Chemical genetics reveals cross-regulation of plant developmental signaling by the immune peptide-receptor pathway

Cells sense and integrate multiple signals to coordinate a response. A receptor-kinase signaling pathway for plant stomatal development shares components with the immunity pathway. The mechanism ensuring their signal specificities remains unclear. Using chemical genetics, here, we report the identification of a small molecule, kC9, that triggers excessive stomatal differentiation by inhibiting the canonical ERECTA pathway. kC9 binds to and inhibits the downstream mitogen-activated protein kinase MPK6, perturbing its substrate interaction. Notably, activation of immune signaling by a bacterial flagellin peptide nullified kC9's effects on stomatal development. This cross-regulation depends on the immune receptor FLS2 (FLAGELLIN SENSING 2) and occurs even in the absence of kC9 if the ERECTA family receptor population becomes suboptimal. Proliferating stomatal lineage cells are vulnerable to this immune signal penetration. Our findings suggest that the signal specificity between development and immunity can be ensured by mitogen-activated protein kinase homeostasis, reflecting the availability of upstream receptors, thereby providing an unanticipated view on signal specificity.

Small molecules and heat treatments reverse vernalization via epigenetic modification in Arabidopsis

Monocarpic plants flower only once and then produce seeds. Many monocarpic plants require a cold treatment known as vernalization before they flower. This requirement delays flowering until the plant senses warm temperatures in the spring. Exposure to high temperatures following vernalization causes devernalization, which cancels the vernalized state, inhibiting flowering and promoting vegetative growth. In this study, we screened over 16,000 chemical compounds and identified five small molecules (devernalizers; DVRs) that induce devernalization in Arabidopsis thaliana at room temperature without requiring a high-temperature treatment. Treatment with DVRs reactivated the expression of FLOWERING LOCUS C (FLC), a master repressor of flowering, by reducing the deposition of repressive histone modifications, thereby delaying flowering time. Three of the DVRs identified shared two structures: a hydantoin-like region and a spiro-like carbon. Treatment with DVR06, which has a simple chemical structure containing these domains, delayed flowering time and reduced the deposition of repressive histone modifications at FLC. RNA-seq and ChIP-seq analyses revealed both shared and specific transcriptomic and epigenetic effects between DVR06- and heat-induced devernalization. Overall, our extensive chemical screening indicated that hydantoin and spiro are key chemical signatures that reduce repressive histone modifications and promote devernalization in plants.

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.

Fungal toxin fusicoccin enhances plant growth by upregulating 14-3-3 interaction with plasma membrane H+-ATPase

Fusicoccin-A (FC-A) is a diterpene glucoside produced by a pathogenic fungus. Since its discovery, FC-A has been widely recognized as a phytotoxin that induces stomatal opening and leaf wilting, eventually leading to plant death. In this study, we present the first evidence that FC-A enhances plant growth by stabilizing the protein-protein interaction between plasma membrane (PM) H+-ATPase and 14-3-3 in guard cells. Long-term treatment of Arabidopsis plants with FC-A resulted in ~ 30% growth enhancement. Structurally similar fusicoccin-J (FC-J) showed a similar degree of growth-promotion activity as FC-A, whereas the more hydrophilic fusicoccin-H (FC-H) exhibited no effect on plant growth, indicating that the enhancement of plant growth observed with FC-A and FC-J involves upregulation of the protein-protein interaction between PM H+-ATPase and 14-3-3 in guard cells, which promotes stomatal opening and photosynthesis.

