or decreased expression level. These genes were enriched with flavonoid biosynthetic process terms in GO analysis, as well as gene set enrichment analysis (GSEA) analysis. Further in silico analysis on expression levels of anthocyanin biosynthetic genes including rate-limiting genes such as StCHS and StCHI followed by RT-PCR and qRT-PCR analysis showed a strong positive correlation with the observed phenotypes. Finally, we identified StWRKY44 from 36 common DEGs as a possible regulator of anthocyanin accumulation, which was further supported by network analysis. In conclusion, we identified StWRKY44 as a putative regulator of tuber-induction-dependent anthocyanin accumulation.

Effects of partial replacement of red by green light in the growth spectrum on photomorphogenesis and photosynthesis in tomato plants

The artificial light used in growth chambers is usually devoid of green (G) light, which is considered to be less photosynthetically efficient than blue (B) or red (R) light. To verify the role of G light supplementation in the spectrum, we modified the RB spectrum by progressively replacing R light with an equal amount of G light. The tomato plants were cultivated under 100 µmol m^-2 s^-1 of five different combinations of R (35-75%) and G light (0-40%) in the presence of a fixed proportion of B light (25%) provided by light-emitting diodes (LEDs). Substituting G light for R altered the plant's morphology and partitioning of biomass. We observed a decrease in the dry biomass of leaves, which was associated with increased biomass accumulation and the length of the roots. Moreover, plants previously grown under the RGB spectrum more efficiently utilized the B light that was applied to assess the effective quantum yield of photosystem II, as well as the G light when estimated with CO₂ fixation using RB + G light-response curves. At the same time, the inclusion of G light in the growth spectrum reduced stomatal conductance (g_s), transpiration (E) and altered stomatal traits, thus improving water-use efficiency. Besides this, the increasing contribution of G light in place of R light in the growth spectrum resulted in the progressive accumulation of phytochrome interacting factor 5, along with a lowered level of chalcone synthase and anthocyanins. However, the plants grown at 40% G light exhibited a decreased net photosynthetic rate (P_n), and consequently, a reduced dry biomass accumulation, accompanied by morphological and molecular traits related to shade-avoidance syndrome.

Biosynthesis and regulation of anthocyanin pathway genes

Anthocyanins are the phenolic compounds responsible for coloring pigments in fruits and vegetables. Anthocyanins offer a wide range of health benefits to human health. Their scope has expanded dramatically in the past decade, making anthocyanin control, influx, and outflow regulation fascinating for many researchers. The main culprit is anthocyanin stability and concentration form, which demands novel ways because these are critical in the food industry. This review aims to examine anthocyanin synthesis via triggering transcription genes that code for anthocyanin-producing enzymes. The balance between production and breakdown determines anthocyanin accumulation. Thus, increasing the anthocyanin content in food requires the stability of molecules in the vacuolar lumen, the pigment fading process, and a better understanding of the mechanism. The promising option is biosynthesis by metabolically engineered microorganisms with a lot of success. This study aims to look into and evaluate the existing literature on anthocyanin production, namely the biosynthesis of anthocyanin pathway genes, production by microbial cell factories, and the regulatory factors that can modulate the production of anthocyanins. Understanding these mechanisms will provide new biotechnological approaches.Key points• Factors affecting the regulation of anthocyanins• Focus on degradation, biosynthesis pathway genes, and alternative systems for the production of anthocyanins• Microbial cell factories can be used to produce large amounts of anthocyanins.

RNA sequencing-based exploration of the effects of blue laser irradiation on mRNAs involved in functional metabolites of D. officinales

Dendrobium officinale Kimura et Migo (D. officinale) has promising lung moisturizing, detoxifying, and immune boosting properties. Light is an important factor influencing functional metabolite synthesis in D. officinale. The mechanisms by which lasers affect plants are different from those of ordinary light sources; lasers can effectively address the shortcomings of ordinary light sources and have significant interactions with plants. Different light treatments (white, blue, blue laser) were applied, and the number of red leaves under blue laser was greater than that under blue and white light. RNA-seq technology was used to analyze differences in D. officinale under different light treatments. The results showed 465, 2,107 and 1,453 differentially expressed genes (DEGs) in LB-B, LB-W and W-B, respectively. GO, KEGG and other analyses of DEGs indicated that D. officinale has multiple blue laser response modes. Among them, the plasma membrane, cutin, suberine and wax biosynthesis, flavone and flavonol biosynthesis, heat shock proteins, etc. play central roles. Physiological and biochemical results verified that blue laser irradiation significantly increases POD, SOD, and PAL activities in D. officinale. The functional metabolite results showed that blue laser had the greatest promoting effect on total flavonoids, polysaccharides, and alkaloids. qPCR verification combined with other results suggested that CRY DASH, SPA1, HY5, and PIF4 in the blue laser signal transduction pathway affect functional metabolite accumulation in D. officinale through positively regulated expression patterns, while CO16 and MYC2 exhibit negatively regulated expression patterns. These findings provide new ideas for the efficient production of metabolites in D. officinale.

