Characterization of Phytochrome Interacting Factors from the Moss Physcomitrella patens Illustrates Conservation of Phytochrome Signaling Modules in Land Plants

Both phytochrome A and phyB interact with PHYTOCHROME-INTERACTING FACTORs through an evolutionary conserved phyOPM-APA interaction

Phytochrome A (phyA) and phyB are red and far-red photoreceptors that interact with PHYTOCHROME-INTERACTING FACTORs (PIFs) via active phyA-binding (APA) or active phyB-binding (APB) motifs. While APB interacts with the N-terminal photosensory module of phyB (phyBPSM), it remains unclear whether APA interacts with phyAPSM. We report that both phyA and phyB interact with APA through C-terminal output module of phy (phyOPM), while phyB interacts additionally with APB through phyBPSM. Marchantia Mp-phy also interacts with PIFs via the phyOPM-APA interaction. The phyBOPM-APA interaction promotes PIF3 degradation but not mutual phyB destruction. The full-length phy-APA interaction is light-dependent, whereas the underlying phyOPM-APA interaction is not. We show that the Pr form, not the Pfr, of phyPSM competes with APA for phyOPM binding, explaining how the light-dependent phy-APA interaction arises from the light-independent phyOPM-APA interaction. Together, our results suggest that the phyOPM-APA interaction is an ancient feature conserved in both Arabidopsis phyA, phyB and Marchantia Mp-phy.

Evolution of the basic helix-loop-helix transcription factor SPATULA and its role in gynoecium development

BACKGROUND AND AIMS

SPATULA (SPT) encodes a basic helix-loop-helix transcription factor in Arabidopsis thaliana that functions in the development of the style, stigma and replum tissues, all of which arise from the carpel margin meristem of the gynoecium. Here we use a comparative approach to investigate the evolutionary history of SPT and identify changes that potentially contributed to its role in gynoecium development.

METHODS

We investigate SPT's molecular and functional evolution using phylogenetic reconstruction, yeast two-hybrid analyses of protein-protein interactions, microarray-based analyses of protein-DNA interactions, plant transformation assays, RNA in situ hybridization, and in silico analyses of promoter sequences.

KEY RESULTS

We demonstrate the SPT lineage to have arisen at the base of euphyllophytes from a clade of potentially light-regulated transcription factors through gene duplication followed by the loss of an active phytochrome binding (APB) domain. We also clarify the more recent evolutionary history of SPT and its paralogue ALCATRAZ (ALC), which appear to have arisen through a large-scale duplication within Brassicales. We find that SPT orthologues from diverse groups of seed plants share strikingly similar capacities for protein-protein and protein-DNA interactions, and that SPT coding regions from a wide taxonomic range of plants are able to complement loss-of-function spt mutations in transgenic Arabidopsis. However, the expression pattern of SPT appears to have evolved significantly within angiosperms, and we identify structural changes in SPT's promoter region that correlate with the acquisition of high expression levels in tissues arising from the carpel margin meristem in Brassicaceae.

CONCLUSIONS

We conclude that changes in SPT's expression pattern made a major contribution to the evolution of its developmental role in the gynoecium of Brassicaceae. By contrast, the main biochemical capacities of SPT, as well as many of its immediate transcriptional targets, appear to have been conserved at least since the base of living angiosperms.

Specific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergence

The basic helix-loop-helix (bHLH) domain via critical amino acid residues on basic region binding to E-box (5'-CANNTG-3') is known in embryophyte. However, the dictated E-box types selection by bHLH dimers and the significant impact of these critical amino acid residues along embryophyte evolution remain unclear. The Arabidopsis thaliana PIF3-bHLH (AtPIF3-bHLH) recombinant protein and a series of AtPIF3-bHLH mutants were synthesized and analyzed. The reduced DNA binding ability and affinity of AtPIF3-bHLH point-mutation proteins, observed via fluorescence-based electrophoretic mobility shift assay (fEMSA) and isothermal titration calorimetry (ITC), suggest the critical role of these DNA-recognition sites in maintaining the AtPIF3-bHLH-DNA interaction. The purifying selection signals and the DNA-recognition-site conservation at the species level suggest the invariant roles of these sites throughout embryophyte evolution. The G-box outcompeted other types of E-box for binding in our competitive fEMSAs. The dynamic hydrogen bond formed between AtPIF3-bHLH and the G-box core indicates flexible identification of the core region. These features highlight a fast fixation of the bHLH-G-box recognition mechanism through embryophyte evolution and serve as a blueprint for studying DNA recognition determinants of other TF families.

The phytochrome-interacting factor genes PIF1 and PIF4 are functionally diversified due to divergence of promoters and proteins

Phytochrome-interacting factors (PIFs) are basic helix-loop-helix transcription factors that regulate light responses downstream of phytochromes. In Arabidopsis (Arabidopsis thaliana), 8 PIFs (PIF1-8) regulate light responses, either redundantly or distinctively. Distinctive roles of PIFs may be attributed to differences in mRNA expression patterns governed by promoters or variations in molecular activities of proteins. However, elements responsible for the functional diversification of PIFs have yet to be determined. Here, we investigated the role of promoters and proteins in the functional diversification of PIF1 and PIF4 by analyzing transgenic lines expressing promoter-swapped PIF1 and PIF4, as well as chimeric PIF1 and PIF4 proteins. For seed germination, PIF1 promoter played a major role, conferring dominance to PIF1 gene with a minor contribution from PIF1 protein. Conversely, for hypocotyl elongation under red light, PIF4 protein was the major element conferring dominance to PIF4 gene with the minor contribution from PIF4 promoter. In contrast, both PIF4 promoter and PIF4 protein were required for the dominant role of PIF4 in promoting hypocotyl elongation at high ambient temperatures. Together, our results support that the functional diversification of PIF1 and PIF4 genes resulted from contributions of both promoters and proteins, with their relative importance varying depending on specific light responses.