Small chemical molecules regulating the phytohormone signalling alter the plant's physiological processes to improve stress adaptation, growth and productivity

Small chemical molecules are attractive agents for improving the plant processes associated with plant growth and stress tolerance. Recent advances in chemical biology and structure-assisted drug discovery approaches have opened up new avenues in plant biology to discover new drug-like molecules to improve plant processes for sustained food production. Several compounds targeting phytohormone biosynthesis or signalling cascades were designed to alter plant physiological mechanisms. Altering Abscisic acid synthesis and its signalling process can improve drought tolerance, and the processes targeted are reversible. Molecules targeting cytokinin, Auxin, and gibberellic acid regulate plant physiological processes and can potentially improve plant growth, biomass and productivity. The potential of molecules may be exploited as agrochemicals to enhance agricultural productivity. The discovery of small molecules provides new avenues to improve crop production in changing climatic conditions and the nutritional quality of foods. We present the rational combinations of small molecules with inhibitory and co-stimulatory effects and discuss future opportunities in this field.

Chemical genetics reveals cross-activation of plant developmental signaling by the immune peptide-receptor pathway

Cells sense and integrate multiple signals to coordinate development and defence. A receptor-kinase signaling pathway for plant stomatal development shares components with the immunity pathway. The mechanism ensuring their signal specificities remains unclear. Using chemical genetics, here we report the identification of a small molecule, kC9, that triggers excessive stomatal differentiation by inhibiting the canonical ERECTA receptor-kinase pathway. kC9 binds to and inhibits the downstream MAP kinase MPK6, perturbing its substrate interaction. Strikingly, activation of immune signaling by a bacterial flagellin peptide nullified kC9's effects on stomatal development. This cross-activation of stomatal development by immune signaling depends on the immune receptor FLS2 and occurs even in the absence of kC9 if the ERECTA-family receptor population becomes suboptimal. Furthermore, proliferating stomatal-lineage cells are vulnerable to the immune signal penetration. Our findings suggest that the signal specificity between development and immunity can be ensured by MAP Kinase homeostasis reflecting the availability of upstream receptors, thereby providing a novel view on signal specificity.

A Small Compound, HYGIC, Promotes Hypocotyl Growth Through Ectopic Ethylene Response

Plant seedlings adjust the growth of the hypocotyl in response to surrounding environmental changes. Genetic studies have revealed key players and pathways in hypocotyl growth, such as phytohormones and light signaling. However, because of genetic redundancy in the genome, it is expected that not-yet-revealed mechanisms can be elucidated through approaches different from genetic ones. Here, we identified a small compound, HYGIC (HG), that simultaneously induces hypocotyl elongation and thickening, accompanied by increased nuclear size and enlargement of cortex cells. HG-induced hypocotyl growth required the ethylene signaling pathway activated by endogenous ethylene, involving CONSTITUTIVE PHOTOMORPHOGENIC 1, ETHYLENE INSENSITIVE 2 (EIN2) and redundant transcription factors for ethylene responses, ETHYLENE INSENSITIVE 3 (EIN3) and EIN3 LIKE 1. By using EBS:GUS, a transcriptional reporter of ethylene responses based on an EIN3-binding-cis-element, we found that HG treatment ectopically activates ethylene responses at the epidermis and cortex of the hypocotyl. RNA-seq and subsequent gene ontology analysis revealed that a significant number of HG-induced genes are related to responses to hypoxia. Indeed, submergence, a representative environment where the hypoxia response is induced in nature, promoted ethylene-signaling-dependent hypocotyl elongation and thickening accompanied by ethylene responses at the epidermis and cortex, which resembled the HG treatment. Collectively, the identification and analysis of HG revealed that ectopic responsiveness to ethylene promotes hypocotyl growth, and this mechanism is activated under submergence.

