Transcriptional regulatory network of the light signaling pathways

Genome-Wide Analysis and Expression Profiling of Soybean RbcS Family in Response to Plant Hormones and Functional Identification of GmRbcS8 in Soybean Mosaic Virus

Rubisco small subunit (RbcS), a core component with crucial effects on the structure and kinetic properties of the Rubisco enzyme, plays an important role in response to plant growth, development, and various stresses. Although Rbcs genes have been characterized in many plants, their muti-functions in soybeans remain elusive. In this study, a total of 11 GmRbcS genes were identified and subsequently divided into three subgroups based on a phylogenetic relationship. The evolutionary analysis revealed that whole-genome duplication has a profound effect on GmRbcSs. The cis-acting elements responsive to plant hormones, development, and stress-related were widely found in the promoter region. Expression patterns based on the RT-qPCR assay exhibited that GmRbcS genes are expressed in multiple tissues, and notably Glyma.19G046600 (GmRbcS8) exhibited the highest expression level compared to other members, especially in leaves. Moreover, differential expressions of GmRbcS genes were found to be significantly regulated by exogenous plant hormones, demonstrating their potential functions in diverse biology processes. Finally, the function of GmRbcS8 in enhancing soybean resistance to soybean mosaic virus (SMV) was further determined through the virus-induced gene silencing (VIGS) assay. All these findings establish a strong basis for further elucidating the biological functions of RbcS genes in soybeans.

B-BOX proteins:Multi-layered roles of molecular cogs in light-mediated growth and development in plants

B-box containing proteins (BBXs) are a class of zinc-ligating transcription factors or regulators that play essential roles in various physiological and developmental processes in plants. They not only directly associate with target genes to regulate their transcription, but also interact with other transcription factors to mediate target genes' expression, thus forming a complex transcriptional network ensuring plants' adaptation to dynamically changing light environments. This review summarizes and highlights the molecular and biochemical properties of BBXs, as well as recent advances with a focus on their critical regulatory functions in photomorphogenesis (de-etiolation), shade avoidance, photoperiodic-mediated flowering, and secondary metabolite biosynthesis and accumulation in plants.

Green light mediates atypical photomorphogenesis by dual modulation of Arabidopsis phytochromes B and A

Although green light (GL) is located in the middle of the visible light spectrum and regulates a series of plant developmental processes, the mechanism by which it regulates seedling development is largely unknown. In this study, we demonstrated that GL promotes atypical photomorphogenesis in Arabidopsis thaliana via the dual regulations of phytochrome B (phyB) and phyA. Although the Pr-to-Pfr conversion rates of phyB and phyA under GL were lower than those under red light (RL) in a fluence rate-dependent and time-dependent manner, long-term treatment with GL induced high Pfr/Pr ratios of phyB and phyA. Moreover, GL induced the formation of numerous small phyB photobodies in the nucleus, resulting in atypical photomorphogenesis, with smaller cotyledon opening angles and longer hypocotyls in seedlings compared to RL. The abundance of phyA significantly decreased after short- and long-term GL treatments. We determined that four major PHYTOCHROME-INTERACTING FACTORs (PIFs: PIF1, PIF3, PIF4, and PIF5) act downstream of phyB in GL-mediated cotyledon opening. In addition, GL plays opposite roles in regulating different PIFs. For example, under continuous GL, the protein levels of all PIFs decreased, whereas the transcript levels of PIF4 and PIF5 strongly increased compared with dark treatment. Taken together, our work provides a detailed molecular framework for understanding the role of the antagonistic regulations of phyB and phyA in GL-mediated atypical photomorphogenesis.

A Novel 10-Base Pair Deletion in the First Exon of GmHY2a Promotes Hypocotyl Elongation, Induces Early Maturation, and Impairs Photosynthetic Performance in Soybean

Plants photoreceptors perceive changes in light quality and intensity and thereby regulate plant vegetative growth and reproductive development. By screening a γ irradiation-induced mutant library of the soybean (Glycine max) cultivar "Dongsheng 7", we identified Gmeny, a mutant with elongated nodes, yellowed leaves, decreased chlorophyll contents, altered photosynthetic performance, and early maturation. An analysis of bulked DNA and RNA data sampled from a population segregating for Gmeny, using the BVF-IGV pipeline established in our laboratory, identified a 10 bp deletion in the first exon of the candidate gene Glyma.02G304700. The causative mutation was verified by a variation analysis of over 500 genes in the candidate gene region and an association analysis, performed using two populations segregating for Gmeny. Glyma.02G304700 (GmHY2a) is a homolog of AtHY2a in Arabidopsis thaliana, which encodes a PΦB synthase involved in the biosynthesis of phytochrome. A transcriptome analysis of Gmeny using the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed changes in multiple functional pathways, including photosynthesis, gibberellic acid (GA) signaling, and flowering time, which may explain the observed mutant phenotypes. Further studies on the function of GmHY2a and its homologs will help us to understand its profound regulatory effects on photosynthesis, photomorphogenesis, and flowering time.

Comprehensive genome-wide analysis of wheat xylanase inhibitor protein (XIP) genes: unveiling their role in Fusarium head blight resistance and plant immune mechanisms

In this comprehensive genome-wide study, we identified and classified 83 Xylanase Inhibitor Protein (XIP) genes in wheat, grouped into five distinct categories, to enhance understanding of wheat's resistance to Fusarium head blight (FHB), a significant fungal threat to global wheat production. Our analysis reveals the unique distribution of XIP genes across wheat chromosomes, particularly at terminal regions, suggesting their role in the evolutionary expansion of the gene family. Several XIP genes lack signal peptides, indicating potential alternative secretion pathways that could be pivotal in plant defense against FHB. The study also uncovers the sequence homology between XIPs and chitinases, hinting at a functional diversification within the XIP gene family. Additionally, the research explores the association of XIP genes with plant immune mechanisms, particularly their linkage with plant hormone signaling pathways like abscisic acid and jasmonic acid. XIP-7A3, in particular, demonstrates a significant increase in expression upon FHB infection, highlighting its potential as a key candidate gene for enhancing wheat's resistance to this disease. This research not only enriches our understanding of the XIP gene family in wheat but also provides a foundation for future investigations into their role in developing FHB-resistant wheat cultivars. The findings offer significant implications for wheat genomics and breeding, contributing to the development of more resilient crops against fungal diseases.

Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.)

The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.

Quantitative RUBY reporter assay for gene regulation analysis

Various reporter genes have been developed to study gene expression pattern and gene regulation. The RUBY reporter gene was recently developed and widely used, because of its visible and noninvasive advantages. However, quantitative analysis of RUBY gene expression levels was lacking. In this study, we introduce a novel betalain quantification method in combination with the tobacco transient expression system. The betalain produced in tobacco leaves was extracted and purified, and its concentration was quantitatively measured. We successfully applied this approach in studying the transcriptional regulation of ARC5 gene by transcription factors CPD25 and CPD45. Furthermore, with this method, we showed that the gene expression of RCA and Rbcs1A gene were regulated by light, transcription factors HY5 and PIFs through G-box and I-box elements. The development of this betalain quantification approach with the tobacco transient expression system offers a cost-effective and intuitive strategy for studying the regulatory mechanism of gene expression.

