Inhibition of the shade avoidance response by formation of non-DNA binding bHLH heterodimers

The BBX7/8-CCA1/LHY transcription factor cascade promotes shade avoidance by activating PIF4

Sun-loving plants undergo shade avoidance syndrome (SAS) to compete with their neighbors for sunlight in shade conditions. Phytochrome B (phyB) plays a dominant role in sensing the shading signals (low red to far-red ratios) and triggering SAS. Shade drives phyB conversion to inactive form, consequently leading to the accumulation of PHYTOCHROMEINTERACTING FACTOR 4 (PIF4) that promotes plant growth. Here, we show B-box PROTEIN 7 (BBX7)/BBX8 and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1)/LATE ELONGATED HYPOCOTYL (LHY) positively regulate the low R : FR-induced PIF4 expression and promote the low R : FR-triggered hypocotyl growth in Arabidopsis. Shade interferes the interactions of phyB with BBX7 or BBX8 and triggers the accumulation of BBX7 and BBX8 independent of phyB. BBX7 and BBX8 associate with CCA1 and LHY to activate their transcription, the gene produces of which subsequently upregulate the expression of PIF4 in shade. Genetically, BBX7 and BBX8 act upstream of CCA1, LHY, and PIF4 with respect to hypocotyl growth in shade conditions. Our study reveals the BBX7/8-CCA1/LHY transcription factor cascade upregulates PIF4 expression and increases its abundance to promote plant growth and development in response to shade.

Temporal and spatial frameworks supporting plant responses to vegetation proximity

After the perception of vegetation proximity by phytochrome photoreceptors, shade-avoider plants initiate a set of responses known as the shade avoidance syndrome (SAS). Shade perception by the phytochrome B (phyB) photoreceptor unleashes the PHYTOCHROME INTERACTING FACTORs and initiates SAS responses. In Arabidopsis (Arabidopsis thaliana) seedlings, shade perception involves rapid and massive changes in gene expression, increases auxin production, and promotes hypocotyl elongation. Other components, such as phyA and ELONGATED HYPOCOTYL 5, also participate in the shade regulation of the hypocotyl elongation response by repressing it. However, why and how so many regulators with either positive or negative activities modulate the same response remains unclear. Our physiological, genetic, cellular, and transcriptomic analyses showed that (i) these components are organized into 2 main branches or modules and (ii) the connection between them is dynamic and changes with the time of shade exposure. We propose a model for the regulation of shade-induced hypocotyl elongation in which the temporal and spatial functional importance of the various SAS regulators analyzed here helps to explain the coexistence of differentiated regulatory branches with overlapping activities.

Chemical inhibition of stomatal differentiation by perturbation of the master-regulatory bHLH heterodimer via an ACT-Like domain

Selective perturbation of protein interactions with chemical compounds enables dissection and control of developmental processes. Differentiation of stomata, cellular valves vital for plant growth and survival, is specified by the basic-helix-loop-helix (bHLH) heterodimers. Harnessing a new amination reaction, we here report a synthesis, derivatization, target identification, and mode of action of an atypical doubly-sulfonylated imidazolone, Stomidazolone, which triggers stomatal stem cell arrest. Our forward chemical genetics followed by biophysical analyses elucidates that Stomidazolone directly binds to the C-terminal ACT-Like (ACTL) domain of MUTE, a master regulator of stomatal differentiation, and perturbs its heterodimerization with a partner bHLH, SCREAM in vitro and in plant cells. On the other hand, Stomidazolone analogs that are biologically inactive do not bind to MUTE or disrupt the SCREAM-MUTE heterodimers. Guided by structural docking modeling, we rationally design MUTE with reduced Stomidazolone binding. These engineered MUTE proteins are fully functional and confer Stomidazolone resistance in vivo. Our study identifies doubly-sulfonylated imidazolone as a direct inhibitor of the stomatal master regulator, further expanding the chemical space for perturbing bHLH-ACTL proteins to manipulate plant development.

Shade-induced ROS/NO reinforce COP1-mediated diffuse cell growth

Canopy shade enhances the activity of PHYTOCHROME INTERACTING FACTORs (PIFs) to boost auxin synthesis in the cotyledons. Auxin, together with local PIFs and their positive regulator CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1), promotes hypocotyl growth to facilitate access to light. Whether shade alters the cellular redox status thereby affecting growth responses, remains unexplored. Here, we show that, under shade, high auxin levels increased reactive oxygen species and nitric oxide accumulation in the hypocotyl of Arabidopsis. This nitroxidative environment favored the promotion of hypocotyl growth by COP1 under shade. We demonstrate that COP1 is S-nitrosylated, particularly under shade. Impairing this redox regulation enhanced COP1 degradation by the proteasome and diminished the capacity of COP1 to interact with target proteins and to promote hypocotyl growth. Disabling this regulation also generated transversal asymmetries in hypocotyl growth, indicating poor coordination among different cells, which resulted in random hypocotyl bending and predictably low ability to compete with neighbors. These findings highlight the significance of redox signaling in the control of diffuse growth during shade avoidance.

MPK4-mediated phosphorylation of PHYTOCHROME INTERACTING FACTOR4 controls thermosensing by regulating histone variant H2A.Z deposition

Plants can perceive a slight upsurge in ambient temperature and respond by undergoing morphological changes, such as elongated hypocotyls and early flowering. The dynamic functioning of PHYTOCHROME INTERACTING FACTOR4 (PIF4) in thermomorphogenesis is well established, although the complete regulatory pathway involved in thermosensing remains elusive. We establish that an increase in temperature from 22 to 28 °C induces upregulation and activation of MITOGEN-ACTIVATED PROTEIN KINASE 4 (MPK4) in Arabidopsis (Arabidopsis thaliana), subsequently leading to the phosphorylation of PIF4. Phosphorylated PIF4 represses the expression of ACTIN-RELATED PROTEIN 6 (ARP6), which is required for mediating the deposition of histone variant H2A.Z at its target loci. Furthermore, we demonstrate that variations in ARP6 expression in PIF4 phosphor-null and phosphor-mimetic seedlings affect hypocotyl growth at 22 and 28 °C by modulating the regulation of ARP6-mediated H2A.Z deposition at the loci of genes involved in elongating hypocotyl cells. Interestingly, the expression of MPK4 is also controlled by H2A.Z deposition in a temperature-dependent manner. Taken together, these findings highlight the regulatory mechanism of thermosensing by which MPK4-mediated phosphorylation of PIF4 affects ARP6-mediated H2A.Z deposition at the genes involved in hypocotyl cell elongation.

HTL/KAI2 signaling substitutes for light to control plant germination

Plants monitor multiple environmental cues, such as light and temperature, to ensure they germinate at the right time and place. Some specialist plants, like ephemeral fire-following weeds and root parasitic plants, germinate primarily in response to small molecules found in specific environments. Although these species come from distinct clades, they use the same HYPOSENSITIVE TO LIGHT/KARRIKIN INSENSITIVE 2 (HTL/KAI2) signaling pathway, to perceive different small molecules suggesting convergent evolution on this pathway. Here, we show that HTL/KAI2 signaling in Arabidopsis thaliana bypasses the light requirement for germination. The HTL/KAI2 downstream component, SUPPRESSOR OF MAX2 1 (SMAX1) accumulates in the dark and is necessary for PHYTOCHROME INTERACTING FACTOR 1/PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIF1/PIL5) to regulate hormone response pathways conducive to germination. The interaction of HTL/KAI2 and light signaling may help to explain how specialist plants like ephemeral and parasitic weeds evolved their germination behaviour in response to specific environments.