Involvement of Transcription Factors and Regulatory Proteins in the Regulation of Carotenoid Accumulation in Plants and Algae

Carotenoids are essential for photosynthesis and photoprotection in photosynthetic organisms, which are widely used in food coloring, feed additives, nutraceuticals, cosmetics, and pharmaceuticals. Carotenoid biofortification in crop plants or algae has been considered as a sustainable strategy to improve human nutrition and health. However, the regulatory mechanisms of carotenoid accumulation are still not systematic and particularly scarce in algae. This article focuses on the regulatory mechanisms of carotenoid accumulation in plants and algae through regulatory factors (transcription factors and regulatory proteins), demonstrating the complexity of homeostasis regulation of carotenoids, mainly including transcriptional regulation as the primary mechanism, subsequent post-translational regulation, and cross-linking with other metabolic processes. Different organs of plants and different plant/algal species usually have specific regulatory mechanisms for the biosynthesis, storage, and degradation of carotenoids in response to the environmental and developmental signals. In plants and algae, regulators such as MYB, bHLH, MADS, bZIP, AP2/ERF, WRKY, and orange proteins can be involved in the regulation of carotenoid metabolism. And many more regulators, regulatory networks, and mechanisms need to be explored. Our paper will provide a basis for multitarget or multipathway engineering for carotenoid biofortification in plants and algae.

The advantages of crosstalk during the evolution of the BZR1-ARF6-PIF4 (BAP) module

The BAP module, comprising BRASSINAZOLE RESISTANT 1 (BZR1), AUXIN RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), functions as a molecular hub to orchestrate plant growth and development. In Arabidopsis thaliana, components of the BAP module physically interact to form a complex system that integrates light, brassinosteroid (BR), and auxin signals. Little is known about the origin and evolution of the BAP module. Here, we conducted comparative genomic and transcriptomic analyses to investigate the evolution and functional diversification of the BAP module. Our results suggest that the BAP module originated in land plants and that the ζ, ε, and γ whole-genome duplication/triplication events contributed to the expansion of BAP module components in seed plants. Comparative transcriptomic analysis suggested that the prototype BAP module arose in Marchantia polymorpha, experienced stepwise evolution, and became established as a mature regulatory system in seed plants. We developed a formula to calculate the signal transduction productivity of the BAP module and demonstrate that more crosstalk among components enables higher signal transduction efficiency. Our results reveal the evolutionary history of the BAP module and provide insights into the evolution of plant signaling networks and the strategies employed by plants to integrate environmental and endogenous signals.

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

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

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.

Functions of Phytochrome-Interacting Factors (PIFs) in the regulation of plant growth and development: A comprehensive review

Transcription factors play important roles in governing plant responses upon changes in their ambient conditions. Any fluctuation in the supply of critical requirements for plants, such as optimum light, temperature, and water leads to the reprogramming of gene-signaling pathways. At the same time, plants also evaluate and shift their metabolism according to the various stages of development. Phytochrome-Interacting Factors are one of the most important classes of transcription factors that regulate both developmental and external stimuli-based growth of plants. This review focuses on the identification of PIFs in various organisms, regulation of PIFs by various proteins, functions of PIFs of Arabidopsis in diverse developmental pathways such as seed germination, photomorphogenesis, flowering, senescence, seed and fruit development, and external stimuli-induced plant responses such as shade avoidance response, thermomorphogenesis, and various abiotic stress responses. Recent advances related to the functional characterization of PIFs of crops such as rice, maize, and tomato have also been incorporated in this review, to ascertain the potential of PIFs as key regulators to enhance the agronomic traits of these crops. Thus, an attempt has been made to provide a holistic view of the function of PIFs in various processes in plants.

Two distinct light-induced reactions are needed to promote germination in spores of Ceratopteris richardii

Germination of Ceratopteris richardii spores is initiated by light and terminates 3-4 days later with the emergence of a rhizoid. Early studies documented that the photoreceptor for initiating this response is phytochrome. However, completion of germination requires additional light input. If no further light stimulus is given after phytochrome photoactivation, the spores do not germinate. Here we show that a crucial second light reaction is required, and its function is to activate and sustain photosynthesis. Even in the presence of light, blocking photosynthesis with DCMU after phytochrome photoactivation blocks germination. In addition, RT-PCR showed that transcripts for different phytochromes are expressed in spores in darkness, and the photoactivation of these phytochromes results in the increased transcription of messages encoding chlorophyll a/b binding proteins. The lack of chlorophyll-binding protein transcripts in unirradiated spores and their slow accumulation makes it unlikely that photosynthesis is required for the initial light reaction. This conclusion is supported by the observation that the transient presence of DCMU, only during the initial light reaction, had no effect on germination. Additionally, the [ATP] in Ceratopteris richardii spores increased coincidentally with the length of light treatment during germination. Overall, these results support the conclusion that two distinct light reactions are required for the germination of Ceratopteris richardii spores.

Co-action of COP1, SPA and cryptochrome in light signal transduction and photomorphogenesis of the moss Physcomitrium patens

The Arabidopsis COP1/SPA ubiquitin ligase suppresses photomorphogenesis in darkness. In the light, photoreceptors inactivate COP1/SPA to allow a light response. While SPA genes are specific to the green lineage, COP1 also exists in humans. This raises the question of when in evolution plant COP1 acquired the need for SPA accessory proteins. We addressed this question by generating Physcomitrium Ppcop1 mutants and comparing their visible and molecular phenotypes with those of Physcomitrium Ppspa mutants. The phenotype of Ppcop1 nonuple mutants resembles that of Ppspa mutants. Most importantly, both mutants produce green chloroplasts in complete darkness. They also exhibit dwarfed gametophores, disturbed branching of protonemata and absent gravitropism. RNA-sequencing analysis indicates that both mutants undergo weak constitutive light signaling in darkness. PpCOP1 and PpSPA proteins form a complex and they interact via their WD repeat domains with the VP motif of the cryptochrome CCE domain in a blue light-dependent manner. This resembles the interaction of Arabidopsis SPA proteins with Arabidopsis CRY1, and is different from that with Arabidopsis CRY2. Taken together, the data indicate that PpCOP1 and PpSPA act together to regulate growth and development of Physcomitrium. However, in contrast to their Arabidopsis orthologs, PpCOP1 and PpSPA proteins execute only partial suppression of light signaling in darkness. Hence, additional repressors may exist that contribute to the repression of a light response in dark-exposed Physcomitrium.