Transcriptomic and Metabolomic Profiling Reveals the Effect of LED Light Quality on Fruit Ripening and Anthocyanin Accumulation in Cabernet Sauvignon Grape

Different light qualities have various impacts on the formation of fruit quality. The present study explored the influence of different visible light spectra (red, green, blue, and white) on the formation of quality traits and their metabolic pathways in grape berries. We found that blue light and red light had different effects on the berries. Compared with white light, blue light significantly increased the anthocyanins (malvidin-3-O-glucoside and peonidin-3-O-glucoside), volatile substances (alcohols and phenols), and soluble sugars (glucose and fructose), reduced the organic acids (citric acid and malic acid), whereas red light achieved the opposite effect. Transcriptomics and metabolomics analyses revealed that 2707, 2547, 2145, and 2583 differentially expressed genes (DEGs) and (221, 19), (254, 22), (189, 17), and (234, 80) significantly changed metabolites (SCMs) were filtered in the dark vs. blue light, green light, red light, and white light, respectively. According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, most of the DEGs identified were involved in photosynthesis and biosynthesis of flavonoids and flavonols. Using weighted gene co-expression network analysis (WGCNA) of 23410 highly expressed genes, two modules significantly related to anthocyanins and soluble sugars were screened out. The anthocyanins accumulation is significantly associated with increased expression of transcription factors (VvHY5, VvMYB90, VvMYB86) and anthocyanin structural genes (VvC4H, Vv4CL, VvCHS3, VvCHI1, VvCHI2, VvDFR), while significantly negatively correlated with VvPIF4. VvISA1, VvISA2, VvAMY1, VvCWINV, VvβGLU12, and VvFK12 were all related to starch and sucrose metabolism. These findings help elucidate the characteristics of different light qualities on the formation of plant traits and can inform the use of supplemental light in the field and after harvest to improve the overall quality of fruit.

Multilevel regulation of anthocyanin-promoting R2R3-MYB transcription factors in plants

Anthocyanins are common secondary metabolites in plants that confer red, blue, and purple colorations in plants and are highly desired by consumers for their visual appearance and nutritional quality. In the last two decades, the anthocyanin biosynthetic pathway and transcriptional regulation of anthocyanin biosynthetic genes (ABGs) have been well characterized in many plants. From numerous studies on model plants and horticultural crops, many signaling regulators have been found to control anthocyanin accumulation via regulation of anthocyanin-promoting R2R3-MYB transcription factors (so-called R2R3-MYB activators). The regulatory mechanism of R2R3-MYB activators is mediated by multiple environmental factors (e.g., light, temperature) and internal signals (e.g., sugar, ethylene, and JA) in complicated interactions at multiple levels. Here, we summarize the transcriptional control of R2R3-MYB activators as a result of natural variations in the promoter of their encoding genes, upstream transcription factors and epigenetics, and posttranslational modifications of R2R3-MYB that determine color variations of horticultural plants. In addition, we focus on progress in elucidating the integrated regulatory network of anthocyanin biosynthesis mediated by R2R3-MYB activators in response to multiple signals. We also highlight a few gene cascade modules involved in the regulation of anthocyanin-related R2R3-MYB to provide insights into anthocyanin production in horticultural plants.

PIF4-PAP1 interaction affects MYB-bHLH-WD40 complex formation and anthocyanin accumulation in Arabidopsis

Anthocyanin accumulation is a marked phenotype of plants under environmental stresses. PHYTOCHROME-INTERACTING FACTORs (PIFs) are involved in environment-induced anthocyanin biosynthesis through interacting with the MYB-bHLH-WD40 (MBW) complex. However, the molecular mechanism of this interaction remains unclear. The present study demonstrated that PIF3 and PIF5 can slightly repress anthocyanin accumulation under NaCl, low nitrogen (-N), or 6-BA treatments; in contrast, PIF4 can significantly repress anthocyanin accumulation. Bimolecular fluorescence complementation and yeast two-hybrid assays showed that PIF4 directly interacts with PRODUCTION OF ANTHOCYANIN PIGMENT 1 (PAP1), a MYB transcription factor in the MBW complex. Further analysis revealed that the active phytochrome binding (APB) domain in the N terminus of PIF4 is necessary for the interaction between PIF4 and PAP1. Yeast three-hybrid analysis showed that PIF4 competes with TRANSPARENT TESTA 8 (TT8) to bind PAP1, thereby interfering with the regulation of the MBW protein complex in anthocyanin synthesis. Consistently, the anthocyanin content in pap1-D/35S::PIF4 and 35S::PAP1/35S::PIF4 seedlings was markedly lower than that in pap1-D and 35S::PAP1 under 6-BA, MeJA, -N, and NaCl stresses, implying that overexpression of PIF4 suppresses anthocyanin accumulation in pap1-D and 35S::PAP1. Thus, PIF4 is genetically epistatic to PAP1. Taken together, PIF4 plays a negative role in modulating anthocyanin biosynthesis in Arabidopsis under different stress environments, and PIF4 interacts with PAP1 to affect the integrity of the MBW complex.