NAC transcription factor ATAF1 negatively modulates the PIF-regulated hypocotyl elongation under a short-day photoperiod

Day length modulates hypocotyl elongation in seedlings to optimize their overall fitness. Variations in cell growth-associated genes are regulated by several transcription factors. However, the specific transcription factors through which the plant clock increases plant fitness are still being elucidated. In this study, we identified the no apical meristem, Arabidopsis thaliana-activating factor (ATAF-1/2), and cup-shaped cotyledon (NAC) family transcription factor ATAF1 as a novel repressor of hypocotyl elongation under a short-day (SD) photoperiod. Variations in day length profoundly affected the transcriptional and protein levels of ATAF1. ATAF1-deficient mutant exhibited increased hypocotyl length and cell growth-promoting gene expression under SD conditions. Moreover, ATAF1 directly targeted and repressed the expression of the cycling Dof factor 1/5 (CDF1/5), two key transcription factors involved in hypocotyl elongation under SD conditions. Additionally, ATAF1 interacted with and negatively modulated the effects of phytochrome-interacting factor (PIF), thus inhibiting PIF-promoted gene expression and hypocotyl elongation. Taken together, our results revealed ATAF1-PIF as a crucial pair modulating the expression of key transcription factors to facilitate plant growth during day/night cycles under fluctuating light conditions.

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.

Organ-specific transcriptional regulation by HFR1 and HY5 in response to shade in Arabidopsis

Light is crucial for plants and serves as a signal for modulating their growth. Under shade, where red to far-red light ratio is low, plants exhibit shade avoidance responses (SAR). LONG HYPOCOTYL IN FAR-RED 1 (HFR1) and ELONGATED HYPOCOTYL 5 (HY5) are known to be negative regulators of SAR and physically interact with one another. However, transcriptional regulatory network underlying SAR by these two transcription factors has not been explored. Here, we performed organ-specific transcriptome analyses of Arabidopsis thaliana hfr1-5, hy5-215 and hfr1hy5 to identify genes that are co-regulated by HFR1 and HY5 in hypocotyls and cotyledons. Genes co-regulated by HFR1 and HY5 were enriched in various processes related to cell wall modification and chlorophyll biosynthesis in hypocotyls. Phytohormone (abscisic acid and jasmonic acid) and light responses were significantly regulated by HFR1 and HY5 in both organs, though it is more prominent under shade in cotyledons. HFR1 and HY5 also differentially regulate the expression of the cell wall-related genes for xyloglucan endotransglucosylase/hydrolase, expansin, arabinogalactan protein and class III peroxidase depending on the organs. Furthermore, HFR1 and HY5 cooperatively regulated hypocotyl responsiveness to shade through auxin metabolism. Together, our study illustrates the importance of the HFR1-HY5 module in regulating organ-specific shade responses in Arabidopsis.

Atmospheric nitrogen dioxide suppresses the activity of phytochrome interacting factor 4 to suppress hypocotyl elongation

MAIN CONCLUSION

Ambient concentrations of atmospheric nitrogen dioxide (NO2) inhibit the binding of PIF4 to promoter regions of auxin pathway genes to suppress hypocotyl elongation in Arabidopsis. Ambient concentrations (10-50 ppb) of atmospheric nitrogen dioxide (NO2) positively regulate plant growth to the extent that organ size and shoot biomass can nearly double in various species, including Arabidopsis thaliana (Arabidopsis). However, the precise molecular mechanism underlying NO2-mediated processes in plants, and the involvement of specific molecules in these processes, remain unknown. We measured hypocotyl elongation and the transcript levels of PIF4, encoding a bHLH transcription factor, and its target genes in wild-type (WT) and various pif mutants grown in the presence or absence of 50 ppb NO2. Chromatin immunoprecipitation assays were performed to quantify binding of PIF4 to the promoter regions of its target genes. NO2 suppressed hypocotyl elongation in WT plants, but not in the pifq or pif4 mutants. NO2 suppressed the expression of target genes of PIF4, but did not affect the transcript level of the PIF4 gene itself or the level of PIF4 protein. NO2 inhibited the binding of PIF4 to the promoter regions of two of its target genes, SAUR46 and SAUR67. In conclusion, NO2 inhibits the binding of PIF4 to the promoter regions of genes involved in the auxin pathway to suppress hypocotyl elongation in Arabidopsis. Consequently, PIF4 emerges as a pivotal participant in this regulatory process. This study has further clarified the intricate regulatory mechanisms governing plant responses to environmental pollutants, thereby advancing our understanding of how plants adapt to changing atmospheric conditions.

Environmental Control of Hypocotyl Elongation

The hypocotyl is the embryonic stem connecting the primary root to the cotyledons. Hypocotyl length varies tremendously depending on the conditions. This developmental plasticity and the simplicity of the organ explain its success as a model for growth regulation. Light and temperature are prominent growth-controlling cues, using shared signaling elements. Mechanisms controlling hypocotyl elongation in etiolated seedlings reaching the light differ from those in photoautotrophic seedlings. However, many common growth regulators intervene in both situations. Multiple photoreceptors including phytochromes, which also respond to temperature, control the activity of several transcription factors, thereby eliciting rapid transcriptional reprogramming. Hypocotyl growth often depends on sensing in green tissues and interorgan communication comprising auxin. Hypocotyl auxin, in conjunction with other hormones, determines epidermal cell elongation. Plants facing cues with opposite effects on growth control hypocotyl elongation through intricate mechanisms. We discuss the status of the field and end by highlighting open questions.

B-Box transcription factor BBX28 requires CONSTITUTIVE PHOTOMORPHOGENESIS1 to induce shade-avoidance response in Arabidopsis thaliana

Shade avoidance syndrome is an important adaptive strategy. Under shade, major transcriptional rearrangements underlie the reallocation of resources to elongate vegetative structures and redefine the plant architecture to compete for photosynthesis. BBX28 is a B-box transcription factor involved in seedling de-etiolation and flowering in Arabidopsis (Arabidopsis thaliana), but its function in shade-avoidance response is completely unknown. Here, we studied the function of BBX28 using two mutant and two transgenic lines of Arabidopsis exposed to white light and simulated shade conditions. We found that BBX28 promotes hypocotyl growth under shade through the phytochrome system by perceiving the reduction of red photons but not the reduction of photosynthetically active radiation or blue photons. We demonstrated that hypocotyl growth under shade is sustained by the protein accumulation of BBX28 in the nuclei in a CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1)-dependent manner at the end of the photoperiod. BBX28 up-regulates the expression of transcription factor- and auxin-related genes, thereby promoting hypocotyl growth under prolonged shade. Overall, our results suggest the role of BBX28 in COP1 signaling to sustain the shade-avoidance response and extend the well-known participation of other members of BBX transcription factors for fine-tuning plant growth under shade.

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.

A warm temperature-released negative feedback loop fine-tunes PIF4-mediated thermomorphogenesis in Arabidopsis

Plants can sense temperature changes and adjust their growth accordingly. In Arabidopsis, high ambient temperatures stimulate stem elongation by activating a key thermoresponsive regulator, PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Here, we show that warmth promotes the nighttime transcription of GI, which is necessary for the high temperature-induced transcription of TOC1. Genetic analyses suggest that GI prevents excessive thermoresponsive growth by inhibiting PIF4, with this regulatory mechanism being partially reliant on TOC1. GI transcription is repressed by ELF3 and HY5, which concurrently inhibit PIF4 expression and activity. Temperature elevation causes the deactivation or degradation of ELF3 and HY5, leading to PIF4 activation and relief of GI transcriptional repression at high temperatures. This allows PIF4 to further activate GI transcription in response to elevated temperatures. GI, in turn, inhibits PIF4, establishing a negative feedback loop that fine-tunes PIF4 activity. In addition, we demonstrate that ELF3, HY5, and PIF4 regulate GI transcription by modulating the enrichment of histone variant H2A.Z at the GI locus. Together, our findings suggest that thermal release of a negative feedback loop finely adjusts plant thermomorphogenesis.