Identification and characterization of cotton PHYTOCHROME-INTERACTING FACTORs in temperature-dependent flowering

PHYTOCHROME INTERACTING FACTORs (PIFs) assimilate with light and temperature signs to control plant growth and development. However, little is known about PIFs in crop plants such as cotton. Here, we identified 68 PIF proteins and their coding genes from an allotetraploid and three diploid ancestors. Cotton PIFs contain typical APA and APB motifs by means of which they bind to phytochrome phyA and phyB, respectively, and have a bHLH domain and a nuclear localization sequence necessary for bHLH-type transcription factors. Bioinformatics analysis showed that the promoter of each PIF gene contains multiple cis-acting elements and that the evolution of cotton genomes likely underwent loss, recombination, and tandem replication. Further observations indicated that the sensitivity of cotton PIF expression to low or high temperature was significantly different, of which allotetraploid Gossypium hirsutum PIF4a (GhPIF4a) was induced by high temperature. GhPIF4a promotes flowering in cotton and Arabidopsis and binds to the promoter of GhFT (FLOWERING LOCUS T) increasing with temperature rise. In conclusion, our work identifies the evolutionary and structural characteristics and functions of PIF family members in cotton.

Genome-Wide Characterization of the PIFs Family in Sweet Potato and Functional Identification of IbPIF3.1 under Drought and Fusarium Wilt Stresses

Phytochrome-interacting factors (PIFs) are essential for plant growth, development, and defense responses. However, research on the PIFs in sweet potato has been insufficient to date. In this study, we identified PIF genes in the cultivated hexaploid sweet potato (Ipomoea batatas) and its two wild relatives, Ipomoea triloba, and Ipomoea trifida. Phylogenetic analysis revealed that IbPIFs could be divided into four groups, showing the closest relationship with tomato and potato. Subsequently, the PIFs protein properties, chromosome location, gene structure, and protein interaction network were systematically analyzed. RNA-Seq and qRT-PCR analyses showed that IbPIFs were mainly expressed in stem, as well as had different gene expression patterns in response to various stresses. Among them, the expression of IbPIF3.1 was strongly induced by salt, drought, H₂O₂, cold, heat, Fusarium oxysporum f. sp. batatas (Fob), and stem nematodes, indicating that IbPIF3.1 might play an important role in response to abiotic and biotic stresses in sweet potato. Further research revealed that overexpression of IbPIF3.1 significantly enhanced drought and Fusarium wilt tolerance in transgenic tobacco plants. This study provides new insights for understanding PIF-mediated stress responses and lays a foundation for future investigation of sweet potato PIFs.

PEATmoss: A Gene Expression Atlas for Bryophytes

PEATmoss is an interactive gene expression atlas for bryophytes, which originally unified Physcomitrium patens RNA-seq and microarray expression data from multiple gene annotation versions. This atlas includes more than 100 experiments of P. patens, is expanding to host Anthoceros agrestis and Marchantia polymorpha, and aims to host data from more species in the future. PEATmoss has multiple visualization methods and tools for data downloading and is connected to the Physcomitrium patens Gene Model Lookup DB (PpGML DB), which links P. patens genes to annotations and resources from several databases and contains tools for gene version lookup and sequence and annotation extraction. Among the new features available in PEATmoss are dataset privacy control, multispecies menu, interactive color scale, co-expression network visualization, and replicate data downloading.

PpPIF8, a DELLA2-interacting protein, regulates peach shoot elongation possibly through auxin signaling

Rapid growth of branches in a peach tree restricts the light penetration and air ventilation within the orchard, which lowers fruit quality and promotes the occurrence of diseases and insects. Our previous works showed that PpDELLA1 and PpDELLA2 repress the rapid growth of annual shoots. Proteins that interact with DELLA are vital for its function. In this study, seven PpPIFs (PpPIF1, -2, -3, -4, -6, -7 and -8) were identified in the peach genome and contain a conserved bHLH domain. Among the seven PpPIFs, PpPIF8 interacted with PpDELLA2 through an unknown motif in the C-terminal and/or the bHLH domain. Overexpression of PpPIF8 in Arabidopsis promotes plant height and branch numbers. Hypocotyl elongation was significantly enhanced by PpPIF8 under weak light intensity. PpPIF8 overexpressed in Arabidopsis and transiently expressed in peach seedlings upregulated the transcription of YUCCA and SAUR19 and downregulated SHY1 and -2. Additionally, PpPIF4 and -8 were significantly induced by weak light. Phylogentic analysis and intron patterns of the bHLH domain strongly suggested that PIFs from six species could be divided into two groups of different evolutionary origins. These results lay a foundation for the further study of the repression of shoot growth by PpDELLA2 through protein interaction with PpPIF8 in peach.

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.

Moss transcription factors regulating development and defense responses to stress

Transcription factors control gene expression, leading to regulation of biological processes that determine plant development and adaptation to the environment. Land colonization by plants occurred 450-470 million years ago and was accompanied by an increase in the complexity of transcriptional regulation associated to transcription factor gene expansions. AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY transcription factor families increased in land plants compared with algae. In angiosperms, they play crucial roles in regulating plant growth and responses to environmental stressors. However, less information is available in bryophytes and only in a few cases is the functional role of moss transcription factors in stress mechanisms known. In this review, we discuss current knowledge of the transcription factor families involved in development and defense responses to stress in mosses and other bryophytes. By exploring and analysing the Physcomitrium patens public database and published transcriptional profiles, we show that a high number of AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY genes are differentially expressed in response to abiotic stresses and during biotic interactions. Expression profiles together with a comprehensive analysis provide insights into relevant transcription factors involved in moss defenses, and hint at distinct and conserved biological roles between bryophytes and angiosperms.

Bagging Strategy and Identification of Coloring Mode of ‘Xinqihong’ Pear

‘Xinqihong’ is a recently selected and well-colored red pear (Pyrus bretschneideri Rehd.) cultivar that is popular in the marketplace owing to the bright red color and high quality of the fruit. The red pigmentation is strongly associated with the light signal. However, its responses to bagging treatment and to light exposure after shading are unknown. In this study, the fruit were treated with three types of fruit bags. ’Xinqihong’ fruit colored rapidly in response to light stimulation. A white fruit bag was optimal for bagging of ‘Xinqihong’ fruit. To ensure satisfactory red pigmentation, the fruit required exposure to 30 days of light after bag removal. A transcriptome analysis was conducted to screen light-signal-related genes and identify their possible functions. PbCRY1 activated the promoter of PbHY5.2 and enhanced its expression. PbHY5.2 activated the promoter activity of PbUFGT and induced anthocyanin synthesis, and also showed self-activation characteristics. Both PbCRY2 and PbPHY1 induced anthocyanin accumulation. Thus, blue-light receptors played an important role in anthocyanin synthesis. This study provides a theoretical basis for the bagging cultivation of new varieties of ‘Xinqihong’, and lays a foundation for the study of the mechanisms of red pear fruit coloring in response to light signals.