PbWRKY75 promotes anthocyanin synthesis by activating PbDFR, PbUFGT, and PbMYB10b in pear

Anthocyanins are common secondary metabolites in plants that impart red coloration to fruits and flowers. The important WRKY transcription factor family plays multifaceted roles in plant growth and development. In this study, we found a WRKY family gene, Pyrus bretschneideri WRKY75, that may be involved in anthocyanin synthesis in pear. Unlike Arabidopsis thaliana WRKY75, PbWRKY75 may be a positive regulator of anthocyanin synthesis. A transient expression assay indicated that PbWRKY75 promoted pear anthocyanin synthesis. The structural genes (PbANS, PbDFR, and PbUFGT) and positive regulators (PbMYB10 and PbMYB10b) of anthocyanin synthesis were significantly upregulated in the fruitlet skins of PbWRKY75-overexpressing "Zaosu" pears. Subsequently, yeast one-hybrid and dual-luciferase assays indicated that PbWRKY75 promoted PbDFR, PbUFGT, and PbMYB10b expression by activating their promoters. These results revealed that PbWRKY75 may promote the expression of both PbMYB10b and anthocyanin late biosynthetic genes (PbDFR and PbUFGT) by activating their promoters, thereby inducing anthocyanin synthesis in pear. This study enhanced our understanding of the mechanism of pear anthocyanin synthesis, which will be beneficial in the improvement of pear peel color.

Terpenoid indole alkaloid biosynthesis in Catharanthus roseus: effects and prospects of environmental factors in metabolic engineering

Plants synthesize a vast array of specialized metabolites that primarily contribute to their defense and survival under adverse conditions. Many of the specialized metabolites have therapeutic values as drugs. Biosynthesis of specialized metabolites is affected by environmental factors including light, temperature, drought, salinity, and nutrients, as well as pathogens and insects. These environmental factors trigger a myriad of changes in gene expression at the transcriptional and posttranscriptional levels. The dynamic changes in gene expression are mediated by several regulatory proteins that perceive and transduce the signals, leading to up- or down-regulation of the metabolic pathways. Exploring the environmental effects and related signal cascades is a strategy in metabolic engineering to produce valuable specialized metabolites. However, mechanistic studies on environmental factors affecting specialized metabolism are limited. The medicinal plant Catharanthus roseus (Madagascar periwinkle) is an important source of bioactive terpenoid indole alkaloids (TIAs), including the anticancer therapeutics vinblastine and vincristine. The emerging picture shows that various environmental factors significantly alter TIA accumulation by affecting the expression of regulatory and enzyme-encoding genes in the pathway. Compared to our understanding of the TIA pathway in response to the phytohormone jasmonate, the impacts of environmental factors on TIA biosynthesis are insufficiently studied and discussed. This review thus focuses on these aspects and discusses possible strategies for metabolic engineering of TIA biosynthesis. PURPOSE OF WORK: Catharanthus roseus is a rich source of bioactive terpenoid indole alkaloids (TIAs). The objective of this work is to present a comprehensive account of the influence of various biotic and abiotic factors on TIA biosynthesis and to discuss possible strategies to enhance TIA production through metabolic engineering.

Crosstalk between Light- and Temperature-Mediated Processes under Cold and Heat Stress Conditions in Plants

Extreme temperatures are among the most important stressors limiting plant growth and development. Results indicate that light substantially influences the acclimation processes to both low and high temperatures, and it may affect the level of stress injury. The interaction between light and temperature in the regulation of stress acclimation mechanisms is complex, and both light intensity and spectral composition play an important role. Higher light intensities may lead to overexcitation of the photosynthetic electron transport chain; while different wavelengths may act through different photoreceptors. These may induce various stress signalling processes, leading to regulation of stomatal movement, antioxidant and osmoregulation capacities, hormonal actions, and other stress-related pathways. In recent years, we have significantly expanded our knowledge in both light and temperature sensing and signalling. The present review provides a synthesis of results for understanding how light influences the acclimation of plants to extreme low or high temperatures, including the sensing mechanisms and molecular crosstalk processes.

Differences in Anthocyanin Accumulation Patterns and Related Gene Expression in Two Varieties of Red Pear

Red pear is a popular fruit that is appreciated for its attractive and distinctive appearance and mild flavor. In this study, we investigated the mechanism underlying the red coloration of pear skin using the ‘Xinqihong’ cultivar—which was selected as a spontaneous bud sport mutant of the ‘Xinli 7′(Pyrus betulifolia Rehd.) variety and has a stronger red color that is retained in the mature fruit—as an experimental model. We compared the phenotype and gene expression patterns of the two varieties and found no significant differences at the early stage of fruit development. However, although the red color of ‘Xinli 7′ fruits began to fade 107 days after full bloom, that of ‘Xinqihong’ fruits persisted until the time of harvest. Transcriptome sequencing identified 639 genes that were differentially expressed between the two varieties, including genes related to light, calcium, and hormone signaling (e.g., PbPIF3, PbGA2ox, and the calmodulin related genes). Moreover, anthocyanin biosynthesis genes were downregulated as the red color of ‘Xinli 7′ fruits faded. These results provide insight into the molecular basis of color differences in red pears that can be useful for improving its fruit quality and commercial value.