Environmentally adaptive reshaping of plant photomorphogenesis by karrikin and strigolactone signaling

Coordinated morphogenic adaptation of growing plants is critical for their survival and propagation under fluctuating environments. Plant morphogenic responses to light and warm temperatures, termed photomorphogenesis and thermomorphogenesis, respectively, have been extensively studied in recent decades. During photomorphogenesis, plants actively reshape their growth and developmental patterns to cope with changes in light regimes. Accordingly, photomorphogenesis is closely associated with diverse growth hormonal cues. Notably, accumulating evidence indicates that light-directed morphogenesis is profoundly affected by two recently identified phytochemicals, karrikins (KARs) and strigolactones (SLs). KARs and SLs are structurally related butenolides acting as signaling molecules during a variety of developmental steps, including seed germination. Their receptors and signaling mediators have been identified, and associated working mechanisms have been explored using gene-deficient mutants in various plant species. Of particular interest is that the KAR and SL signaling pathways play important roles in environmental responses, among which their linkages with photomorphogenesis are most comprehensively studied during seedling establishment. In this review, we focus on how the phytochemical and light signals converge on the optimization of morphogenic fitness. We also discuss molecular mechanisms underlying the signaling crosstalks with an aim of developing potential ways to improve crop productivity under climate changes.

Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses

Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.

Genome-wide identification and comprehensive analysis of the phytochrome-interacting factor (PIF) gene family in wheat

Phytochrome-interacting factors (PIFs) are essential transcription factors for plant growth, development, and stress responses. Although PIF genes have been extensively studied in many plant species, they have not been thoroughly investigated in wheat. Here, we identified 18 PIF genes in cultivated hexaploid wheat (Triticum aestivum L). Phylogenetic analysis, exon-intron structures, and motif compositions revealed the presence of four distinct groups of TaPIFs. Genome-wide collinearity analysis of PIF genes revealed the evolutionary history of PIFs in wheat, Oryza sativa, and Brachypodium distachyon. Cis-regulatory element analysis suggested that TaPIF genes indicated participated in plant development and stress responses. Subcellular localization assays indicated that TaPIF2-1B and TaPIF4-5B were transcriptionally active. Both were found to be localized to the nucleus. Gene expression analyses demonstrated that TaPIFs were primarily expressed in the leaves and were induced by various biotic and abiotic stresses and phytohormone treatments. This study provides new insights into PIF-mediated stress responses and lays a strong foundation for future investigation of PIF genes in wheat.

Supplementary Low Far-Red Light Promotes Proliferation and Photosynthetic Capacity of Blueberry In Vitro Plantlets

Far-red light exerts an important regulatory influence on plant growth and development. However, the mechanisms underlying far-red light regulation of morphogenesis and photosynthetic characteristics in blueberry plantlets in vitro have remained elusive. Here, physiological and transcriptomic analyses were conducted on blueberry plantlets in vitro supplemented with far-red light. The results indicated that supplementation with low far-red light, such as 6 μmol m-2 s-1 and 14 μmol m-2 s-1 far-red (6FR and 14FR) light treatments, significantly increased proliferation-related indicators, including shoot length, shoot number, gibberellin A3, and trans-zeatin riboside content. It was found that 6FR and 14 FR significantly reduced chlorophyll content in blueberry plantlets but enhanced electron transport rates. Weighted correlation network analysis (WGCNA) showed the enrichment of iron ion-related genes in modules associated with photosynthesis. Genes such as NAC, ABCG11, GASA1, and Erf74 were significantly enriched within the proliferation-related module. Taken together, we conclude that low far-red light can promote the proliferative capacity of blueberry plantlets in vitro by affecting hormone pathways and the formation of secondary cell walls, concurrently regulating chlorophyll content and iron ion homeostasis to affect photosynthetic capacity.

The heat response regulators HSFA1s promote Arabidopsis thermomorphogenesis via stabilizing PIF4 during the day

During summer, plants often experience increased light inputs and high temperatures, two major environmental factors with contrasting effects on thermomorphological traits. The integration of light and temperature signaling to control thermomorphogenesis in plants is critical for their acclimation in such conditions, but the underlying mechanisms remain largely unclear. We found that heat shock transcription factor 1d (HSFA1d) and its homologs are necessary for plant thermomorphogenesis during the day. In response to warm daytime temperature, HSFA1s markedly accumulate and move into the nucleus where they interact with phytochrome-interacting factor 4 (PIF4) and stabilize PIF4 by interfering with phytochrome B-PIF4 interaction. Moreover, we found that the HSFA1d nuclear localization under warm daytime temperature is mediated by constitutive photomorphogenic 1-repressed GSK3-like kinase BIN2. These results support a regulatory mechanism for thermomorphogenesis in the daytime mediated by the HSFA1s-PIF4 module and uncover HSFA1s as critical regulators integrating light and temperature signaling for a better acclimation of plants to the summer high temperature.

HISTONE DEACETYLASE 9 promotes hypocotyl-specific auxin response under shade

Vegetative shade causes an array of morphological changes in plants called shade avoidance syndrome, which includes hypocotyl and petiole elongation, leaf hyponasty, reduced leaf growth, early flowering and rapid senescence. Here, we show that loss-of-function mutations in HISTONE DEACETYLASE 9 (HDA9) attenuated the shade-induced hypocotyl elongation in Arabidopsis. However, the hda9 cotyledons and petioles under shade were not significantly different from those in wild-type, suggesting a specific function of HDA9 in hypocotyl elongation in response to shade. HDA9 expression levels were stable under shade and its protein was ubiquitously detected in cotyledon, hypocotyl and root. Organ-specific transcriptome analysis unraveled that shade induced a set of auxin-responsive genes, such as SMALL AUXIN UPREGULATED RNAs (SAURs) and AUXIN/INDOLE-3-ACETIC ACIDs (AUX/IAAs) and their induction was impaired in hda9-1 hypocotyls. In addition, HDA9 binding to loci of SAUR15/65, IAA5/6/19 and ACS4 was increased under shade. The genetic and organ-specific gene expression analyses further revealed that HDA9 may cooperate with PHYTOCHROME-INTERACTING FACTOR 4/7 in the regulation of shade-induced hypocotyl elongation. Furthermore, HDA9 and PIF7 proteins were found to interact together and thus it is suggested that PIF7 may recruit HDA9 to regulate the shade/auxin responsive genes in response to shade. Overall, our study unravels that HDA9 can work as one component of a hypocotyl-specific transcriptional regulatory machinery that activates the auxin response at the hypocotyl leading to the elongation of this organ under shade.

