Organ-specific COP1 control of BES1 stability adjusts plant growth patterns under shade or warmth

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.

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.

A synchronized symphony: Intersecting roles of ubiquitin proteasome system and autophagy in cellular degradation

Eukaryotic cells have evolved dynamic quality control pathways and recycling mechanisms for cellular homeostasis. We discuss here, the two major systems for quality control, the ubiquitin-proteasome system (UPS) and autophagy that regulate cellular protein and organelle turnover and ensure efficient nutrient management, cellular integrity and long-term wellbeing of the plant. Both the pathways rely on ubiquitination signal to identify the targets for proteasomal and autophagic degradation, yet they use distinct degradation machinery to process these cargoes. Nonetheless, both UPS and autophagy operate together as an interrelated quality control mechanism where they communicate with each other at multiple nodes to coordinate and/or compensate the recycling mechanism particularly under development and environmental cues. Here, we provide an update on the cellular machinery of autophagy and UPS, unravel the nodes of their crosstalk and particularly highlight the factors responsible for their differential deployment towards protein, macromolecular complexes and organelles.

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.

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.

Decoding plant adaptation: deubiquitinating enzymes UBP12 and UBP13 in hormone signaling, light response, and developmental processes

Ubiquitination, a vital post-translational modification in plants, plays a significant role in regulating protein activity, localization, and stability. This process occurs through a complex enzyme cascade that involves E1, E2, and E3 enzymes, leading to the covalent attachment of ubiquitin molecules to substrate proteins. Conversely, deubiquitinating enzymes (DUBs) work in opposition to this process by removing ubiquitin moieties. Despite extensive research on ubiquitination in plants, our understanding of the function of DUBs is still emerging. UBP12 and UBP13, two plant DUBs, have received much attention recently and are shown to play pivotal roles in hormone signaling, light perception, photoperiod responses, leaf development, senescence, and epigenetic transcriptional regulation. This review summarizes current knowledge of these two enzymes, highlighting the central role of deubiquitination in regulating the abundance and activity of critical regulators such as receptor kinases and transcription factors during phytohormone and developmental signaling.

Temperature regulation of auxin-related gene expression and its implications for plant growth

Twenty-five years ago, a seminal paper demonstrated that warm temperatures increase auxin levels to promote hypocotyl growth in Arabidopsis thaliana. Here we highlight recent advances in auxin-mediated thermomorphogenesis and identify unanswered questions. In the warmth, PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF7 bind the YUCCA8 gene promoter and, in concert with histone modifications, enhance its expression to increase auxin synthesis in the cotyledons. Once transported to the hypocotyl, auxin promotes cell elongation. The meta-analysis of expression of auxin-related genes in seedlings exposed to temperatures ranging from cold to hot shows complex patterns of response. Changes in auxin only partially account for these responses. The expression of many SMALL AUXIN UP RNA (SAUR) genes reaches a maximum in the warmth, decreasing towards both temperature extremes in correlation with the rate of hypocotyl growth. Warm temperatures enhance primary root growth, the response requires auxin, and the hormone levels increase in the root tip but the impacts on cell division and cell expansion are not clear. A deeper understanding of auxin-mediated temperature control of plant architecture is necessary to face the challenge of global warming.

Shade-induced RTFL/DVL peptides negatively regulate the shade response by directly interacting with BSKs in Arabidopsis

For shade-intolerant species, shade light indicates the close proximity of neighboring plants and triggers the shade avoidance syndrome (SAS), which causes exaggerated growth and reduced crop yield. Here, we report that non-secreted ROT FOUR LIKE (RTFL)/DEVIL (DVL) peptides negatively regulate SAS by interacting with BRASSINOSTEROID SIGNALING KINASEs (BSKs) and reducing the protein level of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) in Arabidopsis. The transcription of at least five RTFLs (RTFL13/16/17/18/21) is induced by low R:FR light. The RTFL18 (DVL1) protein is stabilized under low R:FR conditions and localized to the plasma membrane. A phenotype analysis reveals that RTFL18 negatively regulates low R:FR-promoted petiole elongation. BSK3 and BSK6 are identified as partners of RTFL18 through binding assays and structural modeling. The overexpression of RTFL18 or knockdown of BSK3/6 reduces BRASSINOSTEROID signaling and reduces low R:FR-stabilized PIF4 levels. Genetically, the overexpression of BSK3/6 and PIF4 restores the petiole phenotype acquired by RTFL18-overexpressing lines. Collectively, our work characterizes a signaling cascade (the RTFLs-BSK3/6-PIF4 pathway) that prevents the excessive activation of the shade avoidance response in Arabidopsis.