Light acts as a stressor and influences abiotic and biotic stress responses in plants

Light is important for plants as an energy source and a developmental signal, but it can also cause stress to plants and modulates responses to stress. Excess and fluctuating light result in photoinhibition and reactive oxygen species (ROS) accumulation around photosystems II and I, respectively. Ultraviolet light causes photodamage to DNA and a prolongation of the light period initiates the photoperiod stress syndrome. Changes in light quality and quantity, as well as in light duration are also key factors impacting the outcome of diverse abiotic and biotic stresses. Short day or shady environments enhance thermotolerance and increase cold acclimation. Similarly, shade conditions improve drought stress tolerance in plants. Additionally, the light environment affects the plants' responses to biotic intruders, such as pathogens or insect herbivores, often reducing growth-defence trade-offs. Understanding how plants use light information to modulate stress responses will support breeding strategies to enhance crop stress resilience. This review summarizes the effect of light as a stressor and the impact of the light environment on abiotic and biotic stress responses. There is a special focus on the role of the different light receptors and the crosstalk between light signalling and stress response pathways.

PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) negatively regulates anthocyanin accumulation by inhibiting PAP1 transcription in Arabidopsis seedlings

Anthocyanin accumulation is a striking symptom of plant environmental response and plays an important role in plant adaptation to adverse stimuli. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) is a member of the PIFs family that directly interacts with light-activated phytochromes, and it can not only regulate various light responses but also optimize growth as a key integrator of multiple signaling pathways. However, the mechanism by which PIF4 participates in the regulation of anthocyanin accumulation remains to be elucidated. In this study, we found that anthocyanin accumulation was effectively induced by white light in Arabidopsis Col-0, but such an effect was impaired in the overexpression line PIF4OX. Consistently, the transcript level of PAP1 that encodes a key transcript factor involved in regulating anthocyanin biosynthesis was significantly decreased in PIF4OX compared with Col-0. Moreover, the expression of PAP1 was markedly lower in pap1-D/PIF4OX than pap1-D, as a result, the phenotype that highly accumulates anthocyanins in leaves of pap1-D caused by PAP1 overexpressing was almost eliminated in pap1-D/PIF4OX. Analyses through chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and electrophoretic mobility shift assay (EMSA) revealed that PIF4 could directly bind to the G-box motif present in the promoter of PAP1. Furthermore, transient transcriptional expression analysis showed that PIF4 could weaken the transcriptional activity of the PAP1 promoter, and the G-box motif is necessary for the effect of PIF4. Subsequently, when the seedlings shifted from darkness to light and grew under constant red light and short-day photoperiod, it was found that the PAP1 transcription level and anthocyanin content in pif4-2/pap1-D were significantly higher than pap1-D, implying that PIF4 mutation can strengthen PAP1's effect on anthocyanin biosynthesis under these conditions. Taken together, the results indicate that PIF4 negatively regulates anthocyanin accumulation in Arabidopsis through transcriptional suppression of PAP1 by directly binding to the G-box motif of the promoter.

Transcriptome analysis reveals the mechanism of anthocyanidins biosynthesis during grains development in purple corn (Zea mays L.)

Anthocyanidins are important pigments that cause plant tissues to develop colors. They have attracted much attention due to their crucial regulatory roles in plant growth as well as their health benefits. In order to reveal the molecular mechanism of anthocyanidin synthesis and regulation in purple corn (Zea mays L.) in this study, purple corn 963 was used to compare differences in gene expression during three stages of grain development by transcriptome analysis. A total of 17,168 differentially expressed genes (DEGs) (7564 up-regulated and 9604 down-regulated DGEs) were identified. The DEGs were significantly enriched in "Phenylpropanoid biosynthesis", "Biosynthesis of secondary metabolites", and "Plant hormone signal transduction". In addition, 72 % of the structural genes that regulate anthocyanidin synthesis were up-regulated, and the transcription factors related to the accumulation of anthocyanidins were enriched during grain development. Moreover, the differential expression of phytohormone genes might also be an important factor in anthocyanidin accumulation. Transcriptomic analysis presents a molecular basis for the study of grain color changes in the three stages of grain development, and provides information for further research on the mechanism of anthocyanidin synthesis.