ELONGATED HYPOCOTYL5 (HY5) and HY5 HOMOLOGUE (HYH) maintain shade avoidance suppression in UV-B

Reductions in red to far-red ratio (R:FR) provide plants with an unambiguous signal of vegetational shade and are monitored by phytochrome photoreceptors. Plants integrate this information with other environmental cues to determine the proximity and density of encroaching vegetation. Shade-sensitive species respond to reductions in R:FR by initiating a suite of developmental adaptations termed shade avoidance. These include the elongation of stems to facilitate light foraging. Hypocotyl elongation is driven by increased auxin biosynthesis promoted by PHYTOCHROME INTERACTING FACTORs (PIF) 4, 5 and 7. UV-B perceived by the UV RESISTANCE LOCUS 8 (UVR8) photoreceptor rapidly inhibits shade avoidance, in part by suppressing PIF4/5 transcript accumulation and destabilising PIF4/5 protein. Here, we show that longer-term inhibition of shade avoidance is sustained by ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOGUE (HYH), which regulate transcriptional reprogramming of genes involved in hormone signalling and cell wall modification. HY5 and HYH are elevated in UV-B and suppress the expression of XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE (XTH) genes involved in cell wall loosening. They additionally increase expression GA2-OXIDASE1 (GA2ox1) and GA2ox2, encoding gibberellin catabolism enzymes that act redundantly to stabilise the PIF-inhibiting DELLA proteins. UVR8 therefore regulates temporally distinct signalling pathways to first rapidly inhibit and subsequently maintain suppression of shade avoidance following UV-B exposure.

SALT OVERLY SENSITIVE2 stabilizes phytochrome-interacting factors PIF4 and PIF5 to promote Arabidopsis shade avoidance

Sun-loving plants trigger the shade avoidance syndrome (SAS) to compete against their neighbors for sunlight. Phytochromes are plant red (R) and far-red (FR) light photoreceptors that play a major role in perceiving the shading signals and triggering SAS. Shade induces a reduction in the level of active phytochrome B (phyB), thus increasing the abundance of PHYTOCHROME-INTERACTING FACTORS (PIFs), a group of growth-promoting transcription factors. However, whether other factors are involved in modulating PIF activity in the shade remains largely obscure. Here, we show that SALT OVERLY SENSITIVE2 (SOS2), a protein kinase essential for salt tolerance, positively regulates SAS in Arabidopsis thaliana. SOS2 directly phosphorylates PIF4 and PIF5 at a serine residue close to their conserved motif for binding to active phyB. This phosphorylation thus decreases their interaction with phyB and posttranslationally promotes PIF4 and PIF5 protein accumulation. Notably, the role of SOS2 in regulating PIF4 and PIF5 protein abundance and SAS is more prominent under salt stress. Moreover, phyA and phyB physically interact with SOS2 and promote SOS2 kinase activity in the light. Collectively, our study uncovers an unexpected role of salt-activated SOS2 in promoting SAS by modulating the phyB-PIF module, providing insight into the coordinated response of plants to salt stress and shade.

Transcriptomic and physiological shade avoidance responses in potato (Solanum tuberosum) plants

Plants detect competitors in shaded environments by perceiving a reduction in photosynthetically active radiation (PAR) and the reduction between the red and far-red light (R:FR) ratio and blue photons. These light signals are detected by phytochromes and cryptochromes, which trigger shade avoidance responses such as shoot and petiole elongation and lead to increased susceptibility to pathogen attack. We studied morphological, anatomical, and photosynthesis differences in potato plants (Solanum tuberosum var. Spunta) exposed to sunlight or simulated shade in a greenhouse. We found that simulated shade strongly induced stem and internode elongation with a higher production of free auxin in stems and a lower production of tubers. The mesophyll thickness of the upper leaves of plants grown in simulated shade was lower, but the epidermis was wider compared with the leaves of plants cultivated in sunlight. In addition, the photosynthesis rate was lower in the upper leaves exposed to nonsaturated irradiances and higher in the basal leaves at saturated irradiances compared with control plants. RNA-seq analysis showed that 146 and 155 genes were up- and downregulated by shade, respectively. By quantitative reverse transcription polymerase chain reaction, we confirmed that FLOWERING LOCUS T (FT), WRKY-like, and PAR1b were induced, while FLAVONOL 4-SULFOTRANSFERASE was repressed under shade. In shaded plants, leaves and tubers were more susceptible to the necrotrophic fungus Botrytis cinerea attack. Overall, our work demonstrates configurational changes between growth and defense decisions in potato plants cultivated in simulated shade.

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.

BBX24 Interacts with JAZ3 to Promote Growth by Reducing DELLA Activity in Shade Avoidance

Shade avoidance syndrome (SAS) is a strategy of major adaptive significance and typically includes elongation of the stem and petiole, leaf hyponasty, reduced branching and phototropic orientation of the plant shoot toward canopy gaps. Both cryptochrome 1 and phytochrome B (phyB) are the major photoreceptors that sense the reduction in the blue light fluence rate and the low red:far-red ratio, respectively, and both light signals are associated with plant density and the resource reallocation when SAS responses are triggered. The B-box (BBX)-containing zinc finger transcription factor BBX24 has been implicated in the SAS as a regulator of DELLA activity, but this interaction does not explain all the observed BBX24-dependent regulation in shade light. Here, through a combination of transcriptional meta-analysis and large-scale identification of BBX24-interacting transcription factors, we found that JAZ3, a jasmonic acid signaling component, is a direct target of BBX24. Furthermore, we demonstrated that joint loss of BBX24 and JAZ3 function causes insensitivity to DELLA accumulation, and the defective shade-induced elongation in this mutant is rescued by loss of DELLA or phyB function. Therefore, we propose that JAZ3 is part of the regulatory network that controls the plant growth in response to shade, through a mechanism in which BBX24 and JAZ3 jointly regulate DELLA activity. Our results provide new insights into the participation of BBX24 and JA signaling in the hypocotyl shade avoidance response in Arabidopsis.

Photoperiodic flowering in Arabidopsis: Multilayered regulatory mechanisms of CONSTANS and the florigen FLOWERING LOCUS T

The timing of flowering affects the success of sexual reproduction. This developmental event also determines crop yield, biomass, and longevity. Therefore, this mechanism has been targeted for improvement along with crop domestication. The underlying mechanisms of flowering are highly conserved in angiosperms. Central to these mechanisms is how environmental and endogenous conditions control transcriptional regulation of the FLOWERING LOCUS T (FT) gene, which initiates floral development under long-day conditions in Arabidopsis. Since the identification of FT as florigen, efforts have been made to understand the regulatory mechanisms of FT expression. Although many transcriptional regulators have been shown to directly influence FT, the question of how they coordinately control the spatiotemporal expression patterns of FT still requires further investigation. Among FT regulators, CONSTANS (CO) is the primary one whose protein stability is tightly controlled by phosphorylation and ubiquitination/proteasome-mediated mechanisms. In addition, various CO interaction partners, some of them previously identified as FT transcriptional regulators, positively or negatively modulate CO protein activity. The FT promoter possesses several transcriptional regulatory "blocks," highly conserved regions among Brassicaceae plants. Different transcription factors bind to specific blocks and affect FT expression, often causing topological changes in FT chromatin structure, such as the formation of DNA loops. We discuss the current understanding of the regulation of FT expression mainly in Arabidopsis and propose future directions related to this topic.