PIF4 Promotes Expression of HSFA2 to Enhance Basal Thermotolerance in Arabidopsis

Heat stress (HS) seriously restricts the growth and development of plants. When plants are exposed to extreme high temperature, the heat stress response (HSR) is activated to enable plants to survive. Sessile plants have evolved multiple strategies to sense and cope with HS. Previous studies have established that PHYTOCHROME INTERACTING FACTOR 4 (PIF4) acts as a key component in thermomorphogenesis; however, whether PIF4 regulates plant thermotolerance and the molecular mechanism linking this light transcriptional factor and HSR remain unclear. Here, we show that the overexpression of PIF4 indeed provides plants with a stronger basal thermotolerance and greatly improves the survival ability of Arabidopsis under severe HS. Via phylogenetic analysis, we identified two sets (six) of PIF4 homologs in wheat, and the expression patterns of the PIF4 homologs were conservatively induced by heat treatment in both wheat and Arabidopsis. Furthermore, the PIF4 protein was accumulated under heat stress and had an identical expression level. Additionally, we found that the core regulator of HSR, HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2), was highly responsive to light and heat. Followed by promoter analysis and ChIP-qPCR, we further found that PIF4 can bind directly to the G-box motifs of the HSFA2 promoter. Via effector–reporter assays, we found that PIF4 binding could activate HSFA2 gene expression, thereby resulting in the activation of other HS-inducible genes, such as heat shock proteins. Finally, the overexpression of PIF4 led to a stronger basal thermotolerance under non-heat-treatment conditions, thereby resulting in an enhanced tolerance to severe heat stress. Taken together, our findings propose that PIF4 is linked to heat stress signaling by directly binding to the HSFA2 promoter and triggering the HSR at normal temperature conditions to promote the basal thermotolerance. These functions of PIF4 provide a candidate direction for breeding heat-resistant crop cultivars.

The Land-Sea Connection: Insights Into the Plant Lineage from a Green Algal Perspective

The colonization of land by plants generated opportunities for the rise of new heterotrophic life forms, including humankind. A unique event underpinned this massive change to earth ecosystems-the advent of eukaryotic green algae. Today, an abundant marine green algal group, the prasinophytes, alongside prasinodermophytes and nonmarine chlorophyte algae, is facilitating insights into plant developments. Genome-level data allow identification of conserved proteins and protein families with extensive modifications, losses, or gains and expansion patterns that connect to niche specialization and diversification. Here, we contextualize attributes according to Viridiplantae evolutionary relationships, starting with orthologous protein families, and then focusing on key elements with marked differentiation, resulting in patchy distributions across green algae and plants. We place attention on peptidoglycan biosynthesis, important for plastid division and walls; phytochrome photosensors that are master regulators in plants; and carbohydrate-active enzymes, essential to all manner of carbohydratebiotransformations. Together with advances in algal model systems, these areas are ripe for discovering molecular roles and innovations within and across plant and algal lineages.

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

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

Low R/FR Ratio Affects Pakchoi’s Growth and Nitrate Content under Excess Nitrate Stress

Nitrate accumulation is one of the main factors of secondary soil salinization in protected horticulture in China. Previous studies have shown that a low red(R)/far-red (FR) ratio can improve the salt tolerance of plants under NaCl stress. However, the effect of a low R/FR ratio on plant growth under nitrate stress is not clear. In order to explore the effect of a low R/FR ratio on the adaptability of pakchoi under high nitrogen stress, the growth index, soluble protein content, soluble sugar content, nitrate content, nitrate reductase activity and Nia2 gene expression of pakchoi’s leaves were measured. The results showed that a high level of nitrogen (the addition of 80 mmol · L−1 NO3− (N80) and 160 mmol · L−1 NO3− (N160)) inhibited the growth of pakchoi and promoted the accumulation of osmoregulation substances and nitrate content, respectively. The reduction of the R/FR ratio under high nitrogen stress (L80) increased the fresh weight of the plants under it by 19.0%, reduced the nitrate content in the leaves by 22.7%, increased the NR activity by 29.9%, and made the Nia2 gene expression more significant, compared with N80. There was a similar mitigation effect of a low R/FR ratio under 160 mmol · L−1 excessive NO3− stress. Therefore, the reduction of the R/FR ratio can effectively control the nitrate content and improve the adaptability of pakchoi under high nitrogen stress. Thus, there is a practical application prospect for a low R/FR ratio for the production of pakchoi under a high level of nitrogen.

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.

Direct photoresponsive inhibition of a p53-like transcription activation domain in PIF3 by Arabidopsis phytochrome B

Photoactivated phytochrome B (PHYB) binds to antagonistically acting PHYTOCHROME-INTERACTING transcription FACTORs (PIFs) to regulate hundreds of light responsive genes in Arabidopsis by promoting PIF degradation. However, whether PHYB directly controls the transactivation activity of PIFs remains ambiguous. Here we show that the prototypic PIF, PIF3, possesses a p53-like transcription activation domain (AD) consisting of a hydrophobic activator motif flanked by acidic residues. A PIF3mAD mutant, in which the activator motif is replaced with alanines, fails to activate PIF3 target genes in Arabidopsis, validating the functions of the PIF3 AD in vivo. Intriguingly, the N-terminal photosensory module of PHYB binds immediately adjacent to the PIF3 AD to repress PIF3’s transactivation activity, demonstrating a novel PHYB signaling mechanism through direct interference of the transactivation activity of PIF3. Our findings indicate that PHYB, likely also PHYA, controls the stability and activity of PIFs via structurally separable dual signaling mechanisms.

Photoactivated phytochrome B regulates gene expression by interacting with PIF transcription factors. Here the authors show that PIF3 contains a p53-like transcription activation domain (AD) and that PHYB can directly suppress PIF3 transactivation activity by binding adjacent to the AD.

