Diverse nitrogen signals activate convergent ROP2-TOR signaling in Arabidopsis

Integrative transcriptomic-physiological analysis deciphers nitrogen-mediated carbon reallocation balancing growth and flavonoid metabolism in Epimedium pubescens

Nitrogen availability critically shapes medicinal plant quality by coordinating the "growth-secondary metabolism" trade-off, yet its regulatory mechanisms remain elusive in the non-model species Epimedium pubescens. Through physiological-transcriptomic integration under five nitrogen levels (0, 3.5, 7.5,15, 22.5 mM NO3 -), we demonstrated that moderate nitrogen (MN: 7.5 mM NO3 -) optimally balanced biomass accumulation (22%-53% higher than low nitrogen [LN: 0 mM NO3 -] and high nitrogen [HN: 22.5 mM NO3 -]) with maximal Icariin-type flavonoid production (19%-34% higher than LN/HN). Extreme nitrogen stresses (LN/HN) impaired photosynthetic efficiency (18%-20% reduction), disrupted carbon-nitrogen homeostasis, and restricted flavonoid biosynthesis by hindering carbon reallocation (soluble sugars reduced by 26%-27%, starch by 30%-43%). Time-series transcriptomics revealed distinct response dynamics: LN triggered active transcriptional reprogramming at mid-stage (36 days after treatment, DAT), whereas HN responses were delayed to late-stage (48 DAT). Weighted gene co-expression network analysis (WGCNA) identified the grey60 module as a hub coordinating carbon-nitrogen metabolism and mRNA processing. A tripartite regulatory network linking nitrogen-responsive genes (e.g., EpF3H, UGT), Icariin-type flavonoid/carbon metabolism (e.g., icariin, soluble sugars), and growth phenotypes (e.g., biomass, photosynthesis) elucidated how nitrogen optimizes the trade-off between medicinal quality and yield in E. pubescens. This study provides molecular targets for precision nitrogen management to enhance both medicinal quality and yield, while establishing an integrative framework combining physiological and transcriptomic analyses to investigate metabolic trade-offs in non-model plants.

Early signalling events induced by glycine application in protoplasts of Mimosa pudica motor cells

Some amino acids have been shown to be signalling molecules in various developmental and stress processes, besides their roles in plant nutrition. Glycine is absorbed by pulvinar motor cells of Mimosa pudica according to an H+-Gly cotransport mechanism and under the control of calcium availability. Noteworthy, glycine triggers early plasma membrane depolarization and H+ migration. The unicellular model of protoplasts isolated from pulvini absorbed glycine with characteristics similar to those determined on multicellular motor tissues, considering metabolism regulation, plasma membrane functionality and calcium control. This model allows to observe that a rapid increase of glycine uptake rate occurs in the first 3 min following 10 mM glycine application. Additionally, we monitored a rapid transient increase (within 5-11 s) of the cytoplasmic free calcium ([Ca2+]c) measured by cytofluorimetric determination using Indo-1-loaded protoplasts. The low [Ca2+]c increase seen in nominally Ca2+-free medium and the inhibition of [Ca2+]c increase after treatment with channel inhibitors (LaCl3, nifedipine) argue for a Ca2+ mobilization from external stores. This observation emphasized the signalling role of glycine at the plasma membrane site.

Target of Rapamycin (TOR): A Master Regulator in Plant Growth, Development, and Stress Responses

The target of rapamycin (TOR) is a central regulator of growth, development, and stress adaptation in plants. This review delves into the molecular intricacies of TOR signaling, highlighting its conservation and specificity across eukaryotic lineages. We explore the molecular architecture of TOR complexes, their regulation by a myriad of upstream signals, and their consequential impacts on plant physiology. The roles of TOR in orchestrating nutrient sensing, hormonal cues, and environmental signals are highlighted, illustrating its pivotal function in modulating plant growth and development. Furthermore, we examine the impact of TOR on plant responses to various biotic and abiotic stresses, underscoring its potential as a target for agricultural improvements. This synthesis of current knowledge on plant TOR signaling sheds light on the complex interplay between growth promotion and stress adaptation, offering a foundation for future research and applications in plant biology.

Pupylation-Based Proximity Labeling Unravels a Comprehensive Protein and Phosphoprotein Interactome of the Arabidopsis TOR Complex

Target of rapamycin (TOR) is a signaling hub that integrates developmental, hormonal, and environmental signals to optimize carbon allocation and plant growth. In plant cells, TOR acts together with the proteins LST8-1 and RAPTOR1 to form a core TOR complex (TORC). While these proteins comprise a functional TORC, they engage with many other proteins to ensure precise signal outputs. Although TORC interactions have attracted significant attention in the recent past, large parts of the interactome are still unknown. In this resource study, PUP-IT is adapted, a fully endogenously expressed protein proximity labeling toolbox, to map TORC protein-protein interactions using the core set of TORC as baits. It is outlined how this interactome is differentially phosphorylated during changes in carbon availability, uncovering putative direct TOR kinase targets. An AlphaFold-Multimer approach is further used to validate many interactors, thus outlining a comprehensive TORC interactome that includes over a hundred new candidate interactors and provides an invaluable resource to the plant cell signaling community.

Dihydroxyacetone phosphate generated in the chloroplast mediates the activation of TOR by CO2 and light

Light and CO2 assimilation activate the target of rapamycin (TOR) kinase in photosynthetic cells, but how these signals are transmitted to TOR is unknown. Using the green alga Chlamydomonas reinhardtii as a model system, we identified dihydroxyacetone phosphate (DHAP) as the key metabolite regulating TOR in response to carbon and light cues. Metabolomic analyses of synchronized cells revealed that DHAP levels change more than any other metabolite between dark- and light-grown cells and that the addition of the DHAP precursor, dihydroxyacetone (DHA), was sufficient to activate TOR in the dark. We also demonstrated that TOR was insensitive to light or inorganic carbon but not to exogenous DHA in a Chlamydomonas mutant defective in the export of DHAP from the chloroplast. Our results provide a metabolic basis for the mode of TOR control by light and inorganic carbon and indicate that cytoplasmic DHAP is an important metabolic regulator of TOR.

Plant Nitrogen Assimilation: A Climate Change Perspective

Of all the essential macronutrients necessary for plant growth and development, nitrogen is required in the greatest amounts. Nitrogen is a key component of important biomolecules like proteins and has high nutritive importance for humans and other animals. Climate change factors, such as increasing levels of carbon dioxide, increasing temperatures, and increasing watering regime, directly or indirectly influence plant nitrogen uptake and assimilation dynamics. The impacts of these stressors can directly threaten our primary source of nitrogen as obtained from the soil by plants. In this review, we discuss how climate change factors can influence nitrogen uptake and assimilation in cultivated plants. We examine the effects of these factors alone and in combination with species of both C3 and C4 plants. Elevated carbon dioxide, e[CO2], causes the dilution of nitrogen in tissues of non-leguminous C3 and C4 plants but can increase nitrogen in legumes. The impact of high-temperature (HT) stress varies depending on whether a species is leguminous or not. Water stress (WS) tends to result in a decrease in nitrogen assimilation. Under some, though not all, conditions, e[CO2] can have a buffering effect against the detrimental impacts of other climate change stressors, having an ameliorating effect on the adverse impacts of HT or WS. Together, HT and WS are seen to cause significant reductions in biomass production and nitrogen uptake in non-leguminous C3 and C4 crops. With a steadily rising population and rapidly changing climate, consideration must be given to the morphological and physiological effects that climate change will have on future crop health and nutritional quality of N.