Comparative transcriptome analysis reveals the function of SlPRE2 in multiple phytohormones biosynthesis, signal transduction and stomatal development in tomato

KEY MESSAGE

Transcriptomic, physiological, and qRT-PCR analysis revealed the potential mechanism by which SlPRE2 regulates plant growth and stomatal size via multiple phytohormone pathways in tomato. Paclobutrazol resistance proteins (PREs) are atypical members of the basic/helix-loop-helix (bHLH) transcription factor family that regulate plant morphology, cell size, pigment metabolism and abiotic stress in response to different phytohormones. However, little is known about the network regulatory mechanisms of PREs in plant growth and development in tomato. In this study, the function and mechanism of SlPRE2 in tomato plant growth and development were investigated. The quantitative RT-PCR results showed that the expression of SlPRE2 was regulated by multiple phytohormones and abiotic stresses. It showed light-repressed expression during the photoperiod. The RNA-seq results revealed that SlPRE2 regulated many genes involved in photosynthesis, chlorophyll metabolism, phytohormone metabolism and signaling, and carbohydrate metabolism, suggesting the role of SlPRE2 in gibberellin, brassinosteroid, auxin, cytokinin, abscisic acid and salicylic acid regulated plant development processes. Moreover, SlPRE2 overexpression plants showed widely opened stomata in young leaves, and four genes involved in stomatal development showed altered expression. Overall, the results demonstrated the mechanism by which SlPRE2 regulates phytohormone and stress responses and revealed the function of SlPRE2 in stomatal development in tomato. These findings provide useful clues for understanding the molecular mechanisms of SlPRE2-regulated plant growth and development in tomato.

Shade avoidance in the context of climate change

When exposed to changes in the light environment caused by neighboring vegetation, shade-avoiding plants modify their growth and/or developmental patterns to access more sunlight. In Arabidopsis (Arabidopsis thaliana), neighbor cues reduce the activity of the photosensory receptors phytochrome B (phyB) and cryptochrome 1, releasing photoreceptor repression imposed on PHYTOCHROME INTERACTING FACTORs (PIFs) and leading to transcriptional reprogramming. The phyB-PIF hub is at the core of all shade-avoidance responses, whilst other photosensory receptors and transcription factors contribute in a context-specific manner. CONSTITUTIVELY PHOTOMORPHOGENIC1 is a master regulator of this hub, indirectly stabilizing PIFs and targeting negative regulators of shade avoidance for degradation. Warm temperatures reduce the activity of phyB, which operates as a temperature sensor and further increases the activities of PIF4 and PIF7 by independent temperature sensing mechanisms. The signaling network controlling shade avoidance is not buffered against climate change; rather, it integrates information about shade, temperature, salinity, drought, and likely flooding. We, therefore, predict that climate change will exacerbate shade-induced growth responses in some regions of the planet while limiting the growth potential in others.

LONG HYPOCOTYL IN FAR-RED 1 mediates a trade-off between growth and defense under shade in Arabidopsis

Plants respond to vegetative shade with developmental and physiological changes that is collectively known as shade avoidance syndrome (SAS). Although LONG HYPOCOTYL IN FAR-RED 1 (HFR1) is known to be a negative regulator of SAS by forming heterodimers with other basic helix-loop-helix (bHLH) transcription factors to inhibit them, its function in genome-wide transcriptional regulation is not fully elucidated. Here, we performed RNA-sequencing analyses of hfr1-5 and HFR1 overexpression line (HFR1(ΔN)-OE) to comprehensively identify HFR1-regulated genes at different time points of shade treatment. We found that HFR1 mediates the trade-off between shade-induced growth and shade-repressed defense, by regulating the expression of relevant genes in shade. Genes involved in promoting growth, such as for auxin biosynthesis, transport, signaling and response were induced by shade but suppressed by HFR1 at both short and long durations of shade. Likewise, most ethylene-related genes were shade-induced and HFR1-repressed. On the other hand, shade suppressed defense-related genes while HFR1 induced their expression, especially under long duration of shade treatment. We demonstrated that HFR1 confers increased resistance to bacterial infection under shade.

PHYTOCHROME-INTERACTING FACTOR 4/HEMERA-mediated thermosensory growth requires the Mediator subunit MED14

While moderately elevated ambient temperatures do not trigger stress responses in plants, they do substantially stimulate the growth of specific organs through a process known as thermomorphogenesis. The basic helix-loop-helix transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) plays a central role in regulating thermomorphogenetic hypocotyl elongation in various plant species, including Arabidopsis (Arabidopsis thaliana). Although it is well known that PIF4 and its co-activator HEMERA (HMR) promote plant thermosensory growth by activating genes involved in the biosynthesis and signaling of the phytohormone auxin, the detailed molecular mechanism of such transcriptional activation is not clear. In this report, we investigated the role of the Mediator complex in the PIF4/HMR-mediated thermoresponsive gene expression. Through the characterization of various mutants of the Mediator complex, a tail subunit named MED14 was identified as an essential factor for thermomorphogenetic hypocotyl growth. MED14 was required for the thermal induction of PIF4 target genes but had a marginal effect on the levels of PIF4 and HMR. Further transcriptomic analyses confirmed that the expression of numerous PIF4/HMR-dependent, auxin-related genes required MED14 at warm temperatures. Moreover, PIF4 and HMR physically interacted with MED14 and both were indispensable for the association of MED14 with the promoters of these thermoresponsive genes. While PIF4 did not regulate MED14 levels, HMR was required for the transcript abundance of MED14. Taken together, these results unveil an important thermomorphogenetic mechanism, in which PIF4 and HMR recruit the Mediator complex to activate auxin-related growth-promoting genes when plants sense moderate increases in ambient temperature.

Activation tagging identifies WRKY14 as a repressor of plant thermomorphogenesis in Arabidopsis

Increases in recorded high temperatures around the world are causing plant thermomorphogenesis and decreasing crop productivity. PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is a central positive regulator of plant thermomorphogenesis. However, the molecular mechanisms underlying PIF4-regulated thermomorphogenesis remain largely unclear. In this study, we identified ABNORMAL THERMOMORPHOGENESIS 1 (ABT1) as an important negative regulator of PIF4 and plant thermomorphogenesis. Overexpression of ABT1 in the activation tagging mutant abt1-D caused shorter hypocotyls and petioles under moderately high temperature (HT). ABT1 encodes WRKY14, which belongs to subgroup II of the WRKY transcription factors. Overexpression of ABT1/WRKY14 or its close homologs, including ABT2/WRKY35, ABT3/WRKY65, and ABT4/WRKY69in transgenic plants caused insensitivity to HT, whereas the quadruple mutant abt1 abt2 abt3 abt4 exhibited greater sensitivity to HT. ABTs were expressed in hypocotyls, cotyledons, shoot apical meristems, and leaves, but their expression were suppressed by HT. Biochemical assays showed that ABT1 can interact with TCP5, a known positive regulator of PIF4, and interrupt the formation of the TCP5-PIF4 complex and repress its transcriptional activation activity. Genetic analysis showed that ABT1 functioned antagonistically with TCP5, BZR1, and PIF4 in plant thermomorphogenesis. Taken together, our results identify ABT1/WRKY14 as a critical repressor of plant thermomorphogenesis and suggest that ABT1/WRKY14, TCP5, and PIF4 may form a sophisticated regulatory module to fine-tune PIF4 activity and temperature-dependent plant growth.