Growth Responses of Red-Leaf Lettuce to Temporal Spectral Changes

Lighting is typically static for indoor production of leafy greens. However, temporal spectrum differentiation for distinct growth phases can potentially control age-specific desirable traits. Spectral effects can be persistent yet dynamic as plants mature, necessitating characterization of time-dependent responses. We grew red-leaf lettuce (Lactuca sativa L.) "Rouxai" in a growth room at 23°C and under a 20-h photoperiod created by warm-white (WW), blue (B; peak = 449 nm), green (G; peak = 526 nm), red (R; peak = 664 nm), and/or far-red (FR; peak = 733 nm) light-emitting diodes. From day 0 to 11, plants received six static lighting treatments with the same total photon flux density (400-800 nm): WW₁₈₀, R₁₈₀, B₂₀R₁₆₀, B₂₀G₆₀R₁₀₀, B₂₀R₁₀₀FR₆₀, or B₁₈₀ (subscripts denote photon flux densities in μmol⋅m^-2⋅s^-1). On day 11, plants grown under each of the six treatments were transferred to all treatments, which created 36 temporal spectrum alternations. Plant growth, morphology, and coloration were measured on days 11 and 25. Increasing B radiation from 0 to 100% in static treatments decreased shoot fresh and dry weights and increased foliage redness of seedlings and mature plants. Compared to B₂₀R₁₆₀, B₂₀R₁₀₀FR₆₀ increased shoot fresh weight, but not dry weight, on both days. However, other phenotypic responses under static treatments changed over time. For example, leaf length under B₁₈₀ was 35% lower on day 11 but similar on day 25 compared to that under R₁₈₀. In the B₂₀ background, substituting G₆₀ for R radiation did not influence shoot weight on day 11 but decreased it by 19% on day 25. When plants were switched from one treatment to another on day 11, the treatments applied before day 11 influenced final shoot weight and, to a lesser extent, leaf length and foliage coloration on day 25. In comparison, effects of the treatments applied after day 11 were more pronounced. We conclude some phenotypic responses to light quality depend on time and sequential light quality treatments had cumulative effects on lettuce growth. The temporal complexity of spectral responses is critical in photobiological research and creates opportunities for time-specific spectrum delivery to optimize crop characteristics.

The Regulation of Floral Colour Change in Pleroma raddianum (DC.) Gardner

Floral colour change is a widespread phenomenon in angiosperms, but poorly understood from the genetic and chemical point of view. This article investigates this phenomenon in Pleroma raddianum, a Brazilian endemic species whose flowers change from white to purple. To this end, flavonoid compounds and their biosynthetic gene expression were profiled. By using accurate techniques (Ultra Performance Liquid Chromatography-High-Resolution Mass Spectrometry (UPLC-HRMS)), thirty phenolic compounds were quantified. Five key genes of the flavonoid biosynthetic pathway were partially cloned, sequenced, and the mRNA levels were analysed (RT-qPCR) during flower development. Primary metabolism was also investigated by gas chromatography coupled to mass spectrometry (GC-EIMS), where carbohydrates and organic acids were identified. Collectively, the obtained results suggest that the flower colour change in P. raddianum is determined by petunidin and malvidin whose accumulation coincides with the transcriptional upregulation of early and late biosynthetic genes of the flavonoid pathway, mainly CHS and ANS, respectively. An alteration in sugars, organic acids and phenolic co-pigments is observed together with the colour change. Additionally, an increment in the content of Fe³⁺ ions in the petals, from the pink to purple stage, seemed to influence the saturation of the colour.

Gibberellins modulate local auxin biosynthesis and polar auxin transport by negatively affecting flavonoid biosynthesis in the root tips of rice

As critical signalling molecules, both gibberellin (GA) and auxin play essential roles in regulating root elongation, and many studies have been shown that auxin influences GA biosynthesis and signalling. However, the mechanism by which GA affects auxin in root elongation is still unknown. In this study, root elongation and DR5-GUS activity were analyzed in rice seedlings. Paclobutrazol-induced short root phenotypes could be partially reversed by co-treatment with IAA, and the inhibition of root elongation caused by naphthylphthalamic acid could be partially reversed when plants were co-treated with GA. DR5-GUS activity was increased in the presence of GA and was reduced at the root tip of paclobutrazol-treated seedlings, indicating that GA could regulate local auxin biosynthesis and polar auxin transport (PAT) in rice root tips. Our RNA-seq analysis showed that GA was involved in the regulation of flavonoid biosynthesis. Flavonoid accumulation level in ks1 root tips was significantly increased and negatively correlated with GA content in GA- and PAC-treated seedlings. GA also rescued the decreased DR5-GUS activity induced by quercetin in rice root tips, confirming that flavonoids act as an intermediary in GA-mediated auxin biosynthesis and PAT. Based on RNA-seq and qPCR analyses, we determined that GA regulates local auxin biosynthesis and polar auxin transport by modulating the expression of OsYUCCA6 and PIN. Our findings provide valuable new insights into the interactions between GA and auxin in the root tips of rice.

bHLH transcription factor SmbHLH92 negatively regulates biosynthesis of phenolic acids and tanshinones in Salvia miltiorrhiza

Objective

Salvia miltiorrhiza is a valuable herbal medicine with tanshinone and phenolic acid as the main biological active ingredients. The biosynthetic regulation of these bioactive compounds is controlled by a set of transcription factors (TFs). The basic helix-loop-helix (bHLH) transcription factor plays an important role in various physiological and biochemical processes in plants. However, research on bHLH TFs regulating phenolic acid or tanshinone biosynthesis in S. miltiorrhiza is limited.