RACK1A promotes hypocotyl elongation by scaffolding light signaling components in Arabidopsis

Plants deploy versatile scaffold proteins to intricately modulate complex cell signaling. Among these, RACK1A (Receptors for Activated C Kinase 1A) stands out as a multifaceted scaffold protein functioning as a central integrative hub for diverse signaling pathways. However, the precise mechanisms by which RACK1A orchestrates signal transduction to optimize seedling development remain largely unclear. Here, we demonstrate that RACK1A facilitates hypocotyl elongation by functioning as a flexible platform that connects multiple key components of light signaling pathways. RACK1A interacts with PHYTOCHROME INTERACTING FACTOR (PIF)3, enhances PIF3 binding to the promoter of BBX11 and down-regulates its transcription. Furthermore, RACK1A associates with ELONGATED HYPOCOTYL 5 (HY5) to repress HY5 biochemical activity toward target genes, ultimately contributing to hypocotyl elongation. In darkness, RACK1A is targeted by CONSTITUTIVELY PHOTOMORPHOGENIC (COP)1 upon phosphorylation and subjected to COP1-mediated degradation via the 26 S proteasome system. Our findings provide new insights into how plants utilize scaffold proteins to regulate hypocotyl elongation, ensuring proper skoto- and photo-morphogenic development.

Histone dynamics responding to internal and external cues underlying plant development

Plants necessitate a refined coordination of growth and development to effectively respond to external triggers for survival and successful reproduction. This intricate harmonization of plant developmental processes and adaptability hinges on significant alterations within their epigenetic landscapes. In this review, we first delve into recent strides made in comprehending underpinning the dynamics of histones, driven by both internal and external cues. We encapsulate the prevailing working models through which cis/trans elements navigate the acquisition and removal of histone modifications, as well as the substitution of histone variants. As we look ahead, we anticipate that delving deeper into the dynamics of epigenetic regulation at the level of individual cells or specific cell types will significantly enrich our comprehension of how plant development unfolds under the influence of internal and external cues. Such exploration holds the potential to provide unprecedented resolution in understanding the orchestration of plant growth and development.

Responding to light signals: a comprehensive update on photomorphogenesis in cyanobacteria

Cyanobacteria are ancestors of chloroplast and perform oxygen-evolving photosynthesis similar to higher plants and algae. However, an obligatory requirement of photons for their growth results in the exposure of cyanobacteria to varying light conditions. Therefore, the light environment could act as a signal to drive the developmental processes, in addition to photosynthesis, in cyanobacteria. These Gram-negative prokaryotes exhibit characteristic light-dependent developmental processes that maximize their fitness and resource utilization. The development occurring in response to radiance (photomorphogenesis) involves fine-tuning cellular physiology, morphology and metabolism. The best-studied example of cyanobacterial photomorphogenesis is chromatic acclimation (CA), which allows a selected number of cyanobacteria to tailor their light-harvesting antenna called phycobilisome (PBS). The tailoring of PBS under existing wavelengths and abundance of light gives an advantage to cyanobacteria over another photoautotroph. In this work, we will provide a comprehensive update on light-sensing, molecular signaling and signal cascades found in cyanobacteria. We also include recent developments made in other aspects of CA, such as mechanistic insights into changes in the size and shape of cells, filaments and carboxysomes.

The PIF1/PIF3-MED25-HDA19 transcriptional repression complex regulates phytochrome signaling in Arabidopsis

Light signals are perceived by photoreceptors, triggering the contrasting developmental transition in dark-germinated seedlings. Phytochrome-interacting factors (PIFs) are key regulators of this transition. Despite their prominent functions in transcriptional activation, little is known about PIFs' roles in transcriptional repression. Here, we provide evidence that histone acetylation is involved in regulating phytochrome-PIFs signaling in Arabidopsis. The histone deacetylase HDA19 interacts and forms a complex with PIF1 and PIF3 and the Mediator subunit MED25. The med25/hda19 double mutant mimics and enhances the phenotype of pif1/pif3 in both light and darkness. HDA19 and MED25 are recruited by PIF1/PIF3 to the target loci to reduce histone acetylation and chromatin accessibility, providing a mechanism for PIF1/PIF3-mediated transcriptional repression. Furthermore, MED25 forms liquid-like condensates, which can compartmentalize PIF1/PIF3 and HDA19 in vitro and in vivo, and the number of MED25 puncta increases in darkness. Collectively, our study establishes a mechanism wherein PIF1/PIF3 interact with HDA19 and MED25 to mediate transcriptional repression in the phytochrome signaling pathway and suggests that condensate formation with Mediator may explain the distinct and specific transcriptional activity of PIF proteins.

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.

Emerging Roles of FHY3 and FAR1 as System Integrators in Plant Development

FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its homolog FAR-RED-IMPAIRED RESPONSE1 (FAR1) are transcription factors derived from transposases essential for phytochrome A-mediated light signaling. In addition to their essential role in light signaling, FHY3 and FAR1 also play diverse regulatory roles in plant growth and development, including clock entrainment, seed dormancy and germination, senescence, chloroplast formation, branching, flowering and meristem development. Notably, accumulating evidence indicates that the emerging role of FHY3 and FAR1 in environmental stress signaling has begun to be revealed. In this review, we summarize these recent findings in the context of FHY3 and FAR1 as integrators of light and other developmental and stressful signals. We also discuss the antagonistic action of FHY3/FAR1 and Phytochrome Interating Factors (PIFs) in various cross-talks between light, hormone and environmental cues.

Overexpression of a pseudo-etiolated-in-light-like protein in Taraxacum koksaghyz leads to a pale green phenotype and enables transcriptome-based network analysis of photomorphogenesis and isoprenoid biosynthesis

Introduction

Plant growth and greening in response to light require the synthesis of photosynthetic pigments such as chlorophylls and carotenoids, which are derived from isoprenoid precursors. In Arabidopsis, the pseudo-etiolated-in-light phenotype is caused by the overexpression of repressor of photosynthetic genes 2 (RPGE2), which regulates chlorophyll synthesis and photosynthetic genes.

Methods

We investigated a homologous protein in the Russian dandelion (Taraxacum koksaghyz) to determine its influence on the rich isoprenoid network in this species, using a combination of in silico analysis, gene overexpression, transcriptomics and metabolic profiling.

Results

Homology-based screening revealed a gene designated pseudo-etiolated-in-light-like (TkPEL-like), and in silico analysis identified a light-responsive G-box element in its promoter. TkPEL-like overexpression in dandelion plants and other systems reduced the levels of chlorophylls and carotenoids, but this was ameliorated by the mutation of one or both conserved cysteine residues. Comparative transcriptomics in dandelions overexpressing TkPEL-like showed that genes responsible for the synthesis of isoprenoid precursors and chlorophyll were downregulated, probably explaining the observed pale green leaf phenotype. In contrast, genes responsible for carotenoid synthesis were upregulated, possibly in response to feedback signaling. The evaluation of additional differentially expressed genes revealed interactions between pathways.

Discussion

We propose that TkPEL-like negatively regulates chlorophyll- and photosynthesis-related genes in a light-dependent manner, which appears to be conserved across species. Our data will inform future studies addressing the regulation of leaf isoprenoid biosynthesis and photomorphogenesis and could be used in future breeding strategies to optimize selected plant isoprenoid profiles and generate suitable plant-based production platforms.

Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice

Photoperiods integrate with the circadian clock to coordinate gene expression rhythms and thus ensure plant fitness to the environment. Genome-wide characterization and comparison of rhythmic genes under different light conditions revealed delayed phase under constant darkness (DD) and reduced amplitude under constant light (LL) in rice. Interestingly, ChIP-seq and RNA-seq profiling of rhythmic genes exhibit synchronous circadian oscillation in H3K9ac modifications at their loci and long non-coding RNAs (lncRNAs) expression at proximal loci. To investigate how gene expression rhythm is regulated in rice, we profiled the open chromatin regions and transcription factor (TF) footprints by time-series ATAC-seq. Although open chromatin regions did not show circadian change, a significant number of TFs were identified to rhythmically associate with chromatin and drive gene expression in a time-dependent manner. Further transcriptional regulatory networks mapping uncovered significant correlation between core clock genes and transcription factors involved in light/temperature signaling. In situ Hi-C of ZT8-specific expressed genes displayed highly connected chromatin association at the same time, whereas this ZT8 chromatin connection network dissociates at ZT20, suggesting the circadian control of gene expression by dynamic spatial chromatin conformation. These findings together implicate the existence of a synchronization mechanism between circadian H3K9ac modifications, chromatin association of TF and gene expression, and provides insights into circadian dynamics of spatial chromatin conformation that associate with gene expression rhythms.

Grapevine plantlets respond to different monochromatic lights by tuning photosynthesis and carbon allocation

The quality of planting materials is the foundation for productivity, longevity, and berry quality of perennial grapevines with a long lifespan. Manipulating the nursery light spectrum may speed up the production of healthy and high-quality planting vines but the underlying mechanisms remain elusive. Herein, the effects of different monochromatic lights (green, blue, and red) on grapevine growth, leaf photosynthesis, whole-plant carbon allocation, and transcriptome reprograming were investigated with white light as control. Results showed that blue and red lights were favorable for plantlet growth in comparison with white light. Blue light repressed excessive growth, significantly increased the maximum net photosynthetic rate (Pn) of leaves by 39.58% and leaf specific weight by 38.29%. Red light increased the dry weight of the stem by 53.60%, the starch content of the leaf by 53.63%, and the sucrose content of the stem by 230%. Green light reduced all photosynthetic indexes of the grape plantlet. Photosynthetic photon flux density (PPFD)/Ci-Pn curves indicated that blue light affected photosynthetic rate depending on the light intensity and CO2 concentration. RNA-seq analysis of different organs (leaf, stem, and root) revealed a systematic transcriptome remodeling and VvCOP1 (CONSTITUTIVELY PHOTOMORPHOGENIC 1), VvHY5 (ELONGATED HYPOCOTYL5), VvHYH (HY5 HOMOLOG), VvELIP (early light-induced protein) and VvPIF3 (PHYTOCHROME INTERACTING FACTOR 3) may play important roles in this shoot-to-root signaling. Furthermore, the correlation network between differential expression genes and physiological traits indicated that VvpsbS (photosystem II subunit S), Vvpsb28 (photosystem II subunit 28), VvHYH, VvSUS4 (sucrose synthase 4), and VvALDA (fructose-bisphosphate aldolase) were pertinent candidate genes in responses to different light qualities. Our results provide a foundation for optimizing the light recipe of grape plantlets and strengthen the understanding of light signaling and carbon metabolism under different monochromatic lights.

Phytochrome-interacting factor PIF3 integrates phytochrome B and UV-B signaling pathways to regulate gibberellin- and auxin-dependent growth in cucumber hypocotyls

In Arabidopsis, the photoreceptors phytochrome B (PhyB) and UV-B resistance 8 (UVR8) mediate light responses that play a major role in regulating photomorphogenic hypocotyl growth, but how they crosstalk to coordinate this process is not well understood. Here we report map-based cloning and functional characterization of an ultraviolet (UV)-B-insensitive, long-hypocotyl mutant, lh1, and a wild-type-like mutant, lh2, in cucumber (Cucumis sativus), which show defective CsPhyB and GA oxidase2 (CsGA20ox-2), a key gibberellic acid (GA) biosynthesis enzyme, respectively. The lh2 mutation was epistatic to lh1 and partly suppressed the long-hypocotyl phenotype in the lh1lh2 double mutant. We identified phytochrome interacting factor (PIF) CsPIF3 as playing a critical role in integrating the red/far-red and UV-B light responses for hypocotyl growth. We show that two modules, CsPhyB-CsPIF3-CsGA20ox-2-DELLA and CsPIF3-auxin response factor 18 (CsARF18), mediate CsPhyB-regulated hypocotyl elongation through GA and auxin pathways, respectively, in which CsPIF3 binds to the G/E-box motifs in the promoters of CsGA20ox-2 and CsARF18 to regulate their expression. We also identified a new physical interaction between CsPIF3 and CsUVR8 mediating CsPhyB-dependent, UV-B-induced hypocotyl growth inhibition. Our work suggests that hypocotyl growth in cucumber involves a complex interplay of multiple photoreceptor- and phytohormone-mediated signaling pathways that show both conservation with and divergence from those in Arabidopsis.

ZmCOP1 Regulates Maize Mesocotyl Length and Plant Height through the Phytohormone Pathways

The morphogenesis of crops is critical to their yield performance. COP1 (constitutively photomorphogenic1) is one of the core regulators in plant morphogenesis and has been deeply studied in Arabidopsis thaliana. However, the function of COP1 in maize is still unclear. Here, we found that the mesocotyl lengths of zmcop1 loss-of-function mutants were shorter than those of wild-type B73 in darkness, while the mesocotyl lengths of lines with ZmCOP1 overexpression were longer than those of wild-type B104. The plant height with zmcop1 was shorter than that of B73 in both short- and long-day photoperiods. Using transcriptome RNA sequencing technology, we identified 33 DEGs (differentially expressed genes) between B73's etiolated seedlings and those featuring zmcop1, both in darkness. The DEGs were mainly enriched in the plant phytohormone pathways. Our results provide direct evidence that ZmCOP1 functions in the elongation of etiolated seedlings in darkness and affects plant height in light. Our data can be applied in the improvement of maize plant architecture.

γ-Glutamyl-transpeptidase CsGGT2 functions as light-activated theanine hydrolase in tea plant (Camellia sinensis L.)

Theanine is an important secondary metabolite endowing tea with umami taste and health effects. It is essential to explore the metabolic pathway and regulatory mechanism of theanine to improve tea quality. Here, we demonstrated that the expression patterns of CsGGT2 (γ-glutamyl-transpeptidase), participated in theanine synthesis in vitro in our previous research, are significantly different in the aboveground and underground tissues of tea plants and regulated by light. Light up-regulated the expression of CsHY5, directly binding to the promoter of CsGGT2 and acting as an activator of CsGGT2, with a negative correlation with theanine accumulation. The enzyme activity assays and transient expression in Nicotiana benthamiana showed that CsGGT2, acting as bifunctional protein, synthesize and degrade theanine in vitro and in planta. The results of enzyme kinetics, Surface plasmon resonance (SPR) assays and targeted gene-silencing assays showed that CsGGT2 had a higher substrate affinity of theanine than that of ethylamine, and performed a higher theanine degradation catalytic efficiency. Therefore, light mediates the degradation of theanine in different tissues by regulating the expression of the theanine hydrolase CsGGT2 in tea plants, and these results provide new insights into the degradation of theanine mediated by light in tea plants.