Soybean GmHY2a encodes a phytochromobilin synthase that regulates internode length and flowering time

Plant height and flowering time are important agronomic traits that directly affect soybean [Glycine max (L.) Merr.] adaptability and yield. Here, the Glycine max long internode 1 (Gmlin1) mutant was selected from an ethyl methyl sulfonate (EMS)-mutated Williams 82 population due to its long internodes and early flowering. Using bulked segregant analysis (BSA), the Gmlin1 locus was mapped to Glyma.02G304700, a homologue of the Arabidopsis HY2 gene, which encodes a phytochromobilin (PΦB) synthase involved in phytochrome chromophore synthesis. Mutation of GmHY2a results in failure of the de-etiolation response under both red and far-red light. The Gmlin1 mutant exhibits a constitutive shade avoidance response under normal light, and the mutations influence the auxin and gibberellin pathways to promote internode elongation. The Gmlin1 mutant also exhibits decreased photoperiod sensitivity. In addition, the soybean photoperiod repressor gene E1 is down-regulated in the Gmlin1 mutant, resulting in accelerated flowering. The nuclear import of phytochrome A (GmphyA) and GmphyB following light treatment is decreased in Gmlin1 protoplasts, indicating that the weak light response of the Gmlin1 mutant is caused by a decrease in functional phytochrome. Together, these results indicate that GmHY2a plays an important role in soybean phytochrome biosynthesis and provide insights into the adaptability of the soybean plant.

COP1 SUPPRESSOR 6 represses the PIF4 and PIF5 action to promote light-inhibited hypocotyl growth

Light signaling precisely controls photomorphogenic development in plants. PHYTOCHROME INTERACTING FACTOR 4 and 5 (PIF4 and PIF5) play critical roles in the regulation of this developmental process. In this study, we report CONSTITUTIVELY PHOTOMORPHOGENIC 1 SUPPRESSOR 6 (CSU6) functions as a key regulator of light signaling. Loss of CSU6 function largely rescues the cop1-6 constitutively photomorphogenic phenotype. CSU6 promotes hypocotyl growth in the dark, but inhibits hypocotyl elongation in the light. CSU6 not only associates with the promoter regions of PIF4 and PIF5 to inhibit their expression in the morning, but also directly interacts with both PIF4 and PIF5 to repress their transcriptional activation activity. CSU6 negatively controls a group of PIF4- and PIF5-regulated gene expressions. Mutations in PIF4 and/or PIF5 are epistatic to the loss of CSU6, suggesting that CSU6 acts upstream of PIF4 and PIF5. Taken together, CSU6 promotes light-inhibited hypocotyl elongation by negatively regulating PIF4 and PIF5 transcription and biochemical activity.

COP1 dynamics integrate conflicting seasonal light and thermal cues in the control of Arabidopsis elongation

As the summer approaches, plants experience enhanced light inputs and warm temperatures, two environmental cues with an opposite morphogenic impact. Key components of this response are PHYTOCHROME B (phyB), EARLY FLOWERING 3 (ELF3), and CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). Here, we used single and double mutant/overexpression lines to fit a mathematical model incorporating known interactions of these regulators. The fitted model recapitulates thermal growth of all lines used and correctly predicts thermal behavior of others not used in the fit. While thermal COP1 function is accepted to be independent of diurnal timing, our model shows that it acts at temperature signaling only during daytime. Defective response of cop1-4 mutants is epistatic to phyB-9 and elf3-8, indicating that COP1 activity is essential to transduce phyB and ELF3 thermosensory function. Our thermal model provides a unique toolbox to identify best allelic combinations enhancing climate change resilience of crops adapted to different latitudes.

SUPPRESSOR OF PHYTOCHROME B-4 #3 reduces the expression of PIF-activated genes and increases expression of growth repressors to regulate hypocotyl elongation in short days

SUPPRESSOR OF PHYTOCHROME B-4 #3 (SOB3) is a member of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family of transcription factors that are involved in light-mediated growth in Arabidopsis thaliana, affecting processes such as hypocotyl elongation. The majority of the research on the AHLs has been conducted in continuous light. However, there are unique molecular events that promote growth in short days (SD) compared to constant light conditions. Therefore, we investigated how AHLs affect hypocotyl elongation in SD. Firstly, we observed that AHLs inhibit hypocotyl growth in SD, similar to their effect in constant light. Next, we identified AHL-regulated genes in SD-grown seedlings by performing RNA-seq in two sob3 mutants at different time points. Our transcriptomic data indicate that PHYTOCHROME INTERACTING FACTORS (PIFs) 4, 5, 7, and 8 along with PIF-target genes are repressed by SOB3 and/or other AHLs. We also identified PIF target genes that are repressed and have not been previously described as AHL-regulated, including PRE1, PIL1, HFR1, CDF5, and XTR7. Interestingly, our RNA-seq data also suggest that AHLs activate the expression of growth repressors to control hypocotyl elongation, such as HY5 and IAA17. Notably, many growth-regulating and other genes identified from the RNA-seq experiment were differentially regulated between these two sob3 mutants at the time points tested. Surprisingly, our ChIP-seq data suggest that SOB3 mostly binds to similar genes throughout the day. Collectively, these data suggest that AHLs affect gene expression in a time point-specific manner irrespective of changes in binding to DNA throughout SD.

PEAPOD repressors modulate and coordinate developmental responses to light intensity in Arabidopsis

Higher plants adapt to different light intensities by altering hypocotyl elongation, stomatal density, seed size, and flowering time. Despite the importance of this developmental plasticity, knowledge of the underlying genetic and molecular mechanisms modulating and coordinating responses to light intensity remains incomplete. Here, I report that in Arabidopsis the PEAPOD (PPD) repressors PPD1 and PPD2 prevent exaggerated responses to light intensity. Genetic and transcriptome analyses, of a ppd deletion mutant and a PPD1 overexpression genotype, were used to identify how PPD repressors modulate the light signalling network. A ppd1/ppd2 deletion mutant has elongated hypocotyls, elevated stomatal density, enlarged seed, and delayed flowering, whereas overexpression of PPD1 results in the reverse. Transcription of both PPD1 and PPD2, upregulated in low light and downregulated in higher light, is activated by PHYTOCHROME INTERACTING FACTOR 4. I found PPDs modulate light signalling by negative regulation of SUPPRESSOR OF phyA-105 (SPA1) transcription. Whereas PPDs coordinate many of the responses to light intensity - hypocotyl elongation, flowering time, and stomatal density - by repression/de-repression of SPA1, PPD regulation of seed size occurs independent of SPA1. In conclusion PPD repressors modulate and coordinate developmental responses to light intensity by altering light signal transduction.

EARLY FLOWERING 3 represses the nighttime growth response to sucrose in Arabidopsis

Plant growth depends on the supply of carbohydrates produced by photosynthesis. Exogenously applied sucrose promotes the growth of the hypocotyl in Arabidopsis thaliana seedlings grown under short days. Whether this effect of sucrose is stronger under the environmental conditions where the light input for photosynthesis is limiting remains unknown. We characterised the effects of exogenous sucrose on hypocotyl growth rates under light compared to simulated shade, during different portions of the daily cycle. The strongest effects of exogenous sucrose occurred under shade and during the night; i.e., the conditions where there is reduced or no photosynthesis. Conversely, a faster hypocotyl growth rate, predicted to enhance the demand of carbohydrates, did not associate to a stronger sucrose effect. The early flowering 3 (elf3) mutation strongly enhanced the impact of sucrose on hypocotyl growth during the night of a white-light day. This effect occurred under short, but not under long days. The addition of sucrose enhanced the fluorescence intensity of ELF3 nuclear speckles. The elf3 mutant showed increased abundance of PHYTOCHROME INTERACTING FACTOR4 (PIF4), which is a transcription factor required for a full response to sucrose. Sucrose increased PIF4 protein abundance by post-transcriptional mechanisms. Under shade, elf3 showed enhanced daytime and reduced nighttime effects of sucrose. We conclude that ELF3 modifies the responsivity to sucrose according to the time of the daily cycle and the prevailing light or shade conditions.