Plants and Small Molecules: An Up-and-Coming Synergy

The emergence of Arabidopsis thaliana as a model system has led to a rapid and wide improvement in molecular genetics techniques for studying gene function and regulation. However, there are still several drawbacks that cannot be easily solved with molecular genetic approaches, such as the study of unfriendly species, which are of increasing agronomic interest but are not easily transformed, thus are not prone to many molecular techniques. Chemical genetics represents a methodology able to fill this gap. Chemical genetics lies between chemistry and biology and relies on small molecules to phenocopy genetic mutations addressing specific targets. Advances in recent decades have greatly improved both target specificity and activity, expanding the application of this approach to any biological process. As for classical genetics, chemical genetics also proceeds with a forward or reverse approach depending on the nature of the study. In this review, we addressed this topic in the study of plant photomorphogenesis, stress responses and epigenetic processes. We have dealt with some cases of repurposing compounds whose activity has been previously proven in human cells and, conversely, studies where plants have been a tool for the characterization of small molecules. In addition, we delved into the chemical synthesis and improvement of some of the compounds described.

Identification of a pluripotency-inducing small compound, PLU, that induces callus formation via Heat Shock Protein 90-mediated activation of auxin signaling

Plants retain the ability to generate a pluripotent tissue called callus by dedifferentiating somatic cells. A pluripotent callus can also be artificially induced by culturing explants with hormone mixtures of auxin and cytokinin, and an entire body can then be regenerated from the callus. Here we identified a pluripotency-inducing small compound, PLU, that induces the formation of callus with tissue regeneration potency without the external application of either auxin or cytokinin. The PLU-induced callus expressed several marker genes related to pluripotency acquisition via lateral root initiation processes. PLU-induced callus formation required activation of the auxin signaling pathway though the amount of active auxin was reduced by PLU treatment. RNA-seq analysis and subsequent experiments revealed that Heat Shock Protein 90 (HSP90) mediates a significant part of the PLU-initiated early events. We also showed that HSP90-dependent induction of TRANSPORT INHIBITOR RESPONSE 1, an auxin receptor gene, is required for the callus formation by PLU. Collectively, this study provides a new tool for manipulating and investigating the induction of plant pluripotency from a different angle from the conventional method with the external application of hormone mixtures.

Discovery of 2,6-Dihalopurines as Stomata Opening Inhibitors: Implication of an LRX-Mediated H+-ATPase Phosphorylation Pathway

Stomata are pores in the leaf epidermis of plants and their opening and closing regulate gas exchange and water transpiration. Stomatal movements play key roles in both plant growth and stress responses. In recent years, small molecules regulating stomatal movements have been used as a powerful tool in mechanistic studies, as well as key players for agricultural applications. Therefore, the development of new molecules regulating stomatal movement and the elucidation of their mechanisms have attracted much attention. We herein describe the discovery of 2,6-dihalopurines, AUs, as a new stomatal opening inhibitor, and their mechanistic study. Based on biological assays, AUs may involve in the pathway related with plasma membrane H⁺-ATPase phosphorylation. In addition, we identified leucine-rich repeat extensin proteins (LRXs), LRX3, LRX4 and LRX5 as well as RALF, as target protein candidates of AUs by affinity based pull down assay and molecular dynamics simulation. The mechanism of stomatal movement related with the LRXs-RALF is an unexplored pathway, and therefore further studies may lead to the discovery of new signaling pathways and regulatory factors in the stomatal movement.

Chemical biology to dissect molecular mechanisms underlying plant circadian clocks

Circadian clocks regulate the diel rhythmic physiological activities of plants, enabling them to anticipate and adapt to day-night and seasonal changes. Genetic and biochemical approaches have suggested that transcription-translation feedback loops (TTFL) are crucial for Arabidopsis clock function. Recently, the study of chemical chronobiology has emerged as a discipline within the circadian clock field, with important and complementary discoveries from both plant and animal research. In this review, we introduce recent advances in chemical biology using small molecules to perturb plant circadian clock function through TTFL components. Studies using small molecule clock modulators have been instrumental for revealing the role of post-translational modification in the clock, or the metabolite-dependent clock input pathway, as well as for controlling clock-dependent flowering time.