Integration of light and ABA signaling pathways to combat drought stress in plants

Drought is one of the most critical stresses, which causes an enormous reduction in crop yield. Plants develop various strategies like drought escape, drought avoidance, and drought tolerance to cope with the reduced availability of water during drought. Plants adopt several morphological and biochemical modifications to fine-tune their water-use efficiency to alleviate drought stress. ABA accumulation and signaling plays a crucial role in the response of plants towards drought. Here, we discuss how drought-induced ABA regulates the modifications in stomatal dynamics, root system architecture, and the timing of senescence to counter drought stress. These physiological responses are also regulated by light, indicating the possibility of convergence of light- and drought-induced ABA signaling pathways. In this review, we provide an overview of investigations reporting light-ABA signaling cross talk in Arabidopsis as well as other crop species. We have also tried to describe the potential role of different light components and their respective photoreceptors and downstream factors like HY5, PIFs, BBXs, and COP1 in modulating drought stress responses. Finally, we highlight the possibilities of enhancing the plant drought resilience by fine-tuning light environment or its signaling components in the future.

Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii

Comprehensive utilization of cottonseeds is limited by the presence of pigment glands and its inclusion gossypol. The ideal cotton has glandless seeds but a glanded plant, a trait found in only a few Australian wild cotton species, including Gossypium bickii. Introgression of this trait into cultivated species has proved to be difficult. Understanding the biological processes toward pigment gland morphogenesis and the associated underlying molecular mechanisms will facilitate breeding of cultivated cotton varieties with the trait of glandless seeds and glanded plant. In this study, single-cell RNA sequencing (scRNA-seq) was performed on 12 222 protoplasts isolated from cotyledons of germinating G. bickii seeds 48 h after imbibition. Clustered into 14 distinct clusters unsupervisedly, these cells could be grouped into eight cell populations with the assistance of known cell marker genes. The pigment gland cells were well separated from others and could be separated into pigment gland parenchyma cells, secretory cells, and apoptotic cells. By integrating the pigment gland cell developmental trajectory, transcription factor regulatory networks, and core transcription factor functional validation, we established a model for pigment gland formation. In this model, light and gibberellin were verified to promote the formation of pigment glands. In addition, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11), and GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), were found to affect pigment gland formation. Collectively, these findings provide new insights into pigment gland morphogenesis and lay the cornerstone for future cotton scRNA-seq investigations.

Spectral light quality regulates the morphogenesis, architecture, and flowering in pepper (Capsicum annuum L.)

Transparent plastic films with poor light transmittance seriously affect the mass composition of visible light in many greenhouses, which leads to the reduction of photosynthesis in vegetable crops. Understanding the regulatory mechanisms of monochromatic light in the vegetative and reproductive growth of vegetable crops is of great importance for the application of light-emitting diodes (LEDs) in the greenhouse. In this study, three monochromatic light treatments (red-, green- and blue-light) were simulated by using LEDs to explore light quality-dependent regulation from the stage of seedling to flowering in pepper (Capsicum annuum L.). The results showed that light quality-dependent regulation guides the growth and morphogenesis in pepper plants. Red- and blue-light played opposite roles in determining the plant height, stomatal density, axillary bud growth, photosynthetic characteristics, flowering time and hormone metabolism, while green light treatment resulted in taller plants and fewer branches, which was similar to the red-light treatment. The weighted correlation network analysis (WGCNA) based on mRNA-seq results revealed that the two modules named "MEred" and "MEmidnightblue" were positively correlated with red- and blue-light treatment, respectively, exhibiting high correlations with the traits such as plant hormone content, branching and flowering. Moreover, our results suggest that the light response factor ELONGATED HYPOCOTYL 5 (HY5) is essential for blue light-induced plant growth and development by regulating photosynthesis in pepper plants. Hence, this study uncovers crucial molecular mechanisms of how light quality determines the morphogenesis, architecture, and flowering in pepper plants, thus providing a basic concept of manipulating light quality to regulate pepper plant growth and flowering under greenhouse conditions.

Light plays a critical role in the accumulation of chlorogenic acid in Lonicera macranthoides Hand.-Mazz

Light has important effects on plant metabolism. However, the relationship between the chlorogenic acid (CGA) content and light in plants remains unclear. Here, we investigated the effects of shading treatment on gene expression and CGA content in Lonicera macranthoides Hand.-Mazz. (LM), a widely used medicinal plant. A total of 1891 differentially expressed genes (DEGs) were obtained in flower buds and 819 in leaves in response to light in shading treatment compared to the control sample by RNA-Seq. After shading treatment, the content of CGA in LM leaves decreased significantly by 1.78-fold, the carotenoid content increased, and the soluble sugar and starch contents significantly decreased. WGCNA and the expression of related genes verified by qRT‒PCR revealed that CGA synthesis pathway enzyme genes form a co-expression network with genes for carbohydrate synthesis, photosynthesis, light signalling elements, and transcription factor genes (TFs) that affect the accumulation of CGA. Through a virus-induced gene silencing (VIGS) system and CGA assay in Nicotiana benthamiana (NB), we determined that downregulation of NbHY5 expression decreased the CGA content in NB leaves. In this study, we found that light provides energy and material for the accumulation of CGA in LM, and light affects the expression of CGA accumulation-related genes. Our results show that different light intensities have multiple effects on leaves and flower buds in LM and are able to coregulate LmHY5 expression and CGA synthesis.

A Novel LED Light Radiation Approach Enhances Growth in Green and Albino Tea Varieties

Light, as an energy source, has been proven to strongly affect photosynthesis and, thus, can regulate the yield and quality of tea leaves (Camellia sinensis L.). However, few comprehensive studies have investigated the synergistic effects of light wavelengths on tea growth and development in green and albino varieties. Thus, the objective of this study was to investigate different ratios of red, blue and yellow light and their effects on tea plants' growth and quality. In this study, Zhongcha108 (green variety) and Zhongbai4 (albino variety) were exposed to lights of different wavelengths for a photoperiod of 5 months under the following seven treatments: white light simulated from the solar spectrum, which served as the control, and L1 (red 75%, blue 15% and yellow 10%), L2 (red 60%, blue 30% and yellow 10%), L3 (red 45%, far-red light 15%, blue 30% and yellow 10%), L4 (red 55%, blue 25% and yellow 20%), L5 (red 45%, blue 45% and yellow 10%) and L6 (red 30%, blue 60% and yellow 10%), respectively. We examined how different ratios of red light, blue light and yellow light affected tea growth by investigating the photosynthesis response curve, chlorophyll content, leaf structure, growth parameters and quality. Our results showed that far-red light interacted with red, blue and yellow light (L3 treatments) and significantly promoted leaf photosynthesis by 48.51% in the green variety, Zhongcha108, compared with the control treatments, and the length of the new shoots, number of new leaves, internode length, new leaf area, new shoots biomass and leaf thickness increased by 70.43%, 32.64%, 25.97%, 15.61%, 76.39% and 13.30%, respectively. Additionally, the polyphenol in the green variety, Zhongcha108, was significantly increased by 15.6% compared to that of the plants subjected to the control treatment. In addition, for the albino variety Zhongbai4, the highest ratio of red light (L1 treatment) remarkably enhanced leaf photosynthesis by 50.48% compared with the plants under the control treatment, resulting in the greatest new shoot length, number of new leaves, internode length, new leaf area, new shoot biomass, leaf thickness and polyphenol in the albino variety, Zhongbai4, compared to those of the control treatments, which increased by 50.48%, 26.11%, 69.29%, 31.61%, 42.86% and 10.09%, respectively. Our study provided these new light modes to serve as a new agricultural method for the production of green and albino varieties.