RNA-Seq and Gene Ontology Analysis Reveal Differences Associated With Low R/FR-Induced Shade Responses in Cultivated Lentil and a Wild Relative

Lentil is an important pulse crop not only because of its high nutrient value but also because of its ecological advantage in a sustainable agricultural system. Our previous work showed that the cultivated lentil and wild lentil germplasm respond differently to light environments, especially to low R/FR-induced shade conditions. Little is known about how cultivated and wild lentils respond to shade at the level of gene expression and function. In this study, transcriptomic profiling of a cultivated lentil (Lupa, L. culinaris) and a wild lentil (BGE 016880, L. orientalis) at several growth stages is presented. De novo transcriptomes were assembled for both genotypes, and differential gene expression analysis and gene ontology enrichment analysis were performed. The transcriptomic resources generated in this study provide fundamental information regarding biological processes and genes associated with shade responses in lentils. BGE 016880 and Lupa shared a high similarity in their transcriptomes; however, differential gene expression profiles were not consistent between these two genotypes. The wild lentil BGE 016880 had more differentially expressed genes than the cultivated lentil Lupa. Upregulation of genes involved in gibberellin, brassinosteroid, and auxin synthesis and signaling pathways, as well as cell wall modification, in both genotypes explains their similarity in stem elongation response under the shade. Genes involved in jasmonic acid and flavonoid biosynthesis pathways were downregulated in BGE 016880 only, and biological processes involved in defense responses were significantly enriched in the wild lentil BGE 016880 only. Downregulation of WRKY and MYB transcription factors could contribute to the reduced defense response in BGE 016880 but not in Lupa under shade conditions. A better understanding of shade responses of pulse crop species and their wild relatives will play an important role in developing genetic strategies for crop improvement in response to changes in light environments.

Overexpression of SlPRE5, an atypical bHLH transcription factor, affects plant morphology and chlorophyll accumulation in tomato

The basic helix-loop-helix (bHLH) transcription factors play vital regulatory roles in a series of metabolic, physiological, and developmental processes of plants. Here, SlPRE5, an atypical bHLH gene, was isolated from tomato. SlPRE5 was noticeably expressed in young leaves, sepals, and flowers. SlPRE5-overexpressing plants exhibited rolling leaves with reduced chlorophyll content, increased stem internode length, leaf angle, and compound leaf length. The water loss rate of mature leaves and the content of starch were significantly reduced, while the content of gibberellin was significantly increased in transgenic plants. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) showed that SlPRE5 could interact with SlAIF1, SlAIF2, and SlPAR1. qRT-PCR and RNA-seq results revealed that the expression levels of genes related to chloroplast development, chlorophyll metabolism, gibberellin metabolism and signal transduction, starch, photosynthesis, and cell expansion were significantly altered in SlPRE5-overexpression plants. Collectively, our results suggest that SlPRE5 is a crucial transcription factor involved in plant morphology and chlorophyll accumulation in tomato leaves.

Comparative proteomics analysis of Arabidopsis thaliana response to light-emitting diode of narrow wavelength 450 nm, 595 nm, and 650 nm

Incident light is a central modulator of plant growth and development. However, there are still open questions surrounding wavelength-specific plant proteomic responses. Here we applied tandem mass tag based quantitative proteomics technology to acquire an in-depth view of proteome changes in Arabidopsis thaliana response to narrow wavelength blue (B; 450 nm), amber (A; 595 nm), or red (R; 650 nm) light treatments. A total of 16,707 proteins were identified with 9120 proteins quantified across all three light treatments in three biological replicates. This enabled examination of changes in the abundance for proteins with low abundance and important regulatory roles including transcription factors and hormone signaling. Importantly, 18% (1631 proteins) of the A. thaliana proteome is differentially abundant in response to narrow wavelength lights, and changes in proteome correlate well with different morphologies exhibited by plants. To showcase the usefulness of this resource, data were placed in the context of more than thirty published datasets, providing orthogonal validation and further insights into light-specific biological pathways, including Systemic Acquired Resistance and Shade Avoidance Syndrome. This high-resolution resource for A. thaliana provides baseline data and a tool for defining molecular mechanisms that control fundamental aspects of plant response to changing light conditions, with implications in plant development and adaptation. SIGNIFICANCE: Understanding of molecular mechanisms involved in wavelength-specific response of plant is question of widespread interest both to basic researchers and to those interested in applying such knowledge to the engineering of novel proteins, as well as targeted lighting systems. Here we sought to generate a high-resolution labeling proteomic profile of plant leaves, based on exposure to specific narrow-wavelength lights. Although changes in plant physiology in response to light spectral composition is well documented, there is limited knowledge on the roles of specific light wavelengths and their impact. Most previous studies have utilized relatively broad wavebands in their experiments. These multi-wavelengths lights function in a complex signaling network, which provide major challenges in inference of wavelength-specific molecular processes that underly the plant response. Besides, most studies have compared the effect of blue and red wavelengths comparing with FL, as control. As FL light consists the mixed spectra composition of both red and blue as well as numerous other wavelengths, comparing undeniably results in inconsistent and overlapping responses that will hamper effects to elucidate the plant response to specific wavelengths [1, 2]. Monitoring plant proteome response to specific wavelengths and further compare the changes to one another, rather than comparing plants proteome to FL, is thus necessary to gain the clear insights to specific underlying biological pathways and their effect consequences in plant response. Here, we employed narrow wavelength LED lights in our design to eliminate the potential overlap in molecular responses by ensuring non-overlapping wavelengths in the light treatments. We further applied TMT-labeling technology to gain a high-resolution view on the associates of proteome changes. Our proteomics data provides an in-depth coverage suitable for system-wide analyses, providing deep insights on plant physiological processes particularly because of the tremendous increase in the amount of identified proteins which outreach the other biological data.

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.

Hysteresis in PHYTOCHROME-INTERACTING FACTOR 4 and EARLY-FLOWERING 3 dynamics dominates warm daytime memory in Arabidopsis

Despite the identification of temperature sensors and downstream components involved in promoting stem growth by warm temperatures, when and how previous temperatures affect current plant growth remain unclear. Here we show that hypocotyl growth in Arabidopsis thaliana during the night responds not only to the current temperature but also to preceding daytime temperatures, revealing a short-term memory of previous conditions. Daytime temperature affected the levels of PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) and LONG HYPOCOTYL 5 (HY5) in the nucleus during the next night. These factors jointly accounted for the observed growth kinetics, whereas nighttime memory of prior daytime temperature was impaired in pif4 and hy5 mutants. PIF4 promoter activity largely accounted for the temperature-dependent changes in PIF4 protein levels. Notably, the decrease in PIF4 promoter activity triggered by cooling required a stronger temperature shift than the increase caused by warming, representing a typical hysteretic effect; this hysteretic pattern required EARLY-FLOWERING 3 (ELF3). Warm temperatures promoted the formation of nuclear condensates of ELF3 in hypocotyl cells during the afternoon but not in the morning. These nuclear speckles showed poor sensitivity to subsequent cooling. We conclude that ELF3 achieves hysteresis and drives the PIF4 promoter into the same behavior, enabling a short-term memory of daytime temperature conditions.

