TOR-inhibitor insensitive-1 (TRIN1) regulates cotyledons greening in Arabidopsis

Cucumber (Cucumis sativus L.) translationally controlled tumor protein interacts with CsRab11A and promotes activation of target of rapamycin in response to Podosphaera xanthii

The target of rapamycin (TOR) kinase serves as a central regulator that integrates nutrient and energy signals to orchestrate cellular and organismal physiology in both animals and plants. Despite significant advancements having been made in understanding the molecular and cellular functions of plant TOR kinases, the upstream regulators that modulate TOR activity are not yet fully elucidated. In animals, the translationally controlled tumor protein (TCTP) is recognized as a key player in TOR signaling. This study reveals that two TCTP isoforms from Cucumis sativus, when introduced into Arabidopsis, are instrumental in balancing growth and defense mechanisms against the fungal pathogen Golovinomyces cichoracearum. We hypothesize that plant TCTPs act as upstream regulators of TOR in response to powdery mildew caused by Podosphaera xanthii in Cucumis. Our research further uncovers a stable interaction between CsTCTP and a small GTPase, CsRab11A. Transient transformation assays indicate that CsRab11A is involved in the defense against P. xanthii and promotes the activation of TOR signaling through CsTCTP. Moreover, our findings demonstrate that the critical role of TOR in plant disease resistance is contingent upon its regulated activity; pretreatment with a TOR inhibitor (AZD-8055) enhances cucumber plant resistance to P. xanthii, while pretreatment with a TOR activator (MHY-1485) increases susceptibility. These results suggest a sophisticated adaptive response mechanism in which upstream regulators, CsTCTP and CsRab11A, coordinate to modulate TOR function in response to P. xanthii, highlighting a novel aspect of plant-pathogen interactions.

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.

Overexpression of Nta-miR6155 confers resistance to Phytophthora nicotianae and regulates growth in tobacco (Nicotiana tabacum L.)

Tobacco black shank induced by Phytophthora nicotianae causes significant yield losses in tobacco plants. MicroRNAs (miRNAs) play a pivotal role in plant biotic stress responses and have great potential in tobacco breeding for disease resistance. However, the roles of miRNAs in tobacco plants in response to P. nicotianae infection has not been well characterized. In this study, we found that Nta-miR6155, a miRNA specific to Solanaceae crops, was significantly induced in P. nicotianae infected tobacco. Some of predicted target genes of Nta-miR6155 were also observed to be involved in disease resistance. To further investigate the function of miR6155 in tobacco during P. nicotianae infection, Nta-miR6155 overexpression plants (miR6155-OE) were generated in the Honghua Dajinyuan tobacco variety (HD, the main cultivated tobacco variety in China). We found that the Nta-miR6155 overexpression enhanced the resistance in tobacco towards P. nicotianae infections. The level of reactive oxygen species (ROS) was significantly lower and antioxidant enzyme activities were significantly higher in miR6155-OE plants than those in control HD plants during P. nicotianae infection. In addition, we found that the accumulation of salicylic acid and the expression of salicylic acid biosynthesis and signal transduction-related genes is significantly higher in miR6155-OE plants in comparison to the control HD plants. Furthermore, we found that Nta-miR6155 cleaved target genes NtCIPK18 to modulate resistance towards P. nicotianae in tobacco plants. Additionally, phenotypic analysis of miR6155-OE plants showed that Nta-miR6155 could inhibit the growth of tobacco by suppressing nitrogen uptake and photosynthesis. In conclusion, our findings indicated that miR6155 plays a crucial role in the regulation of growth and resistance against P. nicotianae infections in tobacco plants.

Target of rapamycin (TOR) plays a role in regulating ROS-induced chloroplast damage during cucumber (Cucumis sativus) leaf senescence

In cucumber production, delaying leaf senescence is crucial for improving cucumber yield and quality. Target of rapamycin (TOR) is a highly conserved serine/threonine protein kinase in eukaryotes, which can integrate exogenous and endogenous signals (such as cell energy state levels) to stimulate cell growth, proliferation, and differentiation. However, no studies have yet examined the regulatory role of TOR signalling in cucumber leaf senescence. In this study, the effects of TOR signalling on dark-induced cucumber leaf senescence were investigated using the TOR activator MHY1485 and inhibitor AZD8055 combined with transient transformation techniques. The results indicate that TOR responds to dark-induced leaf senescence, and alterations in TOR activity/expression influence cucumber leaf resistance to dark-induced senescence. Specifically, in plants with elevated TOR activity/expression, we observed reduced expression of senescence-related genes, less membrane lipid damage, decreased cell apoptosis, lower levels of reactive oxygen species production, and less damage to the photosynthetic system compared to the control. In contrast, in plants with reduced TOR activity/expression, we observed higher expression of senescence-related genes, increased membrane lipid damage, enhanced cell apoptosis, elevated levels of reactive oxygen species production, and more damage to the photosynthetic system. These comprehensive results underscore the critical role of TOR in regulating dark-induced cucumber leaf senescence. These findings provide a foundation for controlling premature leaf senescence in cucumber production and offer insights for further exploration of leaf senescence mechanisms and the development of more effective control methods.