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

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

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.

Combined transcriptome and metabolome analysis reveals the effects of light quality on maize hybrids

BACKGROUND

Heterosis, or hybrid vigor, refers to the phenotypic superiority of an F₁ hybrid relative to its parents in terms of growth rate, biomass production, grain yield, and stress tolerance. Light is an energy source and main environmental cue with marked impacts on heterosis in plants. Research into the production applications and mechanism of heterosis has been conducted for over a century and a half, but little is known about the effect of light on plant heterosis.

RESULTS

In this study, an integrated transcriptome and metabolome analysis was performed using maize (Zea mays L.) inbred parents, B73 and Mo17, and their hybrids, B73 × Mo17 (BM) and Mo17 × B73 (MB), grown in darkness or under far-red, red, or blue light. Most differentially expressed genes (73.72-92.50%) and differentially accumulated metabolites (84.74-94.32%) exhibited non-additive effects in BM and MB hybrids. Gene Ontology analysis revealed that differential genes and metabolites were involved in glutathione transfer, carbohydrate transport, terpenoid biosynthesis, and photosynthesis. The darkness, far-red, red, and blue light treatments were all associated with phenylpropanoid-flavonoid biosynthesis by Weighted Gene Co-expression Network Analysis and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Five genes and seven metabolites related to phenylpropanoid-flavonoid biosynthesis pathway were identified as potential contributors to the interactions between maize heterosis and light conditions. Consistent with the strong mid-parent heterosis observed for metabolites, significant increases in both fresh and dry weights were found in the MB and BM hybrids compared with their inbred parents. Unexpectedly, increasing light intensity resulted in higher biomass heterosis in MB, but lower biomass heterosis in BM.

CONCLUSIONS

The transcriptomic and metabolomic results provide unique insights into the effects of light quality on gene expression patterns and genotype-environment interactions, and have implications for gene mining of heterotic loci to improve maize production.

The Integration of Metabolomics and Transcriptomics Provides New Insights for the Identification of Genes Key to Auxin Synthesis at Different Growth Stages of Maize

As a staple food crop, maize is widely cultivated worldwide. Sex differentiation and kernel development are regulated by auxin, but the mechanism regulating its synthesis remains unclear. This study explored the influence of the growth stage of maize on the secondary metabolite accumulation and gene expression associated with auxin synthesis. Transcriptomics and metabonomics were used to investigate the changes in secondary metabolite accumulation and gene expression in maize leaves at the jointing, tasseling, and pollen-release stages of plant growth. In total, 1221 differentially accumulated metabolites (DAMs) and 4843 differentially expressed genes (DEGs) were screened. KEGG pathway enrichment analyses of the DEGs and DAMs revealed that plant hormone signal transduction, tryptophan metabolism, and phenylpropanoid biosynthesis were highly enriched. We summarized the key genes and regulatory effects of the tryptophan-dependent auxin biosynthesis pathways, giving new insights into this type of biosynthesis. Potential MSTRG.11063 and MSTRG.35270 and MSTRG.21978 genes in auxin synthesis pathways were obtained. A weighted gene co-expression network analysis identified five candidate genes, namely TSB (Zm00001d046676 and Zm00001d049610), IGS (Zm00001d020008), AUX2 (Zm00001d006283), TAR (Zm00001d039691), and YUC (Zm00001d025005 and Zm00001d008255), which were important in the biosynthesis of both tryptophan and auxin. This study provides new insights for understanding the regulatory mechanism of auxin synthesis in maize.

Melatonin biosynthesis and signal transduction in plants in response to environmental conditions

Melatonin, the most widely distributed hormone in nature, plays important roles in plants. Many physiological processes in plants are linked to melatonin, including seed germination, anisotropic cell growth, and senescence. Compared with animals, different plants possess diverse melatonin biosynthetic pathways and regulatory networks. Whereas melatonin biosynthesis in animals is known to be regulated by ambient signals, little is known about how melatonin biosynthesis in plants responds to environmental signals. Plants are affected by numerous environmental factors, such as light, temperature, moisture, carbon dioxide, soil conditions, and nutrient availability at all stages of development and in different tissues. Melatonin content exhibits dynamic changes that affect plant growth and development. Melatonin plays various species-specific roles in plant responses to different environmental conditions. However, much remains to be learned, as not all environmental factors have been studied, and little is known about the mechanisms by which these factors influence melatonin biosynthesis. In this review, we provide a detailed, systematic description of melatonin biosynthesis and signaling and of the roles of melatonin in plant responses to different environmental factors, providing a reference for in-depth research on this important issue.

Transcriptional regulation of photomorphogenesis in seedlings of Brassica napus under different light qualities

This study displayed the transcriptional regulation network of key regulators and downstream pathway in seedling morphogenesis of Brassica napus under different light quality. Plants undergo photomorphogenesis upon the presence of light, mediated by different light (e.g., blue, red, and far-red) signaling pathways. Although the light signaling pathway has been well documented in Arabidopsis, the underlying mechanisms were studied to a less extent in other plant species including Brassica napus. In this study, we investigated the effect of different light qualities (white, blue, red, and far-red light) on the hypocotyl elongation in B. napus, and performed the transcriptomic analysis of seedlings in response to different light qualities. The results showed that hypocotyl elongation was slightly inhibited by red light, while it was strongly inhibited by blue/far-red light. Transcriptome analysis identified 9748 differentially expressed genes (DEGs) among treatments. Gene ontology (GO) enrichment analysis of DEGs showed that light-responsive and photosynthesis-related genes were highly expressed in response to blue/far-red light rather than in red light. Furthermore, the key genes in light signaling (i.e., PHYB, HY5, HYH, HFR1, and PIF3) exhibited distinct expression patterns between blue/far-red and red light treatments. In addition, subgenome dominant expression of homoeologous genes were observed for some genes, such as PHYA, PHYB, HFR1, and BBXs. The current study displayed a comprehensive dissection of light-mediated transcriptional regulation network, including light signaling, phytohormone, and cell elongation/modification, which improved the understanding on the underlying mechanism of light-regulated hypocotyl growth in B. napus.

PIFs- and COP1-HY5-mediated temperature signaling in higher plants

Plants have to cope with the surrounding changing environmental stimuli to optimize their physiological and developmental response throughout their entire life cycle. Light and temperature are two critical environmental cues that fluctuate greatly during day-night cycles and seasonal changes. These two external signals coordinately control the plant growth and development. Distinct spectrum of light signals are perceived by a group of wavelength-specific photoreceptors in plants. PIFs and COP1-HY5 are two predominant signaling hubs that control the expression of a large number of light-responsive genes and subsequent light-mediated development in plants. In parallel, plants also transmit low or warm temperature signals to these two regulatory modules that precisely modulate the responsiveness of low or warm temperatures. The core component of circadian clock ELF3 integrates signals from light and warm temperatures to regulate physiological and developmental processes in plants. In this review, we summarize and discuss recent advances and progresses on PIFs-, COP1-HY5- and ELF3-mediated light, low or warm temperature signaling, and highlight emerging insights regarding the interactions between light and low or warm temperature signal transduction pathways in the control of plant growth.