Cannabinoids Accumulation in Hemp (Cannabis sativa L.) Plants under LED Light Spectra and Their Discrete Role as a Stress Marker

Hemp adaptability through physiological and biochemical changes was studied under 10 LED light spectra and natural light in a controlled aeroponic system. Light treatments were imposed on 25 days aged seedlings for 16 h daily (300 µmol m-2 s-1) for 20 days. Plant accumulated highest Cannabidiol (CBD) in R7:B2:G1 light treatment, with relatively higher photosynthetic rate and lower reactive oxygen species, total phenol content, total flavonoid content, DPPH radical scavenging capacity, and antioxidant enzymatic activities. Tetrahydrocannabinol (THC) also accumulated at a higher level in white, R8:B2, and R7:B2:G1 light with less evidence of stress-modulated substances. These results indicated that CBD and THC have no or little relation with light-mediated abiotic stress in hemp plants. On the contrary, Tetrahydrocannabinolic acid (THCA) was accumulated higher in R6:B2:G1:FR1 and R5:B2:W2:FR1 light treatment along with lower photosynthetic rate and higher reactive oxygen species, total phenol content, total flavonoid content, DPPH radical scavenging capacity, and antioxidant enzymatic activities. However, Cannabidiolic acid (CBDA) was accumulated higher in R6:B2:G1:FR1 light treatment with higher stress-modulated substances and lower physiological traits. CBDA was also accumulated higher in R8:B2 and R7:B2:G1 light treatments with less evidence of stress-modulated substances. Besides, Greenlight influenced CBD and CBDA synthesis where FR and UV-A (along with green) play a positive and negative role in this process. Overall, the results indicated that the treatment R7:B2:G1 enhanced the medicinal cannabinoids most, and the role of THCA as a stress marker is more decisive in the hemp plant than in other cannabinoids under attributed light-mediated stress.

Development and Molecular Genetics of Marchantia polymorpha

Bryophytes occupy a basal position in the monophyletic evolution of land plants and have a life cycle in which the gametophyte generation dominates over the sporophyte generation, offering a significant advantage in conducting genetics. Owing to its low genetic redundancy and the availability of an array of versatile molecular tools, including efficient genome editing, the liverwort Marchantia polymorpha has become a model organism of choice that provides clues to the mechanisms underlying eco-evo-devo biology in plants. Recent analyses of developmental mutants have revealed that key genes in developmental processes are functionally well conserved in plants, despite their morphological differences, and that lineage-specific evolution occurred by neo/subfunctionalization of common ancestral genes. We suggest that M. polymorpha is an excellent platform to uncover the conserved and diversified mechanisms underlying land plant development.

Molecular mechanisms involved in functional macroevolution of plant transcription factors

Transcription factors (TFs) are key components of the transcriptional regulation machinery. In plants, they accompanied the evolution from unicellular aquatic algae to complex flowering plants that dominate the land environment. The adaptations of the body plan and physiological responses required changes in the biological functions of TFs. Some ancestral gene regulatory networks are highly conserved, while others evolved more recently and only exist in particular lineages. The recent emergence of novel model organisms provided the opportunity for comparative studies, producing new insights to infer these evolutionary trajectories. In this review, we comprehensively revisit the recent literature on TFs of nonseed plants and algae, focusing on the molecular mechanisms driving their functional evolution. We discuss the particular contribution of changes in DNA-binding specificity, protein-protein interactions and cis-regulatory elements to gene regulatory networks. Current advances have shown that these evolutionary processes were shaped by changes in TF expression pattern, not through great innovation in TF protein sequences. We propose that the role of TFs associated with environmental and developmental regulation was unevenly conserved during land plant evolution.

Evolution of DELLA function and signaling in land plants

DELLA proteins are master growth regulators that repress responses to a group of plant growth hormones called gibberellins (GAs). Manipulation of DELLA function and signaling was instrumental in the development of high‐yielding crop varieties that saved millions from starvation during the “Green Revolution.” Despite decades of extensive research, it is still unclear how DELLA function and signaling mechanisms evolved within the land plant lineage. Here, we review current knowledge on DELLA protein function with reference to structure, posttranslational modifications, downstream transcriptional targets, and protein–protein interactions. Furthermore, we discuss older and recent findings regarding the evolution of DELLA signaling within the land plant lineage, with an emphasis on bryophytes, and identify future avenues of research that would enable us to shed more light on the evolution of DELLA signaling. Unraveling how DELLA function and signaling mechanisms have evolved could enable us to engineer better crops in an attempt to contribute to mitigating the effects of global warming and achieving global food security.

DELLA genes first appeared in the common ancestor of land plants and underwent two major duplications during land plant evolution.

DELLAs repress gibberellin responses in vascular plants but their function in nonvascular plants remains elusive.

Characterization of Phytochrome-Interacting Factor Genes in Pepper and Functional Analysis of CaPIF8 in Cold and Salt Stress

As a subfamily of basic helix-loop-helix (bHLH) transcription factors, phytochrome-interacting factors (PIFs) participate in regulating light-dependent growth and development of plants. However, limited information is available about PIFs in pepper. In the present study, we identified six pepper PIF genes using bioinformatics-based methods. Phylogenetic analysis revealed that the PIFs from pepper and some other plants could be divided into three distinct groups. Motif analysis revealed the presence of many conserved motifs, which is consistent with the classification of PIF proteins. Gene structure analysis suggested that the CaPIF genes have five to seven introns, exhibiting a relatively more stable intron number than other plants such as rice, maize, and tomato. Expression analysis showed that CaPIF8 was up-regulated by cold and salt treatments. CaPIF8-silenced pepper plants obtained by virus-induced gene silencing (VIGS) exhibited higher sensitivity to cold and salt stress, with an obvious increase in relative electrolyte leakage (REL) and variations in the expression of stress-related genes. Further stress tolerance assays revealed that CaPIF8 plays different regulatory roles in cold and salt stress response by promoting the expression of the CBF1 gene and ABA biosynthesis genes, respectively. Our results reveal the key roles of CaPIF8 in cold and salt tolerance of pepper, and lay a solid foundation for clarifying the biological roles of PIFs in pepper and other plants.

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

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

ZEITLUPE is required for shade avoidance in the wild tobacco Nicotiana attenuata

Being shaded is a common environmental stress for plants, especially for densely planted crops. Shade decreases red: far-red (R:FR) ratios that inactivate phytochrome B (PHYB) and subsequently release p̱hytochrome i̱nteraction f̱actors (PIFs). Shaded plants display elongated hypocotyls, internodes, and petioles, hyponastic leaves, early flowering and are inhibited in branching: traits collectively called the shade avoidance syndrome (SAS). ZEITLUPE (ZTL) is a circadian clock component and blue light photoreceptor, which is also involved in floral rhythms and plant defense in Nicotiana attenuata. ztl mutants are hypersensitive to red light and ZTL physically interacts with PHYB, suggesting the involvement of ZTL in R:FR light signaling. Here, we show that N. attenuata ZTL-silenced plants display a phenotype opposite to that of the SAS under normal light. After simulated shade, the normally induced transcript levels of the SAS marker gene, ATHB2 are attenuated in ZTL-silenced plants. The auxin signaling pathway, known to be involved in SAS, was also significantly attenuated. Furthermore, NaZTL directly interacts with NaPHYBs, and regulates the transcript levels of PHYBs, PIF3a, PIF7 and PIF8 under shade. Our results suggest that ZTL may regulate PHYB- and the auxin-mediated signaling pathway, which functions in the SAS of N. attenuata.