Phosphoproteomics analysis of the effect of target of rapamycin kinase inhibition on Cucumis sativus in response to Podosphaera xanthii

Target of rapamycin (TOR) kinase is a conserved sensor of cell growth in yeasts, plants, and mammals. Despite the extensive research on the TOR complex in various biological processes, large-scale phosphoproteomics analysis of TOR phosphorylation events upon environmental stress are scarce. Powdery mildew caused by Podosphaera xanthii poses a major threat to the quality and yield of cucumber (Cucumis sativus L.). Previous studies concluded that TOR participated in abiotic and biotic stress responses. Hence, studying the underlying mechanism of TOR-P. xanthii infection is particularly important. In this study, we performed a quantitative phosphoproteomics studies of Cucumis against P. xanthii attack under AZD-8055 (TOR inhibitor) pretreatment. A total of 3384 phosphopeptides were identified from the 1699 phosphoproteins. The Motif-X analysis showed high sensitivity and specificity of serine sites under AZD-8055-treatment or P. xanthii stress, and TOR exhibited a unique preference for proline at +1 position and glycine at -1 position to enhance the phosphorylation response to P. xanthii. The functional analysis suggested that the unique responses were attributed to proteins related to plant hormone signaling, mitogen-activated protein kinase cascade signaling, phosphatidylinositol signaling system, and circadian rhythm; and calcium signaling- and defense response-related proteins. Our results provided rich resources for understanding the molecular mechanism of how the TOR kinase controlled plant growth and stress adaptation.

Network of the transcriptome and metabolomics reveals a novel regulation of drought resistance during germination in wheat

BACKGROUND AND AIMS

The North China Plain, the highest winter-wheat-producing region of China, is seriously threatened by drought. Traditional irrigation wastes a significant amount of water during the sowing season. Therefore, it is necessary to study the drought resistance of wheat during germination to maintain agricultural ecological security. From several main cultivars in the North China Plain, we screened the drought-resistant cultivar JM47 and drought-sensitive cultivar AK58 during germination using the polyethylene glycol (PEG) drought simulation method. An integrated analysis of the transcriptome and metabolomics was performed to understand the regulatory networks related to drought resistance in wheat germination and verify key regulatory genes.

METHODS

Transcriptional and metabolic changes were investigated using statistical analyses and gene-metabolite correlation networks. Transcript and metabolite profiles were obtained through high-throughput RNA-sequencing data analysis and ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry, respectively.

KEY RESULTS

A total of 8083 and 2911 differentially expressed genes (DEGs) and 173 and 148 differential metabolites were identified in AK58 and JM47, respectively, under drought stress. According to the integrated analysis results, mammalian target of rapamycin (mTOR) signalling was prominently enriched in JM47. A decrease in α-linolenic acid content was consistent with the performance of DEGs involved in jasmonic acid biosynthesis in the two cultivars under drought stress. Abscisic acid (ABA) content decreased more in JM47 than in AK58, and linoleic acid content decreased in AK58 but increased in JM47. α-Tocotrienol was upregulated and strongly correlated with α-linolenic acid metabolism.

CONCLUSIONS

The DEGs that participated in the mTOR and α-linolenic acid metabolism pathways were considered candidate DEGs related to drought resistance and the key metabolites α-tocotrienol, linoleic acid and l-leucine, which could trigger a comprehensive and systemic effect on drought resistance during germination by activating mTOR-ABA signalling and the interaction of various hormones.