Transcription-metabolism analysis of various signal transduction pathways in Brassica chinensis L. exposed to PLA-MPs

Biodegradable plastics, regarded as an ideal substitute for traditional plastics, are increasingly utilized across various industries. However, due to their unique degradation properties, they can generate microplastics (MPs) at a faster rate, potentially posing a threat to plant development. This study employed transcriptomics and metabolomics to investigate the effects of polylactic acid microplastics (PLA-MPs) on the physiological and biochemical characteristics of Brassica chinensis L. over different periods. The findings indicated that exposure to varying concentrations of PLA-MPs had distinct influences on the growth and development of Brassica chinensis L. Transcriptomic analysis showed different concentrations of PLA-MPs directly influenced the expression of genes associated with plant hormones, such as SnRK2 and BnaA01g27170D. In addition, it was observed that these PLA-MPs also impacted plant growth and development by modulating the expression of other genes, eg. related to sulfur metabolism and glycerophosphate metabolism. Metabolomic analysis demonstrated alterations levels of metabolites such as L-glutamine, and arginine in response to PLA-MPs, which influenced pathways related to vitamin B6 metabolism, the one-carbon folate pool, glycerophospholipid metabolism, and cysteine. This study offers new insights into the potential impacts of biodegradable microplastics (BMPs) on plants and underscores the need for further investigation into the potentially more significant effects of BMPs on terrestrial ecosystems.

The Involvement of Amino Acid Metabolism in the Mechanisms of Salt Tolerance Adaptation in Medicago sativa and Medicago truncatula

Amino acid metabolism constitutes a major metabolic pathway in plants, playing an important role in the modulation of plant responses to stress. In this study, we investigated the amino acid metabolism responses of M. sativa (Medicago sativa L.) and M. truncatula (Medicago truncatula L.) plants under salt stress using transcriptomic and proteomic approaches to elucidate their salt stress tolerance mechanisms in relation to the regulation of amino acid homeostasis. Transcriptome and proteome sequencing followed by Kyoto Gene and Genome Encyclopedia enrichment analysis revealed 34 differentially expressed genes and 45 differentially expressed proteins involved in valine, leucine, and isoleucine degradation, tyrosine metabolism, and glutathione metabolism. Significant differences were observed in the expression of glutathione S-transferase (GST) within the glutathione metabolic pathway between M. sativa and M. truncatula. The induction of valine, leucine, and isoleucine metabolism, aldehyde dehydrogenases (ALDHs), and alanine-glyoxylate aminotransferases (AGXTs), involved in intracellular reactive oxygen species scavenging, also significantly differed under salt stress. Significant differences were identified in the expression of tyrosine decarboxylases (TDCs) involved in tyrosine metabolism, which are responsible for tyramine biosynthesis and can enhance plant tolerance to salt stress. This study delved into the effects of amino acid metabolism on the salt tolerance mechanisms of M. sativa and M. truncatula, which is crucial in guiding the future breeding of salt-tolerant alfalfa varieties.

Signalling and regulation of plant development by carbon/nitrogen balance

The two most abundant macronutrients in plant cells are carbon (C) and nitrogen (N). Coordination of their cellular metabolism is a fundamental factor in guaranteeing the optimal growth and development of plants. N availability and assimilation profoundly affect plant gene expression and modulate root and stem architecture, thus affecting whole plant growth and crop yield. N status also affects C fixation, as it is an important component of the photosynthetic machinery in leaves. Reciprocally, increasing C supply promotes N uptake and assimilation. There is extensive knowledge of the different mechanisms that plants use for sensing and signalling their nutritional status to regulate the assimilation, metabolism and transport of C and N. However, the crosstalk between C and N pathways has received much less attention. Plant growth and development are greatly affected by suboptimal C/N balance, which can arise from nutrient deficiencies or/and environmental cues. Mechanisms that integrate and respond to changes in this specific nutritional balance have started to arise. This review will examine the specific responses to C/N imbalance in plants by focusing on the main inorganic and organic metabolites involved, how they are sensed and transported, and the interconnection between the early signalling components and hormonal networks that underlies plants' adaptive responses.

Genome-Wide Association Study Identifies the Serine/Threonine Kinase ClSIK1 for Low Nitrogen Tolerance in Watermelon Species

Plants have evolved multiple complex mechanisms enabling them to adapt to low nitrogen (LN) stress via increased nitrogen use efficiency (NUE) as nitrogen deficiency in soil is a major factor limiting plant growth and development. However, the adaptive process and evolutionary roles of LN tolerance-related genes in plants remain largely unknown. In this study, we resequenced 191 watermelon accessions and examined their phenotypic differences related to LN tolerance. A major gene ClSIK1 encoding a serine/threonine protein kinase involved in the response to LN stress was identified on chromosome 11 using genome-wide association study and RNA-Seq analysis. According to a functional analysis, ClSIK1 overexpression can increase the root area, total biomass, NUE and LN tolerance by manipulating multiple nitrogen-metabolized genes. Interestingly, the desirable LN-tolerant haplotype ClSIK1HapC was detected in only one wild relative (Citrullus mucosospermus) and likely gradually lost during watermelon domestication and improvement. This study clarified the regulatory effects of ClSIK1 on NUE and adaptations to LN stress, which also identifying valuable haplotypes-resolved gene variants for molecular design breeding of 'green' watermelon varieties highly tolerant to LN stress.

A Gln alteration influences leaf morphogenesis by mediating gibberellin levels in tobacco

Nitrogen is a critical nutrient for plant growth and development. While numerous studies have investigated the mechanisms by which nitrate and/or ammonium regulate plant growth, little is known about whether and how amino acids regulate plant leaf development. This study demonstrates that tobacco plants with altered expression levels of an amino acid transporter (LYSINE HISTIDINE TRANSPORTER1, NtLHT1, Ntab0818090) exhibit significant differences in leaf morphology. Knock-out mutants exhibit elongated and narrower leaves compared to wild-type plants, whereas overexpression (OE) lines display orbicular leaves. Additionally, mutant plants exhibit decreased nitrogen use efficiency (NUE) under half MS medium and delayed development under nitrogen-depleted conditions. Moreover, overexpression lines demonstrate better performance. Although the mutant does not show significant lower level of nitrate or total amino acid content in the developing leaves, its amino acid profile, particularly glutamine (Gln), is significantly altered. Supplementation with Gln in the growth medium, rather than glutamate, can restore the morphological differences observed in mutant leaves, suggesting a pivotal role of Gln in regulating leaf shape. To further elucidate the mechanisms underlying leaf shape regulation, we analyzed endogenous hormone levels and applied exogenous hormones to these lines. Our findings suggest that amino acids transported from source organs, particularly glutamine (Gln), play a key role in controlling leaf development and morphology through the modulation of multiple phytohormones, such as gibberellic acid (GA).

Methionine-mediated trade-off between plant growth and salt tolerance

Salt stress is an important environmental factor that limits plant growth and development. A better understanding of the molecular mechanisms underlying plant salt tolerance will help improve plant performance and crop production under saline conditions. Here, we found that the amino acid methionine significantly improves plant salt tolerance. The salinity-induced activation of key genes governing methionine biosynthesis, namely Hcy-S-methyltransferases (HMTs) and methionine synthases (MSs), is controlled by the concerted interplay of abscisic acid (ABA) and reactive oxygen species signaling. This orchestrated gene activation subsequently leads to methionine accumulation, activating ABA signaling and improving plant salt tolerance. Beyond its role in modulating ABA signaling, methionine affects root growth dynamics by suppressing auxin and cytokinin signaling and impeding cell cycle progression. These multiple effects on growth-related signaling pathways lead to an effective redistribution of energy resources to improve the plant's ability to combat salt-induced stress. Our findings underscore methionine's pivotal involvement in enhancing plant adaptation to salinity stress by establishing a delicate balance between growth and salt tolerance. This mechanistic understanding sheds light on a compelling way to increase crop yields in saline soils and provides a strategic framework for sustainable agricultural practices in challenging environments.