The Cell Differentiation of Idioblast Myrosin Cells: Similarities With Vascular and Guard Cells

Idioblasts are defined by abnormal shapes, sizes, and contents that are different from neighboring cells. Myrosin cells are Brassicales-specific idioblasts and accumulate a large amount of thioglucoside glucohydrolases (TGGs, also known as myrosinases) in their vacuoles. Myrosinases convert their substrates, glucosinolates, into toxic compounds when herbivories and pests attack plants. In this review, we highlight the similarities and differences between myrosin cells and vascular cells/guard cells (GCs) because myrosin cells are distributed along vascular cells, especially the phloem parenchyma, and myrosin cells share the master transcription factor FAMA with GCs for their cell differentiation. In addition, we analyzed the overlap of cell type-specific genes between myrosin cells and GCs by using published single-cell transcriptomics (scRNA-seq) data, suggesting significant similarities in the gene expression patterns of these two specialized cells.

Evaluation of the Anti-transpirant Activity of ABA Receptor Agonists in Monocot and Eudicot Plants

ABA receptor agonists capable of improving plant performance under drought conditions have been described during the last years. However, monocot and eudicot plant species respond differently to various agonists. Here, we provide a detailed methodology to evaluate the anti-transpirant activity of ABA receptor agonists in both monocot and eudicot plant species using infrared imaging and image data analysis. Plant growth conditions, chemical application, and infrared image analysis are explained in detail to evaluate the anti-transpirant activity of ABA receptor agonists in the eudicot model Arabidopsis thaliana and in the C4-monocot model Setaria viridis.

An Affordable Image-Analysis Platform to Accelerate Stomatal Phenotyping During Microscopic Observation

Recent technical advances in the computer-vision domain have facilitated the development of various methods for achieving image-based quantification of stomata-related traits. However, the installation cost of such a system and the difficulties of operating it on-site have been hurdles for experimental biologists. Here, we present a platform that allows real-time stomata detection during microscopic observation. The proposed system consists of a deep neural network model-based stomata detector and an upright microscope connected to a USB camera and a graphics processing unit (GPU)-supported single-board computer. All the hardware components are commercially available at common electronic commerce stores at a reasonable price. Moreover, the machine-learning model is prepared based on freely available cloud services. This approach allows users to set up a phenotyping platform at low cost. As a proof of concept, we trained our model to detect dumbbell-shaped stomata from wheat leaf imprints. Using this platform, we collected a comprehensive range of stomatal phenotypes from wheat leaves. We confirmed notable differences in stomatal density (SD) between adaxial and abaxial surfaces and in stomatal size (SS) between wheat-related species of different ploidy. Utilizing such a platform is expected to accelerate research that involves all aspects of stomata phenotyping.

Chemical control of stomatal function and development

Stomata control trade-offs for plants: carbon dioxide uptake for photosynthetic growth and water loss via transpiration. While agrochemical control of transpiration is an old concept, recent discoveries of the core signaling components controlling stomatal function and numbers opened the door to develop chemical compounds with high potency and specificity. ABA agonists with potent anti-transpiration activity have been developed via in silico virtual screens and structure guided design and synthesis. Library-based chemical screens identified new compounds that influence stomatal movement in ABA-independent manners as well as those affecting stomatal numbers and division polarity. Subsequent hit compound derivatization can be employed to separate adverse side effects. Ultimately, such chemicals might help in optimizing plant productivity and water use in agriculture and florist industries.

Identification of a Devernalization Inducer by Chemical Screening Approaches in Arabidopsis thaliana