Phylogeny and evolution of plant Phytochrome Interacting Factors (PIFs) gene family and functional analyses of PIFs in Brachypodium distachyon

Plant PIFs have been characterized, WGDs contributed to the expansion of class II PIFs; BdPIFs localized in the nucleus; BdPIF4/5C most likely response to high temperature and light stress. Phytochrome interacting factors (PIFs) belong to a small subset of basic helix-loop-helix (bHLH) transcription factors (TFs). As cellular signaling hubs, PIFs integrate multiple external and internal signals to orchestrate the regulation of the transcriptional network, thereby actuating the pleiotropic aspects of downstream morphogenesis. Nevertheless, the origin, phylogeny and function of plant PIFs are not well understood. To elucidate their evolution history and biological function, the comprehensive genomic analysis of the PIF genes was conducted using 40 land plant genomes plus additionally four alga lineages and also performed their gene organizations, sequence features and expression patterns in different subfamilies. In this study, phylogenetic analysis displayed that 246 PIF gene members retrieved from all embryophytes could be divided into three main clades, which were further felled into five distinct classes (Class I-V). The duplications of Class II PIFs were associated specially with whole genome duplication (WGD) events during the plant evolution process. Sequence analysis showed that PIF proteins had a conserved APB motif, and its crucial amino acid residues were relatively high proportion in the average abundance. As expected, subcellular localization analysis revealed that all BdPIF proteins were localized to the nucleus. Especially, BdPIF4/5C showed the highest expression level at high temperature, and the most significant hypocotyl elongation phenotype of overexpression of BdPIFs in Arabidopsis, which was consistent with the function and phenotype of AtPIF4. In brief, our findings provide a novel perspective on the origin and evolutionary history of plant PIFs, and lays a foundation for further investigation on its functions in plant growth and development.

Epigenetic regulation of thermomorphogenesis and heat stress tolerance

Many environmental conditions fluctuate and organisms need to respond effectively. This is especially true for temperature cues that can change in minutes to seasons and often follow a diurnal rhythm. Plants cannot migrate and most cannot regulate their temperature. Therefore, a broad array of responses have evolved to deal with temperature cues from freezing to heat stress. A particular response to mildly elevated temperatures is called thermomorphogenesis, a suite of morphological adaptations that includes thermonasty, formation of thin leaves and elongation growth of petioles and hypocotyl. Thermomorphogenesis allows for optimal performance in suboptimal temperature conditions by enhancing the cooling capacity. When temperatures rise further, heat stress tolerance mechanisms can be induced that enable the plant to survive the stressful temperature, which typically comprises cellular protection mechanisms and memory thereof. Induction of thermomorphogenesis, heat stress tolerance and stress memory depend on gene expression regulation, governed by diverse epigenetic processes. In this Tansley review we update on the current knowledge of epigenetic regulation of heat stress tolerance and elevated temperature signalling and response, with a focus on thermomorphogenesis regulation and heat stress memory. In particular we highlight the emerging role of H3K4 methylation marks in diverse temperature signalling pathways.

Unraveling the Dynamic Integration of Auxin, Brassinosteroid and Gibberellin in Early Shade-Induced Hypocotyl Elongation

For shade-intolerant plants, a reduction in the red/far-red (R:FR) light ratio signals the close proximity of competitors and triggers shade-avoidance syndrome (SAS). Auxin, brassinosteroid, gibberellin and some transcriptional regulators have been reported to regulate shade-induced hypocotyl elongation. However, little is understood regarding the coordination of these multiple regulatory pathways. Here, combining time-lapse growth rates and transcriptomic data, we demonstrate that auxin and brassinosteroid affect two phases of shade-induced rapid growth, whereas gibberellin mainly contributes to the second rapid growth phase. PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) acts earlier than other PIFs. PIF4 and PIF5 modulate the second rapid growth phase. LONG HYPOCOTYL IN FAR-RED 1 (HFR1) and PIF3-LIKE 1 (PIL1) modulate two rapid growth phases. Our results reveal that hormonal and transcriptional regulatory programs act together to coordinate dynamic hypocotyl changes in an immediate response to a shade signal and provide a novel understanding of growth kinetics in a changing environment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-022-00044-3.

MicroProteins: Dynamic and accurate regulation of protein activity

Proteins usually assemble oligomers or high-order complexes to increase their efficiency and specificity in biological processes. The dynamic equilibrium of complex formation and disruption imposes reversible regulation of protein function. MicroProteins are small, single-domain proteins that directly bind target protein complexes and disrupt their assembly. Growing evidence shows that microProteins are efficient regulators of protein activity at the post-translational level. In the last few decades, thousands of plant microProteins have been predicted by computational approaches, but only a few have been experimentally validated. Recent studies highlighted the mechanistic working modes of newly-identified microProteins in Arabidopsis and other plant species. Here, we review characterized microProteins, including their biological roles, regulatory targets, and modes of action. In particular, we focus on microProtein-directed allosteric modulation of key components in light signaling pathways, and we summarize the biogenesis and evolutionary trajectory of known microProteins in plants. Understanding the regulatory mechanisms of microProteins is an important step towards potential utilization of microProteins as versatile biotechnological tools in crop bioengineering.

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

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

PIF7 controls leaf cell proliferation through an AN3 substitution repression mechanism

Phytochrome photoreceptors can markedly alter leaf blade growth in response to far-red (FR) rich neighbor shade, yet we have a limited understanding of how this is accomplished. This study identifies ANGUSTIFOLIA3 (AN3) as a central component in phytochrome promotion of leaf cell proliferation and PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) as a potent repressor. AN3 and PIF7 impose opposing regulation on a shared suite of genes through common cis-acting promoter elements. In response to FR light, activated PIF7 blocks AN3 action by evicting and substituting for AN3 at target promoters. This molecular switch module provides a mechanism through which changes in external light quality can dynamically manipulate gene expression, cell division, and leaf size.

Plants are agile, plastic organisms able to adapt to everchanging circumstances. Responding to far-red (FR) wavelengths from nearby vegetation, shade-intolerant species elicit the adaptive shade-avoidance syndrome (SAS), characterized by elongated petioles, leaf hyponasty, and smaller leaves. We utilized end-of-day FR (EODFR) treatments to interrogate molecular processes that underlie the SAS leaf response. Genetic analysis established that PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) is required for EODFR-mediated constraint of leaf blade cell division, while EODFR messenger RNA sequencing data identified ANGUSTIFOLIA3 (AN3) as a potential PIF7 target. We show that PIF7 can suppress AN3 transcription by directly interacting with and sequestering AN3. We also establish that PIF7 and AN3 impose antagonistic control of gene expression via common cis-acting promoter motifs in several cell-cycle regulator genes. EODFR triggers the molecular substitution of AN3 to PIF7 at G-box/PBE-box promoter regions and a switch from promotion to repression of gene expression.

Mutual upregulation of HY5 and TZP in mediating phytochrome A signaling

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

Understanding the Shade Tolerance Responses Through Hints From Phytochrome A-Mediated Negative Feedback Regulation in Shade Avoiding Plants

Based on how plants respond to shade, we typically classify them into two groups: shade avoiding and shade tolerance plants. Under vegetative shade, the shade avoiding species induce a series of shade avoidance responses (SARs) to outgrow their competitors, while the shade tolerance species induce shade tolerance responses (STRs) to increase their survival rates under dense canopy. The molecular mechanism underlying the SARs has been extensively studied using the shade avoiding model plant Arabidopsis thaliana, while little is known about STRs. In Aarabidopsis, there is a PHYA-mediated negative feedback regulation that suppresses exaggerated SARs. Recent studies revealed that in shade tolerance Cardamine hirsuta plants, a hyperactive PHYA was responsible for suppressing shade-induced elongation growth. We propose that similar signaling components may be used by shade avoiding and shade tolerance plants, and different phenotypic outputs may result from differential regulation or altered dynamic properties of these signaling components. In this review, we summarized the role of PHYA and its downstream components in shade responses, which may provide insights into understanding how both types of plants respond to shade.