Methods

qRT-PCR was used for gene expression analysis. The subcellular localization of SmbHLH92 was detected by SmbHLH92-GFP transient transformation into tobacco leaves, and its fluorescence was observed using a confocal laser scanning microscope. The transcriptional activity of SmbHLH92 was confirmed in the AH109 yeast strain. RNA interference hairy roots of SmbHLH92-RNAi transgenic lines were obtained through Agrobacterium-mediated genetic transformation. Ultra performance liquid chromatography (UPLC) was used to detect the changes of phenolic acids and tanshinones.

Results

SmbHLH92 is a bHLH transcription factor that is highly expressed in the root and phloem of S. miltiorrhiza. The subcellular localization and transcriptional activity of SmbHLH92 indicated that SmbHLH92 was located in the nucleus and may be a transcription factor. RNA interference (RNAi) of SmbHLH92 in hairy roots of S. miltiorrhiza significantly increased the accumulation of phenolic acid and tanshinone. Quantitative RT-PCR (RT-qPCR) analysis showed the transcription level of genes encoding the key enzymes involved in the phenolic acid and tanshinone biosynthetic pathways was increased in the hairy roots of the SmbHLH92-RNAi transgenic line, comparing with the control line.

Conclusion

These data indicate that SmbHLH92 is a negative regulator involved in the regulation of phenolic acid and tanshinone biosynthesis in S. miltiorrhiza.

The Effects of Ultraviolet A/B Treatments on Anthocyanin Accumulation and Gene Expression in Dark-Purple Tea Cultivar 'Ziyan' (Camellia sinensis)

‘Ziyan’ is a novel anthocyanin-rich tea cultivar with dark purple young shoots. However, how its anthocyanin accumulation is affected by environmental factors, such as ultraviolet (UV), remains unclear. In this study, we observed that UV light treatments stimulated anthocyanin accumulation in ‘Ziyan’ leaves, and we further analyzed the underlying mechanisms at gene expression and enzyme activity levels. In addition, the catechins and chlorophyll contents of young shoots under different light treatments were also changed. The results showed that the contents of total anthocyanins and three major anthocyanin molecules, i.e., delphinidin, cyanidin, and pelargonidin, were significantly higher in leaves under UV-A, UV-B, and UV-AB treatments than those under white light treatment alone. However, the total catechins and chlorophyll contents in these purple tea plant leaves displayed the opposite trends. The anthocyanin content was the highest under UV-A treatment, which was higher by about 66% than control. Compared with the white light treatment alone, the enzyme activities of chalcone synthase (CHS), flavonoid 3′,5′-hydroxylase (F3′5′H), and anthocyanidin synthase (ANS) under UV treatments increased significantly, whereas the leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR) activities reduced. There was no significant difference in dihydroflavonol 4-reductase (DFR) activity under all treatments. Comparative transcriptome analyses unveiled that there were 565 differentially expressed genes (DEGs) of 29,648 genes in three pair-wise comparisons (white light versus UV-A, W vs. UV-A; white light versus UV-B, W vs. UV-A; white light versus UV-AB, W vs. UV-AB). The structural genes in anthocyanin pathway such as flavanone 3-hydroxylase (F3H), F3′5′H, DFR, and ANS, and regulatory gene TT8 were upregulated under UV-A treatment; F3′5′H, DFR, ANS, and UFGT and regulatory genes EGL1 and TT2 were upregulated under UV-AB treatment. However, most structural genes involved in phenylpropanoid and flavonoid pathways were downregulated under UV-B treatment compared with control. The expression of LAR and ANR were repressed in all UV treatments. Our results indicated that UV-A and UV-B radiations can induce anthocyanin accumulation in tea plant ‘Ziyan’ by upregulating the structural and regulatory genes involved in anthocyanin biosynthesis. In addition, UV radiation repressed the expression levels of LAR, ANR, and FLS, resulting in reduced ANR activity and a metabolic flux shift toward anthocyanin biosynthesis.

Transcriptomic and metabolomic analyses reveal several critical metabolic pathways and candidate genes involved in resin biosynthesis in Pinus massoniana

Pine resin, which typically consists of terpenoids, is a natural product used in various industrial applications. Oleoresin can be obtained from the xylem tissue by wounding the stem bark. Pinus massoniana (masson pine) is an important resin-tapping tree species that originated in southern China. Masson pines with different genetic backgrounds typically have different resin-yielding capacities (RYCs). However, the mechanisms underlying high resin yield in masson pines are unclear. The aim of this study was to identify the possible genetic regulation pathways and functional genes that influence the resin yield. In this study, we conducted transcriptomic and metabolomic studies of masson pine secondary xylem with high, medium, and low RYCs. A total of 230,068 unigenes and 3894 metabolites were identified from the tissue of the secondary xylem. Several differentially expressed regulation factors, including WRKY, bHLH, and ERF, and functional genes such as PKc and LRR-RLKs, were identified among these masson pines. The Kyoto Encyclopedia of Genes and Genomes pathways were mainly focused on diterpenoid biosynthesis, plant hormone signal transduction, and ABC transporters. Furthermore, integration of the transcriptomic and metabolomic data indicated that the PKc- and LRR-RLK-related regulatory and metabolic pathways may play critical roles in the biosynthesis of terpenoids. These above results improve our understanding of the biosynthesis mechanism of oleoresin in P. massoniana and facilitate further research work into the functional analysis of these candidate genes.