Cia Zeaxanthin Biosynthesis, OsZEP and OsVDE Regulate Striped Leaves Occurring in Response to Deep Transplanting of Rice

The rice leaf color mutant B03S was previously generated from the photoperiod- and thermo-sensitive genic male sterile (PTGMS) rice line Efeng 1S, of which male sterility manifests by photoperiod and temperature but exhibits mainly temperature-sensitive characteristics. After these plants were deeply transplanted, the new leaves manifested typical zebra stripe patterns. Here, B03S was subjected to deep and shallow transplanting, shading with soil and aluminum foil, and control conditions in situ to determine the cause of the striped-leaf trait. The direct cause of striped leaves is the base of the leaf sheath being under darkness during deep transplanting, of which the critical shading range reached or exceeds 4 cm above the base. Moreover, typical striped leaves were analyzed based on the targeted metabolome method by ultra-performance liquid chromatography/tandem mass spectrometry (UPLC–MS/MS) combined with transcriptome and real-time quantitative PCR (qPCR)-based verification to clarify the metabolic pathways and transcriptional regulation involved. Carotenoids enter the xanthophyll cycle, and the metabolites that differentially accumulate in the striped leaves include zeaxanthin and its derivatives for photooxidative stress protection, driven by the upregulated expression of OsZEP. These findings improve the understanding of the physiological and metabolic mechanisms underlying the leaf color mutation in rice plants, enrich the theoretical foundation of the nonuniform leaf color phenomenon widely found in nature and highlight key advancements concerning rice production involving the transplanting of seedlings or direct broadcasting of seeds.

Light quality as a driver of photosynthetic apparatus development

Light provides energy for photosynthesis and also acts as an important environmental signal. During their evolution, plants acquired sophisticated sensory systems for light perception and light-dependent regulation of their growth and development in accordance with the local light environment. Under natural conditions, plants adapted by using their light sensors to finely distinguish direct sunlight and dark in the soil, deep grey shade under the upper soil layer or litter, green shade under the canopy and even lateral green reflectance from neighbours. Light perception also allows plants to evaluate in detail the weather, time of day, day length and thus the season. However, in artificial lighting conditions, plants are confronted with fundamentally different lighting conditions. The advent of new light sources - light-emitting diodes (LEDs), which emit narrow-band light - allows growing plants with light of different spectral bands or their combinations. This sets the task of finding out how light of different quality affects the development and functioning of plants, and in particular, their photosynthetic apparatus (PSA), which is one of the basic processes determining plant yield. In this review, we briefly describe how plants perceive environment light signals by their five families of photoreceptors and by the PSA as a particular light sensor, and how they use this information to form their PSA under artificial narrow-band LED-based lighting of different spectral composition. We consider light regulation of the biosynthesis of photosynthetic pigments, photosynthetic complexes and chloroplast ATP synthase function, PSA photoprotection mechanisms, carbon assimilation reactions and stomatal development and function.

Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L

The availability and intensity of sunlight are among the major factors of growth, development and metabolism in plants. However, excessive illumination disrupts the electronic balance of photosystems and leads to the accumulation of reactive oxygen species in chloroplasts, further mediating several regulatory mechanisms at the subcellular, genetic, and molecular levels. We carried out a comprehensive bioinformatic analysis that aimed to identify genetic systems and candidate transcription factors involved in the response to high light stress in Arabidopsis thaliana L. using resources GEO NCBI, string-db, ShinyGO, STREME, and Tomtom, as well as programs metaRE, CisCross, and Cytoscape. Through the meta-analysis of five transcriptomic experiments, we selected a set of 1151 differentially expressed genes, including 453 genes that compose the gene network. Ten significantly enriched regulatory motifs for TFs families ZF-HD, HB, C2H2, NAC, BZR, and ARID were found in the promoter regions of differentially expressed genes. In addition, we predicted families of transcription factors associated with the duration of exposure (RAV, HSF), intensity of high light treatment (MYB, REM), and the direction of gene expression change (HSF, S1Fa-like). We predicted genetic components systems involved in a high light response and their expression changes, potential transcriptional regulators, and associated processes.

MSD2, an apoplastic Mn-SOD, contributes to root skotomorphogenic growth by modulating ROS distribution in Arabidopsis

Reactive oxygen species (ROS) play essential roles as a second messenger in various physiological processes in plants. Due to their oxidative nature, ROS can also be harmful. Thus, the generation and homeostasis of ROS are tightly controlled by multiple enzymes. Membrane-localized NADPH oxidases are well known to generate ROS during developmental and stress responses, but the metabolic pathways of the superoxide (O2^-) generated by them in the apoplast are poorly understood, and the identity of the apoplastic superoxide dismutase (SOD) is unknown in Arabidopsis. Here, we show that a putative manganese SOD, MSD2 is secreted and possesses a SOD activity that can be inhibited by nitration at tyrosine 68. The expression of MSD2 in roots is light condition-dependent, suggesting that MSD2 may act on ROS metabolism in roots during the light-to-dark transition. Root architecture is governed by ROS distribution that exhibits opposite gradient of H₂O₂ and O2^-, which is indeed altered in etiolated msd2 mutants and accompanied by changes in the onset of differentiation. These results provide a missing link in our understanding of ROS metabolism and suggest that MSD2 plays a role in root skotomorphogenesis by regulating ROS distribution, thereby playing a pivotal role in plant growth and development.

BBX16 mediates the repression of seedling photomorphogenesis downstream of the GUN1/GLK1 module during retrograde signalling

Plastid-to-nucleus retrograde signalling (RS) initiated by dysfunctional chloroplasts impact photomorphogenic development. We have previously shown that the transcription factor GLK1 acts downstream of the RS regulator GUN1 in photodamaging conditions to regulate not only the well established expression of photosynthesis-associated nuclear genes (PhANGs) but also to regulate seedling morphogenesis. Specifically, the GUN1/GLK1 module inhibits the light-induced phytochrome-interacting factor (PIF)-repressed transcriptional network to suppress cotyledon development when chloroplast integrity is compromised, modulating the area exposed to potentially damaging high light. However, how the GUN1/GLK1 module inhibits photomorphogenesis upon chloroplast damage remained undefined. Here, we report the identification of BBX16 as a novel direct target of GLK1. BBX16 is induced and promotes photomorphogenesis in moderate light and is repressed via GUN1/GLK1 after chloroplast damage. Additionally, we showed that BBX16 represents a regulatory branching point downstream of GUN1/GLK1 in the regulation of PhANG expression and seedling development upon RS activation. The gun1 phenotype in lincomycin and the gun1-like phenotype of GLK1OX are markedly suppressed in gun1bbx16 and GLK1OXbbx16. This study identified BBX16 as the first member of the BBX family involved in RS, and defines a molecular bifurcation mechanism operated by GLK1/BBX16 to optimise seedling de-etiolation, and to ensure photoprotection in unfavourable light conditions.