Transcriptional regulatory network of the light signaling pathways

The developmental program by which plants respond is tightly controlled by a complex cascade in which photoreceptors perceive and transduce the light signals that drive signaling processes and direct the transcriptional reprogramming, yielding specific cellular responses. The molecular mechanisms involved in the transcriptional regulation include light-regulated nuclear localization (the phytochromes and UVR8) and nuclear accumulation (the cryptochrome, cry2) of photoreceptors. This regulatory cascade also includes master regulatory transcription factors (TFs) that bridge photoreceptor activation with chromatin remodeling and regulate the expression of numerous light-responsive genes. Light signaling-related TFs often function as signal convergence points in concert with TFs in other signaling pathways to integrate complex endogenous and environmental cues that help the plant adapt to the surrounding environment. Increasing evidence suggests that chromatin modifications play a critical role in regulating light-responsive gene expression and provide an additional layer of light signaling regulation. Here, we provide an overview of our current knowledge of the transcriptional regulatory network involved in the light response, particularly the roles of TFs and chromatin in regulating light-responsive gene expression.

Transcriptional regulation and expression network responding to cadmium stress in a Cd-tolerant perennial grass Poa Pratensis

Kentucky bluegrass has good capability to absorb and accumulate cadmium (Cd) through developed root system, thus having potential phytoremediation function in Cd contaminated soils. Understanding the molecular mechanisms of Cd tolerance and accumulation in this species will be crucial to generating novel Cd-tolerance cultivars through genetic improvement, while it has not well documented yet. In the present study, comparative transcriptome analysis was performed for the seedlings of high Cd-tolerant genotype (M) and low Cd-tolerant genotype (R) under Cd stress. A total of 7022 up-regulated and 1033 down-regulated transcripts were identified in M genotype, whereas, only 850 up-regulated and 846 down-regulated transcripts were detected in R. Further transcriptional regulation analysis in M genotype showed that Dof, MADS25, BBR-BPC, B3, bZIP23 and MYB30 might be the hub transcription factors in response to Cd stress due to the orchestrated multiple functional genes associated with carbohydrate, lipid and secondary metabolism, as well as signal transduction. Differential expressed genes involved in auxin, ethylene, brassinosteroid and ABA signalling formed signal transduction cascades, which interacted with hub transcription factors, thereby finally orchestrated the expression of multiple genes associated with cell wall and membrane stability, cell elongation and Cd tolerance, including IAAs, ARFs, SnRK2, PP2C, PIFs, BES1/BZR1, CCR, CAD, FATB, fabF and HACD. Additionally, post-transcriptional modification of CIPKs, MAPKs, WAXs, UBCs, and E3 ubiquitin ligases were identified and also involved in plant signalling pathways and abiotic resistance. The study could contribute to our understanding the transcriptional regulation and complex internal network associated with Cd tolerance in Kentucky bluegrass.

MYB30 Is a Key Negative Regulator of Arabidopsis Photomorphogenic Development That Promotes PIF4 and PIF5 Protein Accumulation in the Light

Phytochromes are red (R) and far-red (FR) light photoreceptors in plants, and PHYTOCHROME-INTERACTING FACTORS (PIFs) are a group of basic helix-loop-helix family transcription factors that play central roles in repressing photomorphogenesis. Here, we report that MYB30, an R2R3-MYB family transcription factor, acts as a negative regulator of photomorphogenesis in Arabidopsis (Arabidopsis thaliana). We show that MYB30 preferentially interacts with the Pfr (active) forms of the phytochrome A (phyA) and phytochrome B (phyB) holoproteins and that MYB30 levels are induced by phyA and phyB in the light. It was previously shown that phytochromes induce rapid phosphorylation and degradation of PIFs upon R light exposure. Our current data indicate that MYB30 promotes PIF4 and PIF5 protein reaccumulation under prolonged R light irradiation by directly binding to their promoters to induce their expression and by inhibiting the interaction of PIF4 and PIF5 with the Pfr form of phyB. In addition, our data indicate that MYB30 interacts with PIFs and that they act additively to repress photomorphogenesis. In summary, our study demonstrates that MYB30 negatively regulates Arabidopsis photomorphogenic development by acting to promote PIF4 and PIF5 protein accumulation under prolonged R light irradiation, thus providing new insights into the complicated but delicate control of PIFs in the responses of plants to their dynamic light environment.

PHYTOCHROME INTERACTING FACTORs in the moss Physcomitrella patens regulate light-controlled gene expression

Phytochromes are red and far-red light receptors in plants that control growth and development in response to changes in the environment. Light-activated phytochromes enter the nucleus and act on a set of downstream signalling components to regulate gene expression. PHYTOCHROME INTERACTING FACTORs (PIFs) belong to the basic helix-loop-helix family of transcription factors and directly bind to light-activated phytochromes. Potential homologues of PIFs have been identified in ferns, bryophytes and streptophyte algae, and it has been shown that the potential PIF homologues from Physcomitrella patens, PIF1 to PIF4, have PIF function when expressed in Arabidopsis. However, their function in Physcomitrella is still unknown. Seed plant PIFs bind to G-box-containing promoters and, therefore, we searched the Physcomitrella genome for genes that contain G-boxes in their promoter. Here, we show that Physcomitrella PIFs activate these promoters in a G-box-dependent manner, suggesting that they could be direct PIF targets. Furthermore, we generated Physcomitrella pif1, pif2, pif3 and pif4 knock out mutant lines and quantified the expression of potential PIF direct target genes. The expression of these genes was generally reduced in pif mutants compared to the wildtype, but for several genes, the relative induction upon a short light treatment was higher in pif mutants than the wildtype. In contrast, expression of these genes was strongly repressed in continuous light, and pif mutants showed partial downregulation of these genes in the dark. Thus, the overall function of PIFs in light-regulated gene expression might be an ancient property of PIFs.

PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo-devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web-based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at https://peatmoss.online.uni-marburg.de.