TOR kinase, a GPS in the complex nutrient and hormonal signaling networks to guide plant growth and development

To survive and sustain growth, sessile plants have developed sophisticated internal signalling networks that respond to various external and internal cues. Despite the central roles of nutrient and hormone signaling in plant growth and development, how hormone-driven processes coordinate with metabolic status remains largely enigmatic. Target of rapamycin (TOR) kinase is an evolutionarily conserved master regulator that integrates energy, nutrients, growth factors, hormones, and stress signals to promote growth in all eukaryotes. Inspired by recent comprehensive systems, chemical, genetic, and genomic studies on TOR in plants, this review discusses a potential role of TOR as a 'global positioning system' that directs plant growth and developmental programs both temporally and spatially by integrating dynamic information in the complex nutrient and hormonal signaling networks. We further evaluate and depict the possible functional and mechanistic models for how a single protein kinase, TOR, is able to recognize, integrate, and even distinguish a plethora of positive and negative input signals to execute appropriate and distinct downstream biological processes via multiple partners and effectors.

Target of Rapamycin Regulates Photosynthesis and Cell Growth in Auxenochlorella pyrenoidosa

Auxenochlorella pyrenoidosa is an efficient photosynthetic microalga with autotrophic growth and reproduction, which has the advantages of rich nutrition and high protein content. Target of rapamycin (TOR) is a conserved protein kinase in eukaryotes both structurally and functionally, but little is known about the TOR signalling in Auxenochlorella pyrenoidosa. Here, we found a conserved ApTOR protein in Auxenochlorella pyrenoidosa, and the key components of TOR complex 1 (TORC1) were present, while the components RICTOR and SIN1 of the TORC2 were absent in Auxenochlorella pyrenoidosa. Drug sensitivity experiments showed that AZD8055 could effectively inhibit the growth of Auxenochlorella pyrenoidosa, whereas rapamycin, Torin1 and KU0063794 had no obvious effect on the growth of Auxenochlorella pyrenoidosaa. Transcriptome data results indicated that Auxenochlorella pyrenoidosa TOR (ApTOR) regulates various intracellular metabolism and signaling pathways in Auxenochlorella pyrenoidosa. Most genes related to chloroplast development and photosynthesis were significantly down-regulated under ApTOR inhibition by AZD8055. In addition, ApTOR was involved in regulating protein synthesis and catabolism by multiple metabolic pathways in Auxenochlorella pyrenoidosa. Importantly, the inhibition of ApTOR by AZD8055 disrupted the normal carbon and nitrogen metabolism, protein and fatty acid metabolism, and TCA cycle of Auxenochlorella pyrenoidosa cells, thus inhibiting the growth of Auxenochlorella pyrenoidosa. These RNA-seq results indicated that ApTOR plays important roles in photosynthesis, intracellular metabolism and cell growth, and provided some insights into the function of ApTOR in Auxenochlorella pyrenoidosa.

Target of Rapamycin Signaling Involved in the Regulation of Photosynthesis and Cellular Metabolism in Chlorella sorokiniana

Target of rapamycin (TOR) is a serine/threonine protein kinase that plays a central regulating role in cell proliferation, growth, and metabolism, but little is known about the TOR signaling pathway in Chlorella sorokiniana. In this study, a Chlorella sorokiniana DP-1 strain was isolated and identified, and its nutritional compositions were analyzed. Based on homologous sequence analysis, the conserved CsTOR protein was found in the genome of Chlorella sorokiniana. In addition, the key components of TOR complex 1 (TORC1) were present, but the components of TORC2 (RICTOR and SIN1) were absent in Chlorella sorokiniana. Pharmacological assays showed that Chlorella sorokiniana DP-1 was insensitive to rapamycin, Torin1 and KU0063794, whereas AZD8055 could significantly inhibit the growth of Chlorella sorokiniana. RNA-seq analysis showed that CsTOR regulated various metabolic processes and signal transduction pathways in AZD8055-treated Chlorella sorokiniana DP-1. Most genes involved in photosynthesis and carbon fixation in Chlorella sorokiniana DP-1 were significantly downregulated under CsTOR inhibition, indicating that CsTOR positively regulated the photosynthesis in Chlorella sorokiniana. Furthermore, CsTOR controlled protein synthesis and degradation by positively regulating ribosome synthesis and negatively regulating autophagy. These observations suggested that CsTOR plays an important role in photosynthesis and cellular metabolism, and provide new insights into the function of CsTOR in Chlorella sorokiniana.