Exploration of the effect of blue light on microRNAs involved in the accumulation of functional metabolites of longan embryonic calli through RNA-sequencing

BACKGROUND

The regulation of functional metabolites under light by structural genes and regulatory genes is understood but the roles of microRNAs in this pathway have rarely been reported and their regulation network is not yet clear.

RESULTS

Blue light was most conducive to promoting the synthesis of some functional metabolites in longan embryonic callus (ECs). In this study, we sequenced three small RNA libraries of constructed longan ECs under different light qualities (dark, blue, and white). A total of 29 and 22 miRNAs were differentially expressed in the dark versus blue (DB) and dark versus white (DW) combinations, respectively. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, most of the differentially expressed miRNA target genes were involved in plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling, biosynthesis of unsaturated fatty acids, and so on. Cytoscape analysis of the target genes of miRNAs indicated that miR396b-5p and miR5139 had the most target genes in DB. Moreover, this study also found that miR171f_3 targeted DELLA, miR390e targeted BRI1, miR396b-5p targeted EBF1/2 and EIN3; these miRNAs participated in the blue light signaling network through their target genes and regulated the accumulation of longan functional metabolites.

CONCLUSIONS

The results of the study revealed that the expressions of phase-specific miRNAs vary with the change of functional metabolites in longan ECs. This study provides new insights into the molecular mechanisms that allow light to influence plant metabolism. © 2018 Society of Chemical Industry.

Gibberellins play dual roles in response to phosphate starvation of tomato seedlings, negatively in shoots but positively in roots

Gibberellins (GAs), a group of plant hormones, and phosphate (Pi), a macronutrient, are essential for numerous aspects of plant growth and development. During Pi starvation, plants develop many adaptive strategies to cope. However, the detailed roles of GAs in Pi deficiency responses of plants are largely unclear. In the present work, we found that low Pi (LP) treatment caused many responses in tomato (Solanum lycopersicum), including anthocyanin accumulation, upregulation of genes encoding high-affinity Pi transporters, and a striking induction of primary root growth. Application of exogeneous GA₃ in the wild-type Micro-Tom (MT) significantly impaired LP-induced shoot anthocyanin accumulation and the upregulation of several key biosynthetic genes, including SlCHS, SlDFR, and SlF3'H. Meanwhile, LP-induced primary root elongation, upregulated SlPT2 and SlPT7 (genes encoding high-affinity Pi transporters), and favored Pi uptake were obviously attenuated in GA biosynthetic mutant gib3. Moreover, LP treatment obviously decreased the content of endogenous GA₄ (a main form of GAs in tomato) in shoots but increased it in roots of MT seedlings. Additionally, in pro, a tomato mutant of DELLA protein, the LP-induced anthocyanin accumulation and expression of SlCHS, SlDFR, and SlF3'H were impaired, whereas the LP-induced primary root growth, expression of genes SlPT2 and SlPT7, and Pi uptake were more enhanced compared with the wild-type MT. Taking these data together, GAs play dual roles in the Pi starvation response of tomato seedlings, negatively in shoots but positively in roots. In addition, the GA-PRO system may play an important role in responding to Pi starvation in tomato.

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

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

Dynamic regulation of PIF5 by COP1-SPA complex to optimize photomorphogenesis in Arabidopsis

Light signal provides the spatial and temporal information for plants to adapt to the prevailing environmental conditions. Alterations in light quality and quantity can trigger robust changes in global gene expression. In Arabidopsis thaliana, two groups of key factors regulating those changes in gene expression are CONSTITUTIVE PHOTOMORPHOGENESIS/DEETIOLATED/FUSCA (COP/DET/FUS) and a subset of basic helix-loop-helix transcription factors called PHYTOCHROME-INTERACTING FACTORS (PIFs). Recently, rapid progress has been made in characterizing the E3 ubiquitin ligases for the light-induced degradation of PIF1, PIF3 and PIF4; however, the E3 ligase(s) for PIF5 remains unknown. Here, we show that the CUL4^COP1-SPA complex is necessary for the red light-induced degradation of PIF5. Furthermore, COP1 and SPA proteins stabilize PIF5 in the dark, but promote the ubiquitination and degradation of PIF5 in response to red light through the 26S proteasome pathway. Genetic analysis illustrates that overexpression of PIF5 can partially suppress both cop1-4 and spaQ seedling de-etiolation phenotypes under dark and red-light conditions. In addition, the PIF5 protein level cycles under both diurnal and constant light conditions, which is also defective in the cop1-4 and spaQ backgrounds. Both cop1-4 and spaQ show defects in diurnal growth pattern. Overexpression of PIF5 partially restores growth defects in cop1-4 and spaQ under diurnal conditions, suggesting that the COP1-SPA complex plays an essential role in photoperiodic hypocotyl growth, partly through regulating the PIF5 level. Taken together, our data illustrate how the CUL4^COP1-SPA E3 ligase dynamically controls the PIF5 level to regulate plant development.