Spatial regulation of plant hormone action

Although many plant cell types are capable of producing hormones, and plant hormones can in most cases act in the same cells in which they are produced, they also act as signaling molecules that coordinate physiological responses between different parts of the plant, indicating that their action is subject to spatial regulation. Numerous publications have reported that all levels of plant hormonal pathways, namely metabolism, transport, and perception/signal transduction, can help determine the spatial ranges of hormone action. For example, polar auxin transport or localized auxin biosynthesis contribute to creating a differential hormone accumulation across tissues that is instrumental for specific growth and developmental responses. On the other hand, tissue specificity of cytokinin actions has been proposed to be regulated by mechanisms operating at the signaling stages. Here, we review and discuss current knowledge about the contribution of the three levels mentioned above in providing spatial specificity to plant hormone action. We also explore how new technological developments, such as plant hormone sensors based on FRET (fluorescence resonance energy transfer) or single-cell RNA-seq, can provide an unprecedented level of resolution in defining the spatial domains of plant hormone action and its dynamics.

Light signaling as cellular integrator of multiple environmental cues in plants

Plants being sessile need to rapidly adapt to the constantly changing environment through modifications in their internal clock, metabolism, and gene expression. They have evolved an intricate system to perceive and transfer the signals from the primary environmental factors namely light, temperature and water to regulate their growth development and survival. Over past few decades rigorous research using molecular genetics approaches, especially in model plant Arabidopsis, has resulted in substantial progress in discovering various photoreceptor systems and light signaling components. In parallel several molecular pathways operating in response to other environmental cues have also been elucidated. Interestingly, the studies have shown that expression profiles of genes involved in photomorphogenesis can undergo modulation in response to other cues from the environment. Recently, the photoreceptor, PHYB, has been shown to function as a thermosensor. Downstream components of light signaling pathway like COP1 and PIF have also emerged as integrating hubs for various kinds of signals. All these findings indicate that light signaling components may act as central integrator of various environmental cues to regulate plant growth and development processes. In this review, we present a perspective on cross talk of signaling mechanisms induced in response to myriad array of signals and their integration with the light signaling components. By putting light signals on the central stage, we propose the possibilities of enhancing plant resilience to the changing environment by fine-tuning the genetic manipulation of its signaling components in the future.

PIF4 enhances the expression of SAUR genes to promote growth in response to nitrate

Nitrate supply is fundamental to support shoot growth and crop performance, but the associated increase in stem height exacerbates the risks of lodging and yield losses. Despite their significance for agriculture, the mechanisms involved in the promotion of stem growth by nitrate remain poorly understood. Here, we show that the elongation of the hypocotyl of Arabidopsis thaliana, used as a model, responds rapidly and persistently to upshifts in nitrate concentration, rather than to the nitrate level itself. The response occurred even in shoots dissected from their roots and required NITRATE TRANSPORTER 1.1 (NRT1.1) in the phosphorylated state (but not NRT1.1 nitrate transport capacity) and NIN-LIKE PROTEIN 7 (NLP7). Nitrate increased PHYTOCHROME INTERACTING FACTOR 4 (PIF4) nuclear abundance by posttranscriptional mechanisms that depended on NRT1.1 and phytochrome B. In response to nitrate, PIF4 enhanced the expression of numerous SMALL AUXIN-UP RNA (SAUR) genes in the hypocotyl. The growth response to nitrate required PIF4, positive and negative regulators of its activity, including AUXIN RESPONSE FACTORs, and SAURs. PIF4 integrates cues from the soil (nitrate) and aerial (shade) environments adjusting plant stature to facilitate access to light.