Histidine limitation alters plant development and influences the TOR network

Plant growth depends on growth regulators, nutrient availability, and amino acid levels, all of which influence cell wall formation and cell expansion. Cell wall integrity and structures are surveyed and modified by a complex array of cell wall integrity sensors, including leucine-rich repeat (LRR)-extensins (LRXs) that bind RALF (rapid alkalinization factor) peptides with high affinity and help to compact cell walls. Expressing the Arabidopsis root hair-specific LRX1 without the extensin domain, which anchors the protein to the cell wall (LRX1ΔE14), has a negative effect on root hair development. The mechanism of this negative effect was investigated by a suppressor screen, which led to the identification of a sune (suppressor of dominant-negative LRX1ΔE14) mutant collection. The sune82 mutant was identified as an allele of HISN2, which encodes an enzyme essential for histidine biosynthesis. This mutation leads to reduced accumulation of histidine and an increase in several amino acids, which appears to have an effect on the TOR (target of rapamycin) network, a major controller of eukaryotic cell growth. It also represents an excellent tool to study the effects of reduced histidine levels on plant development, as it is a rare example of a viable partial loss-of-function allele in an essential biosynthetic pathway.

Plant Rho GTPase ROP6 Is Essential for Manganese Homeostasis in Arabidopsis

Manganese (Mn) is an indispensable mineral for plant growth and development. However, plants cultivated in acidic and poorly drained soils are vulnerable to Mn2+ toxicity due to its heightened increased bioavailability. Despite the crucial roles of the Rho of plant (ROP) GTPases in various cellular processes, their precise function in regulating Mn homeostasis remains elusive. In this study, we unveil a novel ROP6 GTPase signalling pathway that profoundly influences Mn phytotoxicity tolerance in Arabidopsis. Remarkably, the rop6 and dominant-negative ROP6 (rop6DN) mutant plants displayed a dramatically sensitive phenotype to Mn toxicity, whereas ROP6-overexpression and constitutively activated ROP6 (rop6CA) lines exhibited enhanced Mn stress tolerance. Immunoblot analysis corroborated that the ROP6 protein, especially the active form of ROP6, increased in abundance in the presence of high Mn levels. Further, we identified that ROP6 physically interacted and colocalized with Metal Tolerance Protein 8 (MTP8) in vivo. Mn transport complementation assays in yeast, combined with biochemical analyses, emphasized the essentiality of ROP6 for MTP8's transport activity. In addition, genetic analyses indicated that ROP6 acted upstream of MTP8 in the regulatory cascade. Collectively, our findings elucidate that ROP6 GTPase signalling positively modulates and enhances Mn stress tolerance in plants.

Integrative analyses of morpho-physiological, biochemical, and transcriptomic reveal the seedling growth response of Pinus yunnanensis to nitrogen and phosphorus fertilization

Appropriate nitrogen (N) and phosphorus (P) fertilization is critical for plant growth and production. Pinus yunnanensis, a silvicultural tree in southwestern China, faces economic and ecological limitations due to nutrient deficiency in the soils in its distribution areas. The slow growth of this species during the seedling stage exacerbates these problems. Therefore, it is important to realize the regulating effects of N and P proportioning fertilization on seedling growth to enhance nutrient-use efficiency. In this study, variations in morphological, physiological, and biochemical characteristics of seedlings were analyzed under nine treatments of NP proportioning in an open nursery using a regression design. Growth in height and basal diameter increased and showed an approximate tendency in all treatments. The maximum biomass accumulation was observed at 480 d after treatment in roots of T5 (14.714 g) (application N 0.4 g·per-1 and P 3 g·per-1), stems of T5 (12.654 g), leaves of T9 (24.261 g) (application N 0.8 g·per-1 and P 6 g·per-1), aboveground parts of T9 (35.402 g) and individuals of T5 (49 g). The total chlorophyll content peaked in the leaves at 120 d and was correlated with the peak levels of N, P, and K in leaves. The content and reserves of nutrient elements in the organs of seedlings subjected to NP proportioning were significantly higher than those in unfertilized seedlings. Analysis of nutrient utilization efficiency revealed that T5 demonstrated superior seedling growth performance. Appropriate fertilization dosage of N and P for P. yunnanensis seedlings in this study was 0.32 g·per-1-0.58 g·per-1 and 3.02 g·per-1-4.95 g·per-1 respectively, using path analysis and regression equation. Transcriptomic sequencing revealed that there were 2,301 DEGs between T5 and T1 (control), which were involved in the uptake and assimilation of nutrients, biosynthesis of phytohormones and secondary metabolites, and photosynthesis. Additionally, the abundance of genes involved in cell division and proliferation, cellulose biosynthesis, and cell wall extension were dramatically upregulated, which potentially correlated with enhanced seedling growth. In conclusion, this study provides comprehensive information on the response of seedlings to varying proportions of N and P and may promote the growth of P. yunnanensis seedlings by optimizing the proportion of N and P in fertilizers.

HDC1 Promotes Primary Root Elongation by Regulating Auxin and K+ Homeostasis in Response to Low-K+ Stress

Plants frequently encounter relatively low and fluctuating potassium (K+) concentrations in soil, with roots serving as primary responders to this stress. Histone modifications, such as de-/acetylation, can function as epigenetic markers of stress-inducible genes. However, the signaling network between histone modifications and low-K+ (LK) response pathways remains unclear. This study investigated the regulatory role of Histone Deacetylase Complex 1 (HDC1) in primary root growth of Arabidopsis thaliana under K+ deficiency stress. Using a hdc1-2 mutant line, we observed that HDC1 positively regulated root growth under LK conditions. Compared to wild-type (WT) plants, the hdc1-2 mutant exhibited significantly inhibited primary root growth under LK conditions, whereas HDC1-overexpression lines displayed opposite phenotypes. No significant differences were observed under HK conditions. Further analysis revealed that the inhibition of hdc1-2 on root growth was due to reduced apical meristem cell proliferation rather than cell elongation. Notably, the root growth of hdc1-2 showed reduced sensitivity compared to WT after auxin treatment under LK conditions. HDC1 may regulate root growth by affecting auxin polar transport and subsequent auxin signaling, as evidenced by the altered expression of auxin transport genes. Moreover, the organ-specific RT-qPCR analyses unraveled that HDC1 negatively regulates the expression of CBL-CIPK-K+ channel-related genes such as CBL1, CBL2, CBL3, AKT1, and TPK1, thereby establishing a molecular link between histone deacetylation, auxin signaling, and CBLs-CIPKs pathway in response to K+ deficiency.

GRAIN SIZE ON CHROMOSOME 2 orchestrates phytohormone, sugar signaling and energy metabolism to confer thermal resistance in rice

GRAIN SIZE ON CHROMOSOME 2 (GS2) has been reported to enhance rice grain yield and confer tolerance to cold, drought, and salt stress, but its function in heat tolerance of rice remains undocumented. This study aimed to investigate whether GS2 could enhance thermal tolerance by subjecting rice seedlings of Huazhan (HZ) and its near-isogenic line (HZ-GS2) to heat stress. HZ-GS2 plants exhibited less damage compared to HZ plants under heat stress. Transcriptome revealed the involvement of phytohormones, sugar signaling, and energy metabolism in the mechanism by which GS2 influences heat tolerance. Under heat stress, HZ-GS2 plants showed higher increases or lower decreases in glucose, gibberellins (GAs), salicylic acid (SA), indoleacetic acid (IAA), adenosine triphosphate (ATP), energy charge, as well as the activities of hexokinase, NADH dehydrogenase, cytochrome oxidase, ATP synthase, and ATPase. Exogenous GA3 enhanced heat tolerance in rice by increasing energy charge, ATPase, activities of complex V and hexokinase. Additionally, glucose, sucrose, 3-aminobenzamide (3-ab), and Na2SO3 conferred heat tolerance in rice plants. Importantly, a significant increase in Fv/Fm was observed in plants treated with a combination of GA3, glucose, and 3-ab, compared to those sprayed alone. Thus, GS2 coordinates GA3, hexokinase, and energy metabolism to improve energy status, thereby enhancing heat tolerance in rice plants.