Comparative transcriptome analysis revealed the molecular mechanism of the effect of light intensity on the accumulation of rhynchophylline and isorhynchophylline in Uncaria rhynchophylla

Rhynchophylline (RIN) and isorhynchophylline (IRN), the main medicinal components in plant Uncaria rhynchophylla, have potential effects on Alzheimer's disease. Understanding the influence of environmental factors, especially light intensity, on the production of these active ingredients will help to improve cultivation techniques. Compared with the 100% light intensity (CK), the contents of RIN and IRN in U. rhynchophylla leaves significantly increased at 20% light intensity (HS) after 7 and 21 days. Short-term shading (21d) changed some morphological indicators of U. rhynchophylla, but did not affect its biomass. Transcriptome profile analysis was performed on data from two groups (7 and 21 days) of CK and HS samples and yielded 79,817 unigenes with an average length of 1023 bp. Concurrently, 2391 and 2136 differentially expressed genes were identified in the transcriptome data for, respectively, 7 and 21 days of shade treatment. Notably, unigenes known to be involved upstream in the biosynthesis of RIN and IRN, such as G8O, IO, 7-DLGT, LAMT, TDC, and STR, were mostly upregulated. In addition, 1065 putative transcription factors (TFs) were identified and grouped into 55 TF families; 26 TFs showed differential expression in the shade treatment after 7 and 21 days. HY5 and PIFs, two important TFs of the light signaling pathway, also showed differential expression. This study provides insight into how gene expression was affected by light intensity during RIN and IRN accumulation in U. rhynchophylla.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01142-2.

The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues

As sessile organisms, plants are finely tuned to respond dynamically to developmental, circadian and environmental cues. Genome-wide studies investigating these types of cues have uncovered the intrinsically different ways they can impact gene expression over time. Recent advances in single-cell sequencing and time-based bioinformatic algorithms are now beginning to reveal the dynamics of these time-based responses within individual cells and plant tissues. Here, we review what these techniques have revealed about the spatiotemporal nature of gene regulation, paying particular attention to the three distinct ways in which plant tissues are time sensitive. (i) First, we discuss how studying plant cell identity can reveal developmental trajectories hidden in pseudotime. (ii) Next, we present evidence that indicates that plant cell types keep their own local time through tissue-specific regulation of the circadian clock. (iii) Finally, we review what determines the speed of environmental signaling responses, and how they can be contingent on developmental and circadian time. By these means, this review sheds light on how these different scales of time-based responses can act with tissue and cell-type specificity to elicit changes in whole plant systems.

Origin and adaptive evolution of UV RESISTANCE LOCUS 8-mediated signaling during plant terrestrialization

UV RESISTANCE LOCUS 8 (UVR8) mediates photomorphogenic responses and acclimation to UV-B radiation by regulating the transcription of a series of transcription factors (TFs). However, the origin and evolution of UVR8-mediated signaling pathways remain largely unknown. In this study, we investigated the origin and evolution of the major components of the UVR8-mediated signaling pathway (UVR8, REPRESSOR OF UV-B PHOTOMORPHOGENESIS [RUP], BRI1-EMS-SUPPRESSOR1 [BES1], BES1-INTERACTING MYC-LIKE 1 (BIM1), WRKY DNA-BINDING PROTEIN 36 (WRKY36), MYB DOMAIN PROTEIN 73/77/13 [MYB73/MYB77/MYB13], and PHYTOCHROME INTERACTING FACTOR 4/5 [PIF4 and PIF5]) using comparative genomics and phylogenetic approaches. We showed that the central regulator UVR8 presented a conservative evolutionary route during plant evolution, and the evolutionary history of downstream negative regulators and TFs was different from that of green plant phylogeny. The canonical UVR8-CONSTITUTIVELY PHOTOMORPHOGENIC 1(COP1)/SUPPRESSOR OF PHYA-105 (SPA)-ELONGATED HYPOCOTYL 5 (HY5)-RUP signaling pathway originated in chlorophytes and conferred green algae the additional ability to cope with UV-B radiation. Moreover, the emergence of multiple UVR8-mediated signaling pathways in charophytes laid the foundations for the cross-talk between UV-B signals and endogenous hormone responses. Importantly, we observed signatures that reflect plant adaptations to high UV-B irradiance in subaerial/terrestrial environments, including positive selection in UVR8 and RUPs and increased copy number of some vital TFs. These results revealed that green plants not only experienced adaptive modifications in the canonical UVR8-COP1/SPA-HY5-RUP signaling pathway, but also diversified their UV-B signal transduction mechanisms through increasing cross-talk with other pathways, such as those associated with brassinosteroids and auxin. This study greatly expands our understanding of molecular evolution and adaptive mechanisms underlying plant UV-B acclimation.

HY5: A Pivotal Regulator of Light-Dependent Development in Higher Plants

ELONGATED HYPOCOTYL5 (HY5), a bZIP-type transcription factor, acts as a master regulator that regulates various physiological and biological processes in plants such as photomorphogenesis, root growth, flavonoid biosynthesis and accumulation, nutrient acquisition, and response to abiotic stresses. HY5 is evolutionally conserved in function among various plant species. HY5 acts as a master regulator of light-mediated transcriptional regulatory hub that directly or indirectly controls the transcription of approximately one-third of genes at the whole genome level. The transcription, protein abundance, and activity of HY5 are tightly modulated by a variety of factors through distinct regulatory mechanisms. This review primarily summarizes recent advances on HY5-mediated molecular and physiological processes and regulatory mechanisms on HY5 in the model plant Arabidopsis as well as in crops.

The Unicellular Red Alga Cyanidioschyzon merolae-The Simplest Model of a Photosynthetic Eukaryote

Several species of unicellular eukaryotic algae exhibit relatively simple genomic and cellular architecture. Laboratory cultures of these algae grow faster than plants and often provide homogeneous cellular populations exposed to an almost equal environment. These characteristics are ideal for conducting experiments at the cellular and subcellular levels. Many microalgal lineages have recently become genetically tractable, which have started to evoke new streams of studies. Among such algae, the unicellular red alga Cyanidioschyzon merolae is the simplest organism; it possesses the minimum number of membranous organelles, only 4,775 protein-coding genes in the nucleus, and its cell cycle progression can be highly synchronized with the diel cycle. These properties facilitate diverse omics analyses of cellular proliferation and structural analyses of the intracellular relationship among organelles. C. merolae cells lack a rigid cell wall and are thus relatively easily disrupted, facilitating biochemical analyses. Multiple chromosomal loci can be edited by highly efficient homologous recombination. The procedures for the inducible/repressive expression of a transgene or an endogenous gene in the nucleus and for chloroplast genome modification have also been developed. Here, we summarize the features and experimental techniques of C. merolae and provide examples of studies using this alga. From these studies, it is clear that C. merolae-either alone or in comparative and combinatory studies with other photosynthetic organisms-can provide significant insights into the biology of photosynthetic eukaryotes.