Genome-Wide Identification of PIFs in Grapes (Vitis vinifera L.) and Their Transcriptional Analysis under Lighting/Shading Conditions

Phytochrome-interacting factors (PIFs), as the basic helix⁻loop⁻helix (bHLH) transcription factors, are the primary signaling partners for phytochromes (PHY) that play a key role in PHY-mediated light signal transduction. At present, there are few studies on PIFs in fruit trees. In order to clarify the status of PIFs in grapevines, we identified members of the grape PIFs family and conducted phylogenetic and expression analysis. We identified PIF1, PIF3, PIF4, and PIF7 in PIFs families of the grapevine (Vitis vinifera L.), which were distributed on four different chromosomes with similar gene structures. Except for the closer relationship with PIF1 of citrus, PIFs of grape were distant from the other fruit species such as apple, pear, peach, and strawberry. The VvPIFs (except VvPIF4) were located in the syntenic block with those from Arabidopsisthaliana, Solanum lycopersicum, or Citrus sinensis. In addition to PIF1, all PIFs in grapevines have conserved active PHYB binding (APB) sequences. VvPIF1 has a conserved PIF1-specific active PHYA binding (APA) sequence, while amino acid mutations occurred in the specific APA sequence in VvPIF3. Interestingly, two specific motifs were found in the PIF4 amino acid sequence. The photoreceptor-related elements in the VvPIFs promoter region were the most abundant. PIF1, LONG HYPOCOTYL 5 (HY5) and PIF3, PIF4, GIBBERELLIC ACID INSENSITIVE 1 (GAI1) may interact with each other and participate together in light signal transduction. The relative expression levels of the VvPIFs showed diverse patterns in the various organs at different developmental stages, of which PIF4 was most highly expressed. Prior to maturation, the expression of PIF4 and PIF7 in the skin of the different cultivars increased, while the expression of all PIFs in the flesh decreased. The transcription level of PIFs in grape leaves was sensitive to changes in lighting and shading. Shading treatment was beneficial for enhancing the transcription level of VvPIFs, but the effect on VvPIF3 and VvPIF4 was time-controlled. We concluded that PIFs in grapevines are both conservative and species-specific. The identification and analysis of grape PIFs could provide a theoretical foundation for the further construction of grape light regulation networks.

Transcriptomic analysis of light-dependent anthocyanin accumulation in bicolored cherry fruits

Sweet cherry (Prunus avium L.) fruits are classified into dark-red and bicolored cultivars based on their anthocyanin contents; however, the mechanisms regulating the accumulation of these pigments are unclear. Here, we reveal that anthocyanin accumulation is highly dependent on light in bicolored 'Rainier' cherries, while it is only slightly light dependent in the dark-red 'Hongdeng' fruits. To reveal the transcriptional mechanisms regulating light-dependent anthocyanin accumulation in bicolored 'Rainier' cherries, we sequenced the transcriptomes of fruits grown in light or in darkness. Genes encoding the anthocyanin biosynthesis enzymes chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, and flavonoid 3'-hydroxylase were significantly upregulated by light in the bicolored fruits. Most of the differentially expressed regulatory genes were known to be involved in the light or hormone signal transduction pathways, such as those encoding protein phosphatase 2Cs, PHYTOCHROME INTERACTING FACTOR 3, phytochromes, and ELONGATED HYPOCOTYL 5. The expression levels of 32 highly expressed transcription factors were found to be significantly altered by light in the bicolored fruits, including members of the basic leucine zipper, R2R3-MYB, and WRKY transcription factor families. A co-expression network analysis further revealed that many of the light-regulated genes were co-expressed with genes involved in the abscisic acid and gibberellic acid signaling pathways, suggesting that these phytohormones play important roles in light-dependent anthocyanin biosynthesis. Together, our data reveal multiple roles for light in regulating anthocyanin biosynthesis in differently colored cherries.

The bZip transcription factor HY5 mediates CRY1a-induced anthocyanin biosynthesis in tomato

The production of anthocyanin is regulated by light and corresponding photoreceptors. In this study, we found that exposure to blue light and overexpression of CRY1a are associated with increased accumulation of anthocyanin in tomato (Solanum lycopersicum L.). These responses are the result of changes in mRNA and the protein levels of SlHY5, which is a transcription factor. In vitro and in vivo experiments using electrophoretic mobility shift assay and ChIP-qPCR assays revealed that SlHY5 could directly recognize and bind to the G-box and ACGT-containing element in the promoters of anthocyanin biosynthesis genes, such as chalcone synthase 1, chalcone synthase 2, and dihydroflavonol 4-reductase. Silencing of SlHY5 in OE-CRY1a lines decreased the accumulation of anthocyanin. The findings presented here not only deepened our understanding of how light controls anthocyanin biosynthesis and associated photoprotection in tomato leaves, but also allowed us to explore potential targets for improving pigment production.