Identification and Characterization of Key Genes for Nitrogen Utilization from Saccharum spontaneum Sub-Genome in Modern Sugarcane Cultivar

Sugarcane (Saccharum spp.) is globally considered an important crop for sugar and biofuel production. During sugarcane production, the heavy reliance on chemical nitrogen fertilizer has resulted in low nitrogen use efficiency (NUE) and high loss. Up until now, there has been extensive research on the transcriptomic dynamics during sugarcane response to low nitrogen (LN) stress. However, the specific contribution of S. spontaneum to the NUE of modern sugarcane remains unclear. In the present study, the comparative transcriptome analysis of two contrasting sugarcane cultivars in response to nitrogen deficiency was performed via the combination of genomes of S. spontaneum and S. officinarum. Sub-genome analysis indicated that S. spontaneum supports the high NUE of modern sugarcane by providing genes related to nitrogen and carbohydrate metabolism, photosynthesis, and amino acid metabolism. Additionally, the key genes involved in nitrogen metabolism from the S. spontaneum were successfully identified through weighted gene co-expression network analyses (WGCNA), and a high-affinity nitrate transporter named ScNRT2.3 was subsequently cloned. Heterogeneous expression of the ScNRT2.3, a cell membrane-localized protein, could enhance the growth of Arabidopsis under low nitrate conditions. Furthermore, a conserved protein module known as NAR2.1/NRT2.3 was shown to regulate the response to LN stress in sugarcane roots through molecular interaction. This work helps to clarify the contribution of S. spontaneum to the NUE in modern sugarcane, and the function of the ScNRT2.3 in sugarcane.

SnRK1α1-mediated RBOH1 phosphorylation regulates reactive oxygen species to enhance tolerance to low nitrogen in tomato

Nitrogen is essential for plant growth and development. SNF1-related protein kinase 1 (SnRK1) is an evolutionarily conserved protein kinase pivotal for regulating plant responses to nutrient deficiency. Here, we discovered that the expression and activity of the SnRK1 α-catalytic subunit (SnRK1α1) increased in response to low-nitrogen stress. SnRK1α1 overexpression enhanced seedling tolerance, nitrate uptake capacity, apoplastic reactive oxygen species (ROS) accumulation, and NADPH oxidase activity in tomato (Solanum lycopersicum L.) under low-nitrogen stress compared to wild type plants, while snrk1α1 mutants exhibited the opposite phenotypes. Mutation of the NADPH oxidase gene Respiratory burst oxidase homolog 1 (RBOH1) suppressed numerous nitrate uptake and metabolism genes during low-nitrogen stress. rboh1 mutants displayed lower NADPH oxidase activity, apoplastic ROS production, and seedling tolerance to low nitrogen. Silencing RBOH1 expression also compromised SnRK1α1-mediated seedling tolerance to low-nitrogen stress. SnRK1α1 interacts with and activates RBOH1 through phosphorylation of three N-terminal serine residues, leading to increased apoplastic ROS production and enhanced tolerance to low nitrogen conditions. Furthermore, RBOH1-dependent ROS oxidatively modified the transcription factor TGA4 at residue Cys-334, which increased NRT1.1 and NRT2.1 expression under low-nitrogen stress. These findings reveal a SnRK1α1-mediated signaling pathway and highlight the essential role of RBOH1-dependent ROS production in enhancing plant tolerance to low nitrogen.

Photoacclimation strategies of Chlamydomonas reinhardtii in response to high-light stress in stationary phase

Under ideal conditions, Chlamydomonas reinhardtii can photoacclimate to excess light through various short- and long-term mechanisms. However, how microalgae handle excess light stress once they exit exponential growth, and especially in stationary phase, is less understood. Our study explored C. reinhardtii's photoprotection capacity and acclimation strategies during high-light stress once batch culture growth reached stationary phase. We monitored cultures of wildtype strain (CC125) over five days once they reached stationary phase under both low-light (LL) and high-light (HL) conditions. Under HL, many photosynthetic proteins were degraded but the stress-related light harvesting complex protein (LHCSR) was rapidly induced and contributed to the rapid activation of nonphotochemical quenching (NPQ). However, the LHCSR3-defective mutant (CC4614, npq4) lacked the rapid induction of quenching typical of post-exponential cultures, indicating that LHCSR3 is required for this response in stationary phase. Collectively, the main strategy for photoacclimation in stationary phase appears to be a dramatic reduction of photosystems while maintaining LHCII-LHCSR antenna complexes that prime the antenna for rapid activation of quenching upon light exposure. Part of this response to HL involves a resumption of cell growth after two days, that we hypothesized is due to the stimulation of growth-regulating pathways due to increased metabolite pools from the HL-induced protein turnover in the cell, something that remains to be tested. These findings demonstrate how C. reinhardtii manages high-light stress during stationary phases to maximize longevity.

TOR balances plant growth and cold tolerance by orchestrating amino acid-derived metabolism in tomato

The target of rapamycin (TOR) kinase is a central signaling hub that plays a crucial role in precisely orchestrating plant growth, development, and stress responses. This suggests that TOR is intricately involved in maintaining the balance between plant growth and stress responses. Nevertheless, despite the observed effects, the specific mechanisms through which TOR operates in these processes remain obscure. In this study, we investigated how the tomato (Solanum lycopersicum) TOR (SlTOR) affects plant growth and cold responses. We demonstrated that SlTOR inhibition transcriptionally primes cold stress responses, consequently enhancing tomato cold tolerance. A widely targeted metabolomics analysis revealed the disruption of amino acid metabolism homeostasis under cold stress upon SlTOR inhibition, which led to the accumulation of two important cryoprotective metabolites: salicylic acid (SA) and putrescine (Put). Next, we discovered SlPGH1 (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE 1) as a direct substrate of SlTOR. Inhibiting SlTOR led to increased SlCBF1 (C-REPEAT-BINDING FACTOR 1) expression via SlPGH1, potentially triggering the activation of cold-responsive genes and subsequent metabolic alterations. Our study provides a mechanistic framework that elucidates how SlTOR modulates amino acid-related metabolism to enhance tomato cold tolerance, which sheds light on the complex interplay between growth and stress responses orchestrated by TOR.

A Nitrogen-specific Interactome Analysis Sheds Light on the Role of the SnRK1 and TOR Kinases in Plant Nitrogen Signaling

Nitrogen (N) is of utmost importance for plant growth and development. Multiple studies have shown that N signaling is tightly coupled with carbon (C) levels, but the interplay between C/N metabolism and growth remains largely an enigma. Nonetheless, the protein kinases Sucrose Non-fermenting 1 (SNF1)-Related Kinase 1 (SnRK1) and Target Of Rapamycin (TOR), two ancient central metabolic regulators, are emerging as key integrators that link C/N status with growth. Despite their pivotal importance, the exact mechanisms behind the sensing of N status and its integration with C availability to drive metabolic decisions are largely unknown. Especially for SnRK1, it is not clear how this kinase responds to altered N levels. Therefore, we first monitored N-dependent SnRK1 kinase activity with an in vivo Separation of Phase-based Activity Reporter of Kinase (SPARK) sensor, revealing a contrasting N-dependency in Arabidopsis thaliana (Arabidopsis) shoot and root tissues. Next, using affinity purification (AP) and proximity labeling (PL) coupled to mass spectrometry (MS) experiments, we constructed a comprehensive SnRK1 and TOR interactome in Arabidopsis cell cultures during N-starved and N-repleted growth conditions. To broaden our understanding of the N-specificity of the TOR/SnRK1 signaling events, the resulting network was compared to corresponding C-related networks, identifying a large number of novel, N-specific interactors. Moreover, through integration of N-dependent transcriptome and phosphoproteome data, we were able to pinpoint additional N-dependent network components, highlighting for instance SnRK1 regulatory proteins that might function at the crosstalk of C/N signaling. Finally, confirmation of known and identification of novel SnRK1 interactors, such as Inositol-Requiring 1 (IRE1A) and the RAB GTPase RAB18, indicate that SnRK1, present at the ER, is involved in N signaling and autophagy induction.