Vernalization is the promotion of flowering after prolonged exposure to cold. In Arabidopsis thaliana, vernalization induces epigenetic silencing of the floral repressor gene FLOWERING LOCUS C (FLC). The repressive epigenetic mark trimethylation of lysine 27 on histone H3 proteins (H3K27me3) is a critical contributor to the epigenetic silencing of FLC. Interestingly, the deposited H3K27me3 in the FLC locus can be erased by short-term high-temperature treatment. This is referred to as devernalization. In this study, we identified a novel chemical compound, 4-Isoxazolecarboxylic acid, 3,5-dimethyl-2-(4-fluorophenyl)-4-isoxazole carboxylic acid 1-methyl-2-oxoethyl ester named as DEVERNALIZER01 (DVR01), which induces devernalization in Arabidopsis seedlings, by an FLC-luciferase reporter-based high-throughput screening assay. DVR01 decreased the amount of H3K27me3 in the FLC locus in vernalized plants, resulting in the upregulation of FLC in the whole plant, including the vasculature and meristem, where FLC represses floral induction genes. We also showed that a 2-week treatment with DVR01 reverted plants with a vernalized status back to a fully non-vernalized status. Collectively, this study provides a novel structure of DVR01, which modulates devernalization via demethylation of H3K27me3 in the FLC locus.

Biosystems Design to Accelerate C3-to-CAM Progression

Global demand for food and bioenergy production has increased rapidly, while the area of arable land has been declining for decades due to damage caused by erosion, pollution, sea level rise, urban development, soil salinization, and water scarcity driven by global climate change. In order to overcome this conflict, there is an urgent need to adapt conventional agriculture to water-limited and hotter conditions with plant crop systems that display higher water-use efficiency (WUE). Crassulacean acid metabolism (CAM) species have substantially higher WUE than species performing C3 or C4 photosynthesis. CAM plants are derived from C3 photosynthesis ancestors. However, it is extremely unlikely that the C3 or C4 crop plants would evolve rapidly into CAM photosynthesis without human intervention. Currently, there is growing interest in improving WUE through transferring CAM into C3 crops. However, engineering a major metabolic plant pathway, like CAM, is challenging and requires a comprehensive deep understanding of the enzymatic reactions and regulatory networks in both C3 and CAM photosynthesis, as well as overcoming physiometabolic limitations such as diurnal stomatal regulation. Recent advances in CAM evolutionary genomics research, genome editing, and synthetic biology have increased the likelihood of successful acceleration of C3-to-CAM progression. Here, we first summarize the systems biology-level understanding of the molecular processes in the CAM pathway. Then, we review the principles of CAM engineering in an evolutionary context. Lastly, we discuss the technical approaches to accelerate the C3-to-CAM transition in plants using synthetic biology toolboxes.

3,4-Dibromo-7-Azaindole Modulates Arabidopsis Circadian Clock by Inhibiting Casein Kinase 1 Activity

The circadian clock is a timekeeping system for regulation of numerous biological daily rhythms. One characteristic of the circadian clock is that period length remains relatively constant in spite of environmental fluctuations, such as temperature change. Here, using the curated collection of in-house small molecule chemical library (ITbM chemical library), we show that small molecule 3,4-dibromo-7-azaindole (B-AZ) lengthened the circadian period of Arabidopsis thaliana (Arabidopsis). B-AZ has not previously been reported to have any biological and biochemical activities. Target identification can elucidate the mode of action of small molecules, but we were unable to make a molecular probe of B-AZ for target identification. Instead, we performed other analysis, gene expression profiling that potentially reveals mode of action of molecules. Short-term treatment of B-AZ decreased the expression of four dawn- and morning-phased clock-associated genes, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7. Consistently, amounts of PRR5 and TIMING OF CAB EXPRESSION 1 (TOC1) proteins, transcriptional repressors of CCA1, LHY, PRR9 and PRR7 were increased upon B-AZ treatment. B-AZ inhibited Casein Kinase 1 family (CK1) that phosphorylates PRR5 and TOC1 for targeted degradation. A docking study and molecular dynamics simulation suggested that B-AZ interacts with the ATP-binding pocket of human CK1 delta, whose amino acid sequences are highly similar to those of Arabidopsis CK1. B-AZ-induced period-lengthening effect was attenuated in prr5 toc1 mutants. Collectively, this study provides a novel and simple structure CK1 inhibitor that modulates circadian clock via accumulation of PRR5 and TOC1.