Calmodulin7: recent insights into emerging roles in plant development and stress

Analyses of the function of Arabidopsis Calmodulin7 (CAM7) in concert with multiple regulatory proteins involved in various signal transduction processes. Calmodulin (CaM) plays various regulatory roles in multiple signaling pathways in eukaryotes. Arabidopsis CALMODULIN 7 (CAM7) is a unique member of the CAM family that works as a transcription factor in light signaling pathways. CAM7 works in concert with CONSTITUTIVE PHOTOMORPHOGENIC 1 and ELONGATED HYPOCOTYL 5, and plays an important role in seedling development. Further, it is involved in the regulation of the activity of various Ca²⁺-gated channels such as cyclic nucleotide gated channel 6 (CNGC6), CNGC14 and auto-inhibited Ca²⁺ ATPase 8. Recent studies further indicate that CAM7 is also an integral part of multiple signaling pathways including hormone, immunity and stress. Here, we review the recent advances in understanding the multifaceted role of CAM7. We highlight the open-ended questions, and also discuss the diverse aspects of CAM7 characterization that need to be addressed for comprehensive understanding of its cellular functions.

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

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

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.

BBX11 promotes red light-mediated photomorphogenic development by modulating phyB-PIF4 signaling

phytochrome B (phyB) acts as the red light photoreceptor and negatively regulates the growth-promoting factor PHYTOCHROME INTERACTING 4 (PIF4) through a direct physical interaction, which in turn changes the expression of a large number of genes. phyB-PIF4 module regulates a variety of biological and developmental processes in plants. In this study, we demonstrate that B-BOX PROTEIN 11 (BBX11) physically interacts with both phyB and PIF4. BBX11 negatively regulates PIF4 accumulation as well as its biochemical activity, consequently leading to the repression of PIF4-controlled genes' expression and promotion of photomorphogenesis in the prolonged red light. This study reveals a regulatory mechanism that mediates red light signal transduction and sheds a light on phyB-PIF4 module in promoting red light-dependent photomorphognenesis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-021-00037-2.

Transformation of Long-Lived Albino Epipremnum aureum 'Golden Pothos' and Restoring Chloroplast Development

Chloroplasts are organelles responsible for chlorophyll biosynthesis, photosynthesis, and biosynthesis of many metabolites, which are one of key targets for crop improvement. Elucidating and engineering genes involved in chloroplast development are important approaches for studying chloroplast functions as well as developing new crops. In this study, we report a long-lived albino mutant derived from a popular ornamental plant Epipremnum aureum 'Golden Pothos' which could be used as a model for analyzing the function of genes involved in chloroplast development and generating colorful plants. Albino mutant plants were isolated from regenerated populations of variegated 'Golden Pothos' whose albino phenotype was previously found to be due to impaired expression of EaZIP, encoding Mg-protoporphyrin IX monomethyl ester cyclase. Using petioles of the mutant plants as explants with a traceable sGFP gene, an efficient transformation system was developed. Expressing Arabidopsis CHL27 (a homolog of EaZIP) but not EaZIP in albino plants restored green color and chloroplast development. Interestingly, in addition to the occurrence of plants with solid green color, plants with variegated leaves and pale-yellow leaves were also obtained in the regenerated populations. Nevertheless, our study shows that these long-lived albino plants along with the established efficient transformation system could be used for creating colorful ornamental plants. This system could also potentially be used for investigating physiological processes associated with chlorophyll levels and chloroplast development as well as certain biological activities, which are difficult to achieve using green plants.

Transcriptional Dynamics of Genes Purportedly Involved in the Control of Meiosis, Carbohydrate, and Secondary Metabolism during Sporulation in Ganoderma lucidum

Ganoderma lucidum spores (GLS), the mature germ cells ejected from the abaxial side of the pileus, have diverse pharmacological effects. However, the genetic regulation of sporulation in this fungus remains unknown. Here, samples corresponding to the abaxial side of the pileus were collected from strain YW-1 at three sequential developmental stages and were then subjected to a transcriptome assay. We identified 1598 differentially expressed genes (DEGs) and found that the genes related to carbohydrate metabolism were strongly expressed during spore morphogenesis. In particular, genes involved in trehalose and malate synthesis were upregulated, implying the accumulation of specific carbohydrates in mature G. lucidum spores. Furthermore, the expression of genes involved in triterpenoid and ergosterol biosynthesis was high in the young fruiting body but gradually decreased with sporulation. Finally, spore development-related regulatory pathways were explored by analyzing the DNA binding motifs of 24 transcription factors that are considered to participate in the control of sporulation. Our results provide a dataset of dynamic gene expression during sporulation in G. lucidum. They also shed light on genes potentially involved in transcriptional regulation of the meiotic process, metabolism pathways in energy provision, and ganoderic acids and ergosterol biosynthesis.

Ambient Ultraviolet B Signal Modulates Tea Flavor Characteristics via Shifting a Metabolic Flux in Flavonoid Biosynthesis

Tea leaves contain an extraordinarily high level of flavonoids that contribute to tea health benefits and flavor characteristics, but the regulatory mechanism of ambient ultraviolet B (UV-B) on tea flavonoid enrichment remains unclear. Here, we report that ambient UV-B modulates tea quality by inducing a metabolic flux in flavonoid biosynthesis. UV-B absence decreased bitter- and astringent-tasting flavonol glycosides (kaempferol-7-O-glucoside, myricetin-3-O-glucoside, and quercetin-7-O-glucoside) but increased non-galloylated catechins. Conversely, supplementary UV-B increased flavonols and decreased catechins in tea leaves. These responses were achieved via CsHY5, which mediates the UV-B-induced MYB12 activation and binds to the promoters of flavonoid biosynthetic genes (CsFLS, CsLARa, and CsDFRa), leading to flavonoid changes. Transcriptomic data indicated that UV-B-induced tea flavonoid regulation is responsive to multiple biotic and abiotic environmental stresses. These findings improve our understanding of light-regulated tea astringency and bitterness underlying shading effects and seasonal light changes and provide novel insights into tea cultivation management and processing.

The SNL-HDA19 histone deacetylase complex antagonizes HY5 activity to repress photomorphogenesis in Arabidopsis

Reprogramming of the transcriptome during photomorphogenesis requires dynamic changes in chromatin and distribution of histone modifications. However, the chromatin-based regulation of this process remains to be elucidated. Here, we identify the conserved SWI-INDEPENDENT3 LIKE (SNL)-HISTONE DEACETYLASE19 (HDA19) deacetylase complex, including HDA19 and SNL1-SNL6, as a negative regulator of the light signaling pathway. Light-repression of HDA19 and SNLs expression is mediated by photoreceptors. HDA19 and SNLs are required for histone deacetylation and chromatin inactivation of PHYA gene. We further examined the interaction between SNL-HDA19 complex and ELONGATED HYPOCOTYL5 (HY5), and their antagonistic regulation on the expressions of target genes. The HDA19 deacetylase complex is recruited by HY5 to the chromatin regions of two positive light signaling genes, HY5 and B-BOX CONTAINING PROTEIN 22 (BBX22), thereby reduces the accessibility and histone acetylation and represses their expression. HDA19, SNL1, and HY5 associate with the same regulatory regions of HY5 and BBX22, and HY5 binding to these loci is enhanced upon SNL-HDA19 dysfunction. Our study reveals a crucial role for the HDA19 deacetylase complex in light signaling and demonstrates that the functional interplay between chromatin regulators and transcription factors regulates photomorphogenetic responses to the changing light environments.