FYVE1/FREE1 is involved in glutamine-responsive TORC1 activation in plants

Target of rapamycin complex 1 (TORC1) integrates nutrient availability, growth factors, and stress signals to regulate cellular metabolism according to its environment. Similar to mammals, amino acids have been shown to activate TORC1 in plants. However, as the Rag complex that controls amino acid-responsive TORC1 activation mechanisms in many eukaryotes is not conserved in plants, the amino acid-sensing mechanisms upstream of TORC1 in plants remain unknown. In this study, we report that Arabidopsis FYVE1/FREE1 is involved in glutamine-induced TORC1 activation, independent of its previously reported function in ESCRT-dependent processes. FYVE1/FREE1 has a domain structure similar to that of the yeast glutamine sensor Pib2 that directly activates TORC1. Similar to Pib2, FYVE1/FREE1 interacts with TORC1 in response to glutamine. Furthermore, overexpression of a FYVE1/FREE1 variant lacking the presumptive TORC1 activation motif hindered the glutamine-responsive activation of TORC1. Overall, these observations suggest that FYVE1/FREE1 acts as an intracellular amino acid sensor that triggers TORC1 activation in plants.

Nitrogen starvation leads to TOR kinase-mediated downregulation of fatty acid synthesis in the algae Chlorella sorokiniana and Chlamydomonas reinhardtii

BACKGROUND

When subject to stress conditions such as nutrient limitation microalgae accumulate triacylglycerol (TAG). Fatty acid, a substrate for TAG synthesis is derived from de novo synthesis or by membrane remodeling. The model industrial alga Chlorellasorokiniana accumulates TAG and other storage compounds under nitrogen (N)-limited growth. Molecular mechanisms underlying these processes are still to be elucidated.

RESULT

Previously we used transcriptomics to explore the regulation of TAG synthesis in C. sorokiniana. Surprisingly, our analysis showed that the expression of several key genes encoding enzymes involved in plastidic fatty acid synthesis are significantly repressed. Metabolic labeling with radiolabeled acetate showed that de novo fatty acid synthesis is indeed downregulated under N-limitation. Likewise, inhibition of the Target of Rapamycin kinase (TOR), a key regulator of metabolism and growth, decreased fatty acid synthesis. We compared the changes in proteins and phosphoprotein abundance using a proteomics and phosphoproteomics approach in C. sorokiniana cells under N-limitation or TOR inhibition and found extensive overlap between the N-limited and TOR-inhibited conditions. We also identified changes in the phosphorylation status of TOR complex proteins, TOR-kinase, and RAPTOR, under N-limitation. This indicates that TOR signaling is altered in a nitrogen-dependent manner. We find that TOR-mediated metabolic remodeling of fatty acid synthesis under N-limitation is conserved in the chlorophyte algae Chlorella sorokiniana and Chlamydomonas reinhardtii.

CONCLUSION

Our results indicate that under N-limitation there is significant metabolic remodeling, including fatty acid synthesis, mediated by TOR signaling. This process is conserved across chlorophyte algae. Using proteomic and phosphoproteomic analysis, we show that N-limitation affects TOR signaling and this in-turn affects the metabolic status of the cells. This study presents a link between N-limitation, TOR signaling and fatty acid synthesis in green-lineage.

Glutamine induces lateral root initiation, stress responses, and disease resistance in Arabidopsis

The production of glutamine (Gln) from NO3- and NH4+ requires ATP, reducing power, and carbon skeletons. Plants may redirect these resources to other physiological processes using Gln directly. However, feeding Gln as the sole nitrogen (N) source has complex effects on plants. Under optimal concentrations, Arabidopsis (Arabidopsis thaliana) seedlings grown on Gln have similar primary root lengths, more lateral roots, smaller leaves, and higher amounts of amino acids and proteins compared to those grown on NH4NO3. While high levels of Gln accumulate in Arabidopsis seedlings grown on Gln, the expression of GLUTAMINE SYNTHETASE1;1 (GLN1;1), GLN1;2, and GLN1;3 encoding cytosolic GS1 increases and expression of GLN2 encoding chloroplastic GS2 decreases. These results suggest that Gln has distinct effects on regulating GLN1 and GLN2 gene expression. Notably, Arabidopsis seedlings grown on Gln have an unexpected gene expression profile. Compared with NH4NO3, which activates growth-promoting genes, Gln preferentially induces stress- and defense-responsive genes. Consistent with the gene expression data, exogenous treatment with Gln enhances disease resistance in Arabidopsis. The induction of Gln-responsive genes, including PATHOGENESIS-RELATED1, SYSTEMIC ACQUIRED RESISTANCE DEFICIENT1, WRKY54, and WALL ASSOCIATED KINASE1, is compromised in salicylic acid (SA) biosynthetic and signaling mutants under Gln treatments. Together, these results suggest that Gln may partly interact with the SA pathway to trigger plant immunity.

Posttranslational regulation of photosynthetic activity via the TOR kinase in plants

Chloroplasts are the powerhouse of the plant cell, and their activity must be matched to plant growth to avoid photooxidative damage. We have identified a posttranslational mechanism linking the eukaryotic target of rapamycin (TOR) kinase that promotes growth and the guanosine tetraphosphate (ppGpp) signaling pathway of prokaryotic origins that regulates chloroplast activity and photosynthesis in particular. We find that RelA SpoT homolog 3 (RSH3), a nuclear-encoded enzyme responsible for ppGpp biosynthesis, interacts directly with the TOR complex via a plant-specific amino-terminal region which is phosphorylated in a TOR-dependent manner. Down-regulating TOR activity causes a rapid increase in ppGpp synthesis in RSH3 overexpressors and reduces photosynthetic capacity in an RSH-dependent manner in wild-type plants. The TOR-RSH3 signaling axis therefore regulates the equilibrium between chloroplast activity and plant growth, setting a precedent for the regulation of organellar function by TOR.

Sensing and regulation of C and N metabolism - novel features and mechanisms of the TOR and SnRK1 signaling pathways

Carbon (C) and nitrogen (N) metabolisms are tightly integrated to allow proper plant growth and development. Photosynthesis is dependent on N invested in chlorophylls, enzymes, and structural components of the photosynthetic machinery, while N uptake and assimilation rely on ATP, reducing equivalents, and C-skeletons provided by photosynthesis. The direct connection between N availability and photosynthetic efficiency allows the synthesis of precursors for all metabolites and building blocks in plants. Thus, the capacity to sense and respond to sudden changes in C and N availability is crucial for plant survival and is mediated by complex yet efficient signaling pathways such as TARGET OF RAPAMYCIN (TOR) and SUCROSE-NON-FERMENTING-1-RELATED PROTEIN KINASE 1 (SnRK1). In this review, we present recent advances in mechanisms involved in sensing C and N status as well as identifying current gaps in our understanding. We finally attempt to provide new perspectives and hypotheses on the interconnection of diverse signaling pathways that will allow us to understand the integration and orchestration of the major players governing the regulation of the CN balance.