Stomatal Development and Perspectives toward Agricultural Improvement

Stomata are small pores on the surface of land plants that facilitate gas exchange-acquiring CO₂ from surrounding atmosphere and releasing water vapor. In adverse conditions, such as drought, stomata close to minimize water loss. The activities of stomata are vital for plant growth and survival. In the last two decades, key players for stomatal development have been discovered thanks to the model plant Arabidopsis thaliana Our knowledge about the formation of stomata and their response to environmental changes are accumulating. In this review, we summarize the genetic and molecular mechanisms of stomatal development, with specific emphasis on recent findings and potential applications toward enhancing the sustainability of agriculture.

Identification and Characterization of Compounds that Affect Stomatal Movements

Regulation of stomatal aperture is essential for plant growth and survival in response to environmental stimuli. Opening of stomata induces uptake of CO2 for photosynthesis and transpiration, which enhances uptake of nutrients from roots. Light is the most important stimulus for stomatal opening. Under drought stress, the plant hormone ABA induces stomatal closure to prevent water loss. However, the molecular mechanisms of stomatal movements are not fully understood. In this study, we screened chemical libraries to identify compounds that affect stomatal movements in Commelina benghalensis and characterize the underlying molecular mechanisms. We identified nine stomatal closing compounds (SCL1-SCL9) that suppress light-induced stomatal opening by >50%, and two compounds (temsirolimus and CP-100356) that induce stomatal opening in the dark. Further investigations revealed that SCL1 and SCL2 had no effect on autophosphorylation of phototropin or the activity of the inward-rectifying plasma membrane (PM) K+ channel, KAT1, but suppressed blue light-induced phosphorylation of the penultimate residue, threonine, in PM H+-ATPase, which is a key enzyme for stomatal opening. SCL1 and SCL2 had no effect on ABA-dependent responses, including seed germination and expression of ABA-induced genes. These results suggest that SCL1 and SCL2 suppress light-induced stomatal opening at least in part by inhibiting blue light-induced activation of PM H+-ATPase, but not by the ABA signaling pathway. Interestingly, spraying leaves onto dicot and monocot plants with SCL1 suppressed wilting of leaves, indicating that inhibition of stomatal opening by these compounds confers tolerance to drought stress in plants.

Specialized Vacuoles of Myrosin Cells: Chemical Defense Strategy in Brassicales Plants

Plant vacuoles display many versatile functions. Vacuoles in vegetative tissues are generally involved in protein degradation, and are called lytic vacuoles. However, vegetative vacuoles in specialized cells can accumulate large concentrations of proteins, such as those in idioblast myrosin cells along veins in the order Brassicales, which store large amounts of myrosinases (thioglucoside glucohydrolase and thioglucoside glucohydrolase). Myrosinases cleave the bond between sulfur and glucose in sulfur-rich compounds (glucosinolates) to produce toxic compounds (isothiocyanates) when plants are damaged by pests. This defense strategy is called the myrosinase-glucosinolate system. Recent studies identified atypical myrosinases, PENETRATION 2 (PEN2) and PYK10, along with key components for development of myrosin cells. In this review, we discuss three topics in the myrosinase-glucosinolate system. First, we summarize the complexity and importance of the myrosinase-glucosinolate system, including classical myrosinases, atypical myrosinases and the system that counteracts the myrosinase-glucosinolate system. Secondly, we describe molecular machineries underlying myrosin cell development, including specific reporters, cell lineage, cell differentiation and cell fate determination. The master regulators for myrosin cell differentiation, FAMA and SCREAM, are key transcription factors involved in guard cell differentiation. This indicates that myrosin cells and guard cells share similar transcriptional networks. Finally, we hypothesize that the myrosinase-glucosinolate system may have originated in stomata of ancestral Brassicales plants and, after that, plants co-opted this defense strategy into idioblasts near veins at inner tissue layers.