Brassinosteroid signaling regulator BIM1 integrates brassinolide and jasmonic acid signaling during cold tolerance in apple

Although brassinolide (BR) and jasmonic acid (JA) play essential roles in the regulation of cold stress responses, the molecular basis of their crosstalk remains elusive. Here, we show a key component of BR signaling in apple (Malus × domestica), BR INSENSITIVE1 (BRI1)-EMS-SUPPRESSOR1 (BES1)-INTERACTING MYC-LIKE PROTEIN1 (MdBIM1), increases cold tolerance by directly activating expression of C-REPEAT BINDING FACTOR1 (MdCBF1) and forming a complex with C-REPEAT BINDING FACTOR2 (MdCBF2) to enhance MdCBF2-activated transcription of cold-responsive genes. Two repressors of JA signaling, JAZMONATE ZIM-DOMAIN1 (MdJAZ1) and JAZMONATE ZIM-DOMAIN2 (MdJAZ2), interact with MdBIM1 to integrate BR and JA signaling under cold stress. MdJAZ1 and MdJAZ2 reduce MdBIM1-promoted cold stress tolerance by attenuating transcriptional activation of MdCBF1 expression by MdBIM1 and interfering with the formation of the MdBIM1-MdCBF2 complex. Furthermore, the E3 ubiquitin ligase ARABIDOPSIS TÓXICOS en LEVADURA73 (MdATL73) decreases MdBIM1-promoted cold tolerance by targeting MdBIM1 for ubiquitination and degradation. Our results not only reveal crosstalk between BR and JA signaling mediated by a JAZ-BIM1-CBF module but also provide insights into the posttranslational regulatory mechanism of BR signaling.

Interplay between autophagy and proteasome during protein turnover

Protein homeostasis is epitomized by an equilibrium between protein biosynthesis and degradation: the 'life and death' of proteins. Approximately one-third of newly synthesized proteins are degraded. As such, protein turnover is required to maintain cellular integrity and survival. Autophagy and the ubiquitin-proteasome system (UPS) are the two principal degradation pathways in eukaryotes. Both pathways orchestrate many cellular processes during development and upon environmental stimuli. Ubiquitination of degradation targets is used as a 'death' signal by both processes. Recent findings revealed a direct functional link between both pathways. Here, we summarize key findings in the field of protein homeostasis, with an emphasis on the newly revealed crosstalk between both degradation machineries and how it is decided which pathway facilitates target degradation.

Light Regulation of LoCOP1 and Its Role in Floral Scent Biosynthesis in Lilium 'Siberia'

Light is an important environmental signal that governs plant growth, development, and metabolism. Constitutive photomorphogenic 1 (COP1) is a light signaling component that plays a vital role in plant light responses. We isolated the COP1 gene (LoCOP1) from the petals of Lilium 'Siberia' and investigated its function. The LoCOP1 protein was found to be the most similar to Apostasia shenzhenica COP1. LoCOP1 was found to be an important factor located in the nucleus and played a negative regulatory role in floral scent production and emission using the virus-induced gene silencing (VIGS) approach. The yeast two-hybrid, β-galactosidase, and bimolecular fluorescence complementation (BiFC) assays revealed that LoCOP1 interacts with LoMYB1 and LoMYB3. Furthermore, light modified both the subcellular distribution of LoCOP1 and its interactions with LoMYB1 and MYB3 in onion cells. The findings highlighted an important regulatory mechanism in the light signaling system that governs scent emission in Lilium 'Siberia' by the ubiquitination and degradation of transcription factors via the proteasome pathway.

Thermomorphogenesis: Opportunities and challenges in posttranscriptional regulation

Plants exposed to mildly elevated temperatures display morphological and developmental changes collectively termed thermomorphogenesis. This adaptative process has several undesirable consequences to food production, including yield reduction and increased vulnerability to pathogens. Understanding thermomorphogenesis is, thus, critical for understanding how plants will respond to increasingly warmer temperature conditions, such as those caused by climate change. Recently, we have made major advances in that direction, and it has become apparent that plants resource to a broad range of molecules and molecular mechanisms to perceive and respond to increases in environmental temperature. However, most of our efforts have been focused on regulation of transcription and protein abundance and activity, with an important gap encompassing nearly all processes involving RNA (i.e., posttranscriptional regulation). Here, I summarized our current knowledge of thermomorphogenesis involving transcriptional, posttranscriptional, and posttranslational regulation, focused on opportunities and challenges in understanding posttranscriptional regulation-a fertile field for exciting new discoveries.

Light signaling-mediated growth plasticity in Arabidopsis grown under high-temperature conditions

Growing concern around global warming has led to an increase in research focused on plant responses to increased temperature. In this review, we highlight recent advances in our understanding of plant adaptation to high ambient temperature and heat stress, emphasizing the roles of plant light signaling in these responses. We summarize how high temperatures regulate plant cotyledon expansion and shoot and root elongation and explain how plants use light signaling to combat severe heat stress. Finally, we discuss several future avenues for this research and identify various unresolved questions within this field.