What, where, and how: Regulation of translation and the translational landscape in plants

Translation is a crucial step in gene expression and plays a vital role in regulating various aspects of plant development and environmental responses. It is a dynamic and complex program that involves interactions between mRNAs, transfer RNAs, and the ribosome machinery through both cis- and trans-regulation while integrating internal and external signals. Translational control can act in a global (transcriptome-wide) or mRNA-specific manner. Recent advances in genome-wide techniques, particularly ribosome profiling and proteomics, have led to numerous exciting discoveries in both global and mRNA-specific translation. In this review, we aim to provide a "primer" that introduces readers to this fascinating yet complex cellular process and provide a big picture of how essential components connect within the network. We begin with an overview of mRNA translation, followed by a discussion of the experimental approaches and recent findings in the field, focusing on unannotated translation events and translational control through cis-regulatory elements on mRNAs and trans-acting factors, as well as signaling networks through 3 conserved translational regulators TOR, SnRK1, and GCN2. Finally, we briefly touch on the spatial regulation of mRNAs in translational control. Here, we focus on cytosolic mRNAs; translation in organelles and viruses is not covered in this review.

Histone dynamics responding to internal and external cues underlying plant development

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

TOR in plants: Multidimensional regulators of plant growth and signaling pathways

Target Of Rapamycin (TOR) represents a ubiquitous kinase complex that has emerged as a central regulator of cell growth and metabolism in nearly all eukaryotic organisms. TOR is an evolutionarily conserved protein kinase, functioning as a central signaling hub that integrates diverse internal and external cues to regulate a multitude of biological processes. These processes collectively exert significant influence on plant growth, development, nutrient assimilation, photosynthesis, fruit ripening, and interactions with microorganisms. Within the plant domain, the TOR complex comprises three integral components: TOR, RAPTOR, and LST8. This comprehensive review provides insights into various facets of the TOR protein, encompassing its origin, structure, function, and the regulatory and signaling pathways operative in photosynthetic organisms. Additionally, we explore future perspectives related to this pivotal protein kinase.

Cytochrome c levels affect the TOR pathway to regulate growth and metabolism under energy-deficient conditions

Mitochondrial function is essential for plant growth, but the mechanisms involved in adjusting growth and metabolism to changes in mitochondrial energy production are not fully understood. We studied plants with reduced expression of CYTC-1, one of two genes encoding the respiratory chain component cytochrome c (CYTc) in Arabidopsis, to understand how mitochondria communicate their status to coordinate metabolism and growth. Plants with CYTc deficiency show decreased mitochondrial membrane potential and lower ATP content, even when carbon sources are present. They also exhibit higher free amino acid content, induced autophagy, and increased resistance to nutritional stress caused by prolonged darkness, similar to plants with triggered starvation signals. CYTc deficiency affects target of rapamycin (TOR)-pathway activation, reducing S6 kinase (S6K) and RPS6A phosphorylation, as well as total S6K protein levels due to increased protein degradation via proteasome and autophagy. TOR overexpression restores growth and other parameters affected in cytc-1 mutants, even if mitochondrial membrane potential and ATP levels remain low. We propose that CYTc-deficient plants coordinate their metabolism and energy availability by reducing TOR-pathway activation as a preventive signal to adjust growth in anticipation of energy exhaustion, thus providing a mechanism by which changes in mitochondrial activity are transduced to the rest of the cell.

TON1 recruiting motif 21 positively regulates the flavonoid metabolic pathway at the translational level in Arabidopsis thaliana

MAIN CONCLUSION

This study reveals that TRM21 acts as a positive regulator of flavonoid biosynthesis at the translational level in Arabidopsis, impacting both secondary metabolites and genes associated with root hair growth. TRM (TONNEAU1-recruiting motif) superfamily proteins are reported to be involved in microtubule assembly. However, the functions of this protein family are just beginning to be uncovered. Here, we provide metabolomic and genetic evidence that 1 of the 34 TRM members, TRM21, positively regulates the biosynthesis of flavonoids at the translational level in Arabidopsis thaliana. A loss-of-function mutation in TRM21 led to root hair growth defects and stunted plant growth, accompanied by significant alterations in secondary metabolites, particularly a marked reduction in flavonoid content. Interestingly, our study revealed that the transcription levels of genes involved in the flavonoid biosynthesis pathway remained unchanged in the trm21 mutants, but there was a significant downregulation in the translation levels of certain genes [flavanone 3-hydroxylase (F3H), dihydroflavonol-4-reductase (DFR), anthocyanidin reductase (ANR), flavanone 3'-hydroxylase (F3'H), flavonol synthase (FLS), chalcone synthase (CHS)]. Additionally, the translation levels of some genes related to root hair growth [RHO-related GTPases of plant 2 (ROP2), root hair defective 6 (RHD6), root hair defective 2 (RHD2)] were also reduced in the trm21 mutants. Taken together, these results indicate that TRM21 functions as a positive regulator of flavonoid biosynthesis at the translational level in Arabidopsis.

Mitigating growth-stress tradeoffs via elevated TOR signaling in rice

Rice production accounts for approximately half of the freshwater resources utilized in agriculture, resulting in greenhouse gas emissions such as methane (CH4) from flooded paddy fields. To address this challenge, environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice cultivation. However, the implementation of water-saving treatments (WSTs) in paddy-field rice has been associated with a substantial yield loss of up to 50% as well as a reduction in nitrogen use efficiency (NUE). In this study, we discovered that the target of rapamycin (TOR) signaling pathway is compromised in rice under WST. Polysome profiling-coupled transcriptome sequencing (polysome-seq) analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR activity. Molecular, biochemical, and genetic analyses revealed new insights into the impact of the positive TOR-S6K-RPS6 and negative TOR-MAF1 modules on translation repression under WST. Intriguingly, ammonium exhibited a greater ability to alleviate growth constraints under WST by enhancing TOR signaling, which simultaneously promoted uptake and utilization of ammonium and nitrogen allocation. We further demonstrated that TOR modulates the ammonium transporter AMT1;1 as well as the amino acid permease APP1 and dipeptide transporter NPF7.3 at the translational level through the 5' untranslated region. Collectively, these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and NUE. Our study will contribute to the breeding of new rice varieties with increased water and fertilizer utilization efficiency.

TOR coordinates cytokinin and gibberellin signals mediating development and defense

Plants constantly perceive and process environmental signals and balance between the energetic demands of growth and defense. Growth arrest upon pathogen attack was previously suggested to result from a redirection of the plants' metabolic resources towards the activation of plant defense. The energy sensor Target of Rapamycin (TOR) kinase is a conserved master coordinator of growth and development in all eukaryotes. Although TOR is positioned at the interface between development and defense, little is known about the mechanisms by which TOR may potentially regulate the relationship between these two modalities. The plant hormones cytokinin (CK) and gibberellin (GA) execute various aspects of plant development and defense. The ratio between CK and GA was reported to determine the outcome of developmental programmes. Here, investigating the interplay between TOR-mediated development and TOR-mediated defense in tomato, we found that TOR silencing resulted in rescue of several different aberrant developmental phenotypes, demonstrating that TOR is required for the execution of developmental cues. In parallel, TOR inhibition enhanced immunity in genotypes with a low CK/GA ratio but not in genotypes with a high CK/GA ratio. TOR-inhibition mediated disease resistance was found to depend on developmental status, and was abolished in strongly morphogenetic leaves, while being strongest in mature, differentiated leaves. CK repressed TOR activity, suggesting that CK-mediated immunity may rely on TOR downregulation. At the same time, TOR activity was promoted by GA, and TOR silencing reduced GA sensitivity, indicating that GA signalling requires normal TOR activity. Our results demonstrate that TOR likely acts in concert with CK and GA signalling, executing signalling cues in both defense and development. Thus, differential regulation of TOR or TOR-mediated processes could regulate the required outcome of development-defense prioritisation.

Can nutrients act as signals under abiotic stress?