Contrasted evolutionary trajectories of plant transcription factors

Because of their prominent roles in plant development, transcription factors (TF) play central roles as drivers of innovation in the evolution of the green lineage (viridiplantae). The advent of massive sequencing combined with comparative genetics/genomics allows a rigorous investigation of how TF families have contributed to plant diversification from charophyte algae to bryophytes to angiosperms. Here, we review recent progress on TF family reconstruction and the identification of distantly related TFs present throughout the evolutionary timeline from algae to angiosperms. These data provide examples of contrasting evolutionary trajectories of TF families and illustrate how conserved TFs adopt diverse roles over the course of evolution.

PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Mediated Far-Red Light Responses in Arabidopsis

PHYTOCHROME INTERACTING FACTORs (PIFs) are a group of basic helix-loop-helix (bHLH) transcription factors that repress plant light responses. PIF8 is one of the less-characterized Arabidopsis (Arabidopsis thaliana) PIFs, whose putative orthologs are conserved in other plant species. PIF8 possesses a bHLH motif and an active phytochrome B motif but not an active phytochrome A motif. Consistent with this motif composition, PIF8 binds to G-box elements and interacts with the Pfr form of phyB but only very weakly, if at all, with that of phyA. PIF8 differs, however, from other PIFs in its protein accumulation pattern and functional roles in different light conditions. First, PIF8 inhibits phyA-induced seed germination, suppression of hypocotyl elongation, and randomization of hypocotyl growth orientation in far-red light, but it does not inhibit phyB-induced red light responses. Second, PIF8 protein accumulates more in far-red light than in darkness or red light. This is distinct from the pattern observed with PIF3, which accumulates more in darkness. This PIF8 accumulation pattern requires degradation of PIF8 by CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) in darkness, inhibition of COP1 by phyA in far-red light, and promotion of PIF8 degradation by phyB in red light. Together, our results indicate that PIF8 is a genuine PIF that represses phyA-mediated light responses.

Characterization of spa mutants in the moss Physcomitrella provides evidence for functional divergence of SPA genes during the evolution of land plants

The Arabidopsis COP1/SPA complex is a key repressor of photomorphogenesis that suppresses light signaling in the dark. Both COP1 and SPA proteins are essential components of this complex. Although COP1 also exists in humans, SPA genes are specific to the green lineage. To elucidate the evolution of SPA genes we analyzed SPA functions in the moss Physcomitrella patens by characterizing knockout mutants in the two Physcomitrella SPA genes PpSPAa and PpSPAb. Light-grown PpspaAB double mutants exhibit smaller gametophores than the wild-type. In the dark, PpspaAB mutant gametophores show enhanced continuation of growth but etiolate normally. Gravitropism in the dark is reduced in PpspaAB mutant protonemata. The expression of light-regulated genes is mostly not constitutive in PpspaAB mutants. PpSPA and PpCOP1 interact; PpCOP1 also interacts with the transcription factor PpHY5 and, indeed, PpHY5 is destabilized in dark-grown Physcomitrella. Degradation of PpHY5 in darkness, however, does not require PpSPAa and PpSPAb. The data suggest that COP1/SPA-mediated light signaling is only partially conserved between Arabidopsis and Physcomitrella. Whereas COP1/SPA interaction and HY5 degradation in darkness is conserved, the role of SPA proteins appears to have diverged. PpSPA genes, unlike their Arabidopsis counterparts, are only required to suppress a subset of light responses in darkness.

Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants

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

Identification of TIMING OF CAB EXPRESSION 1 as a temperature-sensitive negative regulator of tuberization in potato

For many potato cultivars, tuber yield is optimal at average daytime temperatures in the range 14-22 °C. Above this range, tuber yield is reduced for most cultivars. We previously reported that moderately elevated temperature increases steady-state expression of the core circadian clock gene TIMING OF CAB EXPRESSION 1 (StTOC1) in developing tubers, whereas expression of the StSP6A tuberization signal is reduced, along with tuber yield. In this study we provide evidence that StTOC1 links environmental signalling with potato tuberization by suppressing StSP6A autoactivation in the stolons. We show that transgenic lines silenced in StTOC1 expression exhibit enhanced StSP6A transcript levels and changes in gene expression in developing tubers that are indicative of an elevated sink strength. Nodal cuttings of StTOC1 antisense lines displayed increased tuber yields at moderately elevated temperatures, whereas tuber yield and StSP6A expression were reduced in StTOC1 overexpressor lines. Here we identify a number of StTOC1 binding partners and demonstrate that suppression of StSP6A expression is independent of StTOC1 complex formation with the potato homolog StPIF3. Down-regulation of StTOC1 thus provides a strategy to mitigate the effects of elevated temperature on tuber yield.

Origin and Evolution of Core Components Responsible for Monitoring Light Environment Changes during Plant Terrestrialization

Light serves as the source of energy as well as an information signal for photosynthetic plants. During evolution, plants have acquired the ability to monitor environmental light radiation and adjust their developmental patterns to optimally utilize light energy for photosynthesis. The mechanisms of light perception and signal transduction have been comprehensively studied in past decades, mostly in a few model plants, including Arabidopsis thaliana. However, systematic analyses of the origin and evolution of core components involved in light perception and signaling are still lacking. In this study, we took advantage of the recently sequenced genomes and transcriptomes covering all the main Archaeplastida clades in the public domain to identify orthologous genes of core components involved in light perception and signaling and to reconstruct their evolutionary history. Our analyses suggested that acclimation to different distribution of light quality in new environments led to the origination of specific light signaling pathways in plants. The UVR8 (UV Resistance Locus 8) signaling pathway originated during the movement of plants from the deeper sea to shallow water and enabled plants to deal with ultraviolet B light (UV-B). After acquisition of UV-B adaptation, origination of the phytochrome signaling pathway helped plants to colonize water surface where red light became the prominent light energy source. The seedling emergence pathway, which is mediated by a combination of light and phytohormone signals that orchestrate plant growth pattern transitions, originated before the emergence of seed plants. Although cryptochromes and some key components of E3 ubiquitin ligase systems already existed before the divergence of the plant and animal kingdoms, the coevolution and optimization of light perception and downstream signal transduction components, including key transcription factors and E3 ubiquitin ligase systems, are evident during plant terrestrialization.