Plant cells are in constant communication to coordinate development processes and environmental reactions. Under stressful conditions, such communication allows the plant cells to adjust their activities and development. This is due to intercellular signaling events which involve several components. In plant development, cell-to-cell signaling is ensured by mobile signals hormones, hydrogen peroxide (H2O2), nitric oxide (NO), or hydrogen sulfide (H2S), as well as several transcription factors and small RNAs. Mineral nutrients, including macro and microelements, are determinant factors for plant growth and development and are, currently, recognized as potential signal molecules. This review aims to highlight the role of nutrients, particularly calcium, potassium, magnesium, nitrogen, phosphorus, and iron as signaling components with special attention to the mechanism of response against stress conditions.

Insights into molecular links and transcription networks integrating drought stress and nitrogen signaling

Drought and the availability of nitrate, the predominant source of nitrogen (N) in agriculture, are major factors limiting plant growth and crop productivity. The dissection of the transcriptional networks' components integrating droght stress and nitrate responses provides valuable insights into how plants effectively balance stress response with growth programs. Recent evidence in Arabidopsis thaliana indicates that transcription factors (TFs) involved in abscisic acid (ABA) signaling affect N metabolism and nitrate responses, and reciprocally, components of nitrate signaling might affect ABA and drought gene responses. Advances in understanding regulatory circuits of nitrate and drought crosstalk in plant tissues empower targeted genetic modifications to enhance plant development and stress resistance, critical traits for optimizing crop yield and promoting sustainable agriculture.

The exception to the rule? TORC1 triggers growth under low nutrient environments

Eukaryotic cells' proliferation and growth are controlled by the target of rapamycin kinase (TOR). TOR usually activates in favorable energy and nutritional circumstances. This is challenged by recent research, suggesting that plant cells optimized for nutrient absorption in low nutritional conditions may activate the TOR pathway in a polarized manner.

Glutamine Metabolism, Sensing and Signaling in Plants

Glutamine (Gln) is the first amino acid synthesized in nitrogen (N) assimilation in plants. Gln synthetase (GS), converting glutamate (Glu) and NH4+ into Gln at the expense of ATP, is one of the oldest enzymes in all life domains. Plants have multiple GS isoenzymes that work individually or cooperatively to ensure that the Gln supply is sufficient for plant growth and development under various conditions. Gln is a building block for protein synthesis and an N-donor for the biosynthesis of amino acids, nucleic acids, amino sugars and vitamin B coenzymes. Most reactions using Gln as an N-donor are catalyzed by Gln amidotransferase (GAT) that hydrolyzes Gln to Glu and transfers the amido group of Gln to an acceptor substrate. Several GAT domain-containing proteins of unknown function in the reference plant Arabidopsis thaliana suggest that some metabolic fates of Gln have yet to be identified in plants. In addition to metabolism, Gln signaling has emerged in recent years. The N regulatory protein PII senses Gln to regulate arginine biosynthesis in plants. Gln promotes somatic embryogenesis and shoot organogenesis with unknown mechanisms. Exogenous Gln has been implicated in activating stress and defense responses in plants. Likely, Gln signaling is responsible for some of the new Gln functions in plants.

TORC pathway intersects with a calcium sensor kinase network to regulate potassium sensing in Arabidopsis

Potassium (K) is an essential macronutrient for plant growth, and its availability in the soil varies widely, requiring plants to respond and adapt to the changing K nutrient status. We show here that plant growth rate is closely correlated with K status in the medium, and this K-dependent growth is mediated by the highly conserved nutrient sensor, target of rapamycin (TOR). Further study connected the TOR complex (TORC) pathway with a low-K response signaling network consisting of calcineurin B-like proteins (CBL) and CBL-interacting kinases (CIPK). Under high K conditions, TORC is rapidly activated and shut down the CBL-CIPK low-K response pathway through regulatory-associated protein of TOR (RAPTOR)-CIPK interaction. In contrast, low-K status activates CBL-CIPK modules that in turn inhibit TORC by phosphorylating RAPTOR, leading to dissociation and thus inactivation of the TORC. The reciprocal regulation of the TORC and CBL-CIPK modules orchestrates plant response and adaptation to K nutrient status in the environment.

Dynamic transcriptome analysis unravels key regulatory genes of maize root growth and development in response to potassium deficiency

MAIN CONCLUSION

Integrated root phenotypes and transcriptome analysis have revealed key candidate genes responsible for maize root growth and development in potassium deficiency. Potassium (K) is a vital macronutrient for plant growth, but our understanding of its regulatory mechanisms in maize root system architecture (RSA) and K+ uptake remains limited. To address this, we conducted hydroponic and field trials at different growth stages. K+ deficiency significantly inhibited maize root growth, with metrics like total root length, primary root length, width and maximum root number reduced by 50% to 80% during early seedling stages. In the field, RSA traits exhibited maximum values at the silking stage but continued to decline thereafter. Furthermore, K deprivation had a pronounced negative impact on root morphology and RSA growth and grain yield. RNA-Seq analysis identified 5972 differentially expressed genes (DEGs), including 17 associated with K+ signaling, transcription factors, and transporters. Weighted gene co-expression network analysis revealed 23 co-expressed modules, with enrichment of transcription factors at different developmental stages under K deficiency. Several DEGs and transcription factors were predicted as potential candidate genes responsible for maize root growth and development. Interestingly, some of these genes exhibited homology to well-known regulators of root architecture or development in Arabidopsis, such as Zm00001d014467 (AtRCI3), Zm00001d011237 (AtWRKY9), and Zm00001d030862 (AtAP2/ERF). Identifying these key genes helps to provide a deeper understanding of the molecular mechanisms governing maize root growth and development under nutrient deficient conditions offering potential benefits for enhancing maize production and improving stress resistance through targeted manipulation of RSA traits in modern breeding efforts.

Sailing in complex nutrient signaling networks: Where I am, where to go, and how to go?

To ensure survival and promote growth, sessile plants have developed intricate internal signaling networks tailored in diverse cells and organs with both shared and specialized functions that respond to various internal and external cues. A fascinating question arises: how can a plant cell or organ diagnose the spatial and temporal information it is experiencing to know "where I am," and then is able to make the accurate specific responses to decide "where to go" and "how to go," despite the absence of neuronal systems found in mammals. Drawing inspiration from recent comprehensive investigations into diverse nutrient signaling pathways in plants, this review focuses on the interactive nutrient signaling networks mediated by various nutrient sensors and transducers. We assess and illustrate examples of how cells and organs exhibit specific responses to changing spatial and temporal information within these interactive plant nutrient networks. In addition, we elucidate the underlying mechanisms by which plants employ posttranslational modification codes to integrate different upstream nutrient signals, thereby conferring response specificities to the signaling hub proteins. Furthermore, we discuss recent breakthrough studies that demonstrate the potential of modulating nutrient sensing and signaling as promising strategies to enhance crop yield, even with reduced fertilizer application.

Understanding signaling pathways governing the polar development of root hairs in low-temperature, nutrient-deficient environments

Plants exposed to freezing and above-freezing low temperatures must employ a variety of strategies to minimize fitness loss. There is a considerable knowledge gap regarding how mild low temperatures (around 10 °C) affect plant growth and developmental processes, even though the majority of the molecular mechanisms that plants use to adapt to extremely low temperatures are well understood. Root hairs (RH) have become a useful model system for studying how plants regulate their growth in response to both cell-intrinsic cues and environmental inputs. Here, we'll focus on recent advances in the molecular mechanisms underpinning Arabidopsis thaliana RH growth at mild low temperatures and how these discoveries may influence our understanding of nutrient sensing mechanisms by the roots. This highlights how intricately linked mechanisms are necessary for plant development to take place under specific circumstances and to produce a coherent response, even at the level of a single RH cell.

How metabolism and development are intertwined in space and time

Developmental transitions, occurring throughout the life cycle of plants, require precise regulation of metabolic processes to generate the energy and resources necessary for the committed growth processes. In parallel, the establishment of new cells, tissues, and even organs, alongside their differentiation provoke profound changes in metabolism. It is increasingly being recognized that there is a certain degree of feedback regulation between the components and products of metabolic pathways and developmental regulators. The generation of large-scale metabolomics datasets during developmental transitions, in combination with molecular genetic approaches has helped to further our knowledge on the functional importance of metabolic regulation of development. In this perspective article, we provide insights into studies that elucidate interactions between metabolism and development at the temporal and spatial scales. We additionally discuss how this influences cell growth-related processes. We also highlight how metabolic intermediates function as signaling molecules to direct plant development in response to changing internal and external conditions.

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.

The Levels of DAHP Synthase, the First Enzyme of the Shikimate Pathway, Are Related to Free Aromatic Amino Acids and Glutamine Content in Nicotiana plumbaginifolia Cell Cultures

Aromatic amino acid homeostasis was investigated in cell suspension cultures of Nicotiana plumbaginifolia and was related to the activity of the first enzyme in aromatic biosynthesis, 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase. An inverse relationship was found between the intracellular content of free phenylalanine, tyrosine and tryptophan and enzyme specific activity levels, suggesting the occurrence of end-product control mechanisms. Two DAHP synthase isogenes are present in wild tobacco that showed a different expression pattern during the culture growth cycle. Intracellular levels of aromatic amino acids were increased or decreased by adding the culture medium with phenylalanine, tyrosine and tryptophan, or with sublethal doses of the shikimate pathway inhibitor glyphosate, respectively. As a consequence, enzyme levels varied in the opposite direction. The concomitant exogenous supply of glutamine further reduced enzyme activity in mid-log cells, suggesting induction by both aromatic amino acid depletion and nitrogen starvation.

Emerging role of small GTPases and their interactome in plants to combat abiotic and biotic stress

Plants are frequently subjected to abiotic and biotic stress which causes major impediments in their growth and development. It is emerging that small guanosine triphosphatases (small GTPases), also known as monomeric GTP-binding proteins, assist plants in managing environmental stress. Small GTPases function as tightly regulated molecular switches that get activated with the aid of guanosine triphosphate (GTP) and deactivated by the subsequent hydrolysis of GTP to guanosine diphosphate (GDP). All small GTPases except Rat sarcoma (Ras) are found in plants, including Ras-like in brain (Rab), Rho of plant (Rop), ADP-ribosylation factor (Arf) and Ras-like nuclear (Ran). The members of small GTPases in plants interact with several downstream effectors to counteract the negative effects of environmental stress and disease-causing pathogens. In this review, we describe processes of stress alleviation by developing pathways involving several small GTPases and their associated proteins which are important for neutralizing fungal infections, stomatal regulation, and activation of abiotic stress-tolerant genes in plants. Previous reviews on small GTPases in plants were primarily focused on Rab GTPases, abiotic stress, and membrane trafficking, whereas this review seeks to improve our understanding of the role of all small GTPases in plants as well as their interactome in regulating mechanisms to combat abiotic and biotic stress. This review brings to the attention of scientists recent research on small GTPases so that they can employ genome editing tools to precisely engineer economically important plants through the overexpression/knock-out/knock-in of stress-related small GTPase genes.

Metabolic regulation of quiescence in plants

Quiescence is a crucial survival attribute in which cell division is repressed in a reversible manner. Although quiescence has long been viewed as an inactive state, recent studies have shown that it is an actively monitored process that is influenced by environmental stimuli. Here, we provide a perspective of the quiescent state and discuss how this process is tuned by energy, nutrient and oxygen status, and the pathways that sense and transmit these signals. We not only highlight the governance of canonical regulators and signalling mechanisms that respond to changes in nutrient and energy status, but also consider the central significance of mitochondrial functions and cues as key regulators of nuclear gene expression. Furthermore, we discuss how reactive oxygen species and the associated redox processes, which are intrinsically linked to energy carbohydrate metabolism, also play a key role in the orchestration of quiescence.

Comprehensive insight into an amino acid metabolic network in postharvest horticultural products: a review

Amino acid (AA) metabolism plays a vital role in the central metabolism of plants. In addition to protein biosynthesis, AAs are involved in secondary metabolite biosynthesis, signal transduction, stress response, defense against pathogens, flavor formation, and so on. Besides these functions, AAs can be degraded into precursors or intermediates of the tricarboxylic acid cycle to substitute respiratory substrates and restore energy homeostasis, as well as directly acting as signal molecules or be involved in the regulation of plant signals to delay senescence of postharvest horticultural products (PHPs). AA metabolism and its role in plants growth have been clarified; however, only a few studies about their roles exist concerning the postharvest preservation of fruit and vegetables. This study reviews the potential functions of various AAs by comparing the difference in AA metabolism at the postharvest stage and then discusses the crosstalk of AA metabolism and energy metabolism, the target of rapamycin/sucrose nonfermenting-related kinase 1 signaling and secondary metabolism. Finally, the roles and effect mechanism of several exogenous AAs in the preservation of PHPs are highlighted. This review provides a comprehensive insight into the AA metabolism network in PHPs. © 2023 Society of Chemical Industry.

The Arabidopsis Target of Rapamycin (TOR) kinase regulates ammonium assimilation and glutamine metabolism

In eukaryotes, Target of Rapamycin (TOR) is a well conserved kinase that controls cell metabolism and growth in response to nutrients and environmental factors. Nitrogen (N) is an essential element for plants, and TOR functions as a crucial N and amino acid sensor in animals and yeast. However, knowledge on the connections between TOR and the overall N metabolism and assimilation in plants is still limited. In this study, we investigated the regulation of TOR in Arabidopsis (Arabidopsis thaliana) by the N source as well as the impact of TOR deficiency on N metabolism. Inhibition of TOR globally decreased ammonium uptake while triggering a massive accumulation of amino acids, such as Gln, but also of polyamines. Consistently, TOR complex mutants were hypersensitive to Gln. We also showed that the glutamine synthetase inhibitor glufosinate abolishes Gln accumulation resulting from TOR inhibition and improves the growth of TOR complex mutants. These results suggest that a high level of Gln contributes to the reduction in plant growth resulting from TOR inhibition. Glutamine synthetase activity was reduced by TOR inhibition while the enzyme amount increased. In conclusion, our findings show that the TOR pathway is intimately connected to N metabolism and that a decrease in TOR activity results in glutamine synthetase-dependent Gln and amino acid accumulation.

Cell surface receptor kinase FERONIA linked to nutrient sensor TORC signaling controls root hair growth at low temperature linked to low nitrate in Arabidopsis thaliana

Root hairs (RH) are excellent model systems for studying cell size and polarity since they elongate several hundred-fold their original size. Their tip growth is determined both by intrinsic and environmental signals. Although nutrient availability and temperature are key factors for a sustained plant growth, the molecular mechanisms underlying their sensing and downstream signaling pathways remain unclear. We use genetics to address the roles of the cell surface receptor kinase FERONIA (FER) and the nutrient sensing TOR Complex 1 (TORC) in RH growth. We identified that low temperature (10°C) triggers a strong RH elongation response in Arabidopsis thaliana involving FER and TORC. We found that FER is required to perceive limited nutrient availability caused by low temperature. FERONIA interacts with and activates TORC-downstream components to trigger RH growth. In addition, the small GTPase Rho of plants 2 (ROP2) is also involved in this RH growth response linking FER and TOR. We also found that limited nitrogen nutrient availability can mimic the RH growth response at 10°C in a NRT1.1-dependent manner. These results uncover a molecular mechanism by which a central hub composed by FER-ROP2-TORC is involved in the control of RH elongation under low temperature and nitrogen deficiency.