Reproductive Induction is a Far-Red High Irradiance Response that is Mediated by Phytochrome and PHYTOCHROME INTERACTING FACTOR in Marchantia polymorpha

Land plants have evolved a series of photoreceptors to precisely perceive environmental information. Among these, phytochromes are the sole photoreceptors for red light (R) and far-red light (FR), and play pivotal roles in modulating various developmental processes. Most extant land plants possess multiple phytochromes that probably evolved from a single phytochrome in the common ancestor of land plants. However, the ancestral phytochrome signaling mechanism remains unknown due to a paucity of knowledge regarding phytochrome functions in basal land plants. It has recently been reported that Mpphy, a single phytochrome in the liverwort Marchantia polymorpha, regulates typical photoreversible responses collectively classified as low fluence response (LFR). Here, we show that Mpphy also regulates the gametangiophore formation analogous to the mode of action of the far-red high irradiance response (FR-HIR) in angiosperms. Our phenotypic analyses using mutant plants obtained by CRISPR/Cas9-based genome editing revealed that MpFHY1, an ortholog of FAR-RED ELONGATED HYPOCOTYL1, as well as Mpphy is critical for the FR-HIR signaling in M. polymorpha. In addition, knockout of MpPIF, a single PHYTOCHROME INTERACTING FACTOR gene in M. polymorpha, completely abolished the FR-HIR-dependent gametangiophore formation, while overexpression of MpPIF accelerated the response. FR-HIR-dependent transcriptional regulation was also disrupted in the Mppif mutant. Our findings suggest that plants had already acquired the FR-HIR signaling mediated by phytochrome and PIF at a very early stage during the course of land plant evolution, and that a single phytochrome in the common ancestor of land plants could mediate both LFR and FR-HIR.

CRISPR/Cas9-Mediated Knockout of Physcomitrella patens Phytochromes

Here we describe procedures for gene disruption and excision in Physcomitrella using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat/CRISPR-associated 9) methods, exemplarily targeting phytochrome (PHY) gene loci. Thereby double-strand breaks (DSBs) are induced using a single guide RNA (sgRNA) with the Cas9 nuclease, leading to insertions or deletions (indels) due to incorrect repair by the nonhomologous-end joining (NHEJ) mechanism. We also include protocols for excision of smaller genomic fragments or whole genes either with or without homologous recombination-assisted repair. The protocol can be adapted to target several loci simultaneously, thereby allowing the physiological analysis of phenotypes that would be masked by functional redundancy. In our particular case, multiple PHY gene knockouts would likely be valuable in understanding phytochrome functions in mosses and, perhaps, higher plants too. Target sites for site-directed induction of DSBs are predicted with the CRISPOR online-tool and are inserted in silico into sequence matrices for the design of sgRNA expression cassettes. The resulting DNAs are cloned into Gateway DONOR vectors and the respective expression plasmids used for moss cotransformation with a Cas9 expression plasmid and a selectable marker (either on a separate plasmid or on one of the other plasmids). After the selection process, genomic DNA is extracted and transformants are analyzed by PCR fingerprinting.

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.

Exposure to lower red to far-red light ratios improve tomato tolerance to salt stress

BACKGROUND

Red (R) and far-red (FR) light distinctly influence phytochrome-mediated initial tomato growth and development, and more recent evidence indicates that these spectra also modulate responses to a multitude of abiotic and biotic stresses. This research investigated whether different R: FR values affect tomato growth response and salinity tolerance. Tomato seedlings were exposed to different R: FR conditions (7.4, 1.2 and 0.8) under salinity stress (100 mM NaCl), and evaluated for their growth, biochemical changes, active reactive oxygen species (ROS) and ROS scavenging enzymes, pigments, rate of photosynthesis, and chlorophyll fluorescence.

RESULTS

The results showed that under conditions of salinity, tomato seedlings subjected to a lower R: FR value (0.8) significantly increased both their growth, proline content, chlorophyll content and net photosynthesis rate (Pn), while they decreased malondialdehyde (MDA) compared to the higher R: FR value (7.4). Under conditions of salinity, the lower R: FR value caused a decrease in both the superoxide anion (O₂^•-) and in hydrogen peroxide (H₂O₂) generation, an increase in the activities of superoxidase dismutase (SOD, EC 1.15.1.1), peroxidase (POD, EC 1.11.1.7) and catalase (CAT, EC 1.11.1.7). Tomato seedlings grown under the lower R: FR value and conditions of salinity showed a higher actual quantum yield of photosynthesis (ΦPSII), electron transport rate (ETR), and photochemical quenching (qP) than those exposed to a higher R: FR, indicating overall healthier growth. However, the salinity tolerance induced at the lower R: FR condition disappeared in the tomato phyB1 mutant.

CONLUSION

These results suggest that growing tomato with a lower R: FR value could improve seedlings' salinity tolerance, and phytochrome B1 play an very important role in this process. Therefore, different qualities of light can be used to efficiently develop abiotic stress tolerance in tomato cultivation.

Great moments in evolution: the conquest of land by plants

500Ma ago the terrestrial habitat was a barren, unwelcoming place for species other than, for example, bacteria or fungi. Most probably, filamentous freshwater algae adapted to aerial conditions and eventually conquered land. Adaptation to a severely different habitat apparently included sturdy cell walls enabling an erect body plan as well as protection against abiotic stresses such as ultraviolet radiation, drought and varying temperature. To thrive on land, plants probably required more elaborate signaling pathways to react to diverse environmental conditions, and phytohormones to control developmental programs. Many such plant-typical features have been studied in flowering plants, but their evolutionary origins were long clouded. With the sequencing of a moss genome a decade ago, inference of ancestral land plant states using comparative genomics, phylogenomics and evolutionary developmental approaches began in earnest. In the past few years, the ever increasing availability of genomic and transcriptomic data of organisms representing the earliest common ancestors of the plant tree of life has much informed our understanding of the conquest of land by plants.

Phytochromes and Phytochrome Interacting Factors

The basic helix-loop-helix domain-containing transcription factors that interact physically with the red and far-red light photoreceptors, phytochromes, are called PHYTOCHROME INTERACTING FACTORS (PIFs). In the last two decades, the phytochrome-PIF signaling module has been shown to be conserved from Physcomitrella patens to higher plants. Exciting recent studies highlight the discovery of at least four distinct kinases (PPKs, CK2, BIN2, and phytochrome itself) and four families of ubiquitin ligases (SCFEBF1/2, CUL3LRB, CUL3BOP, and CUL4COP1-SPA) that regulate PIF abundance both in dark and light conditions. This review discusses these recent discoveries with a focus on the central phytochrome signaling mechanisms that have a profound impact on plant growth and development in response to light.