TARGET OF RAPAMYCIN is essential for asexual vegetative reproduction in Kalanchoë

The unique mechanism by which leaf margin cells regain potency and then form a plantlet in Kalanchoë spp. remains elusive but involves organogenesis and embryogenesis in response to age, day length, nutrient availability, and drought stress. In light of this, we investigated whether TARGET OF RAPAMYCIN (TOR), a conserved protein kinase in eukaryotes that controls cell growth and metabolism in response to nutrient and energy availability, may regulate plantlet formation. Kalanchoë daigremontiana TOR (KdTOR) was expressed in the leaf margin at the site of plantlet initiation, in the early plantlet cotyledons, and in the root tip of the developed plantlet. Both chemical and genetic inhibition of TOR Kinase activity in Kalanchoë daigremontiana leaves disrupted plantlet formation. Furthermore, downregulation of KdTOR in transgenic plants led to wide-ranging transcriptional changes, including decreased K. daigremontiana SHOOTMERISTEMLESS and K. daigremontiana LEAFYCOTYLEDON1 expression, whereas auxin treatments induced KdTOR expression in the plantlet roots. These results suggest that the KdTOR pathway controls plantlet development in cooperation with auxin, organogenesis, and embryogenesis pathways. The ancient and highly conserved TOR Kinase therefore controls diverse and unique developmental pathways, such as asexual reproduction within the land plant lineage.

Contributions of TOR Signaling on Photosynthesis

The target of rapamycin (TOR) protein kinase is an atypical Ser/Thr protein kinase and evolutionally conserved among yeasts, plants, and mammals. TOR has been established as a central hub for integrating nutrient, energy, hormone, and environmental signals in all the eukaryotes. Despite the conserved functions across eukaryotes, recent research has shed light on the multifaceted roles of TOR signaling in plant-specific functional and mechanistic features. One of the most specific features is the involvement of TOR in plant photosynthesis. The recent development of tools for the functional analysis of plant TOR has helped to uncover the involvement of TOR signaling in several steps preceding photoautotrophy and maintenance of photosynthesis. Here, we present recent novel findings relating to TOR signaling and its roles in regulating plant photosynthesis, including carbon nutrient sense, light absorptions, and leaf and chloroplast development. We also provide some gaps in our understanding of TOR function in photosynthesis that need to be addressed in the future.

Target of rapamycin, PvTOR, is a key regulator of arbuscule development during mycorrhizal symbiosis in Phaseolus

Target of rapamycin (TOR) is a conserved central growth regulator in eukaryotes that has a key role in maintaining cellular nutrient and energy status. Arbuscular mycorrhizal (AM) fungi are mutualistic symbionts that assist the plant in increasing nutrient absorption from the rhizosphere. However, the role of legume TOR in AM fungal symbiosis development has not been investigated. In this study, we examined the function of legume TOR in the development and formation of AM fungal symbiosis. RNA-interference-mediated knockdown of TOR transcripts in common bean (Phaseolus vulgaris) hairy roots notably suppressed AM fungus-induced lateral root formation by altering the expression of root meristem regulatory genes, i.e., UPB1, RGFs, and sulfur assimilation and S-phase genes. Mycorrhized PvTOR-knockdown roots had significantly more extraradical hyphae and hyphopodia than the control (empty vector) roots. Strong promoter activity of PvTOR was observed at the site of hyphal penetration and colonization. Colonization along the root length was affected in mycorrhized PvTOR-knockdown roots and the arbuscules were stunted. Furthermore, the expression of genes induced by AM symbiosis such as SWEET1, VPY, VAMP713, and STR was repressed under mycorrhized conditions in PvTOR-knockdown roots. Based on these observations, we conclude that PvTOR is a key player in regulating arbuscule development during AM symbiosis in P. vulgaris. These results provide insight into legume TOR as a potential regulatory factor influencing the symbiotic associations of P. vulgaris and other legumes.

Sweet Modifications Modulate Plant Development

Plant development represents a continuous process in which the plant undergoes morphological, (epi)genetic and metabolic changes. Starting from pollination, seed maturation and germination, the plant continues to grow and develops specialized organs to survive, thrive and generate offspring. The development of plants and the interplay with its environment are highly linked to glycosylation of proteins and lipids as well as metabolism and signaling of sugars. Although the involvement of these protein modifications and sugars is well-studied, there is still a long road ahead to profoundly comprehend their nature, significance, importance for plant development and the interplay with stress responses. This review, approached from the plants' perspective, aims to focus on some key findings highlighting the importance of glycosylation and sugar signaling for plant development.

The tip of the iceberg: emerging roles of TORC1, and its regulatory functions in plant cells

Target of Rapamycin (TOR) is an evolutionarily conserved protein kinase that plays a central role in coordinating cell growth with light availability, the diurnal cycle, energy availability, and hormonal pathways. TOR Complex 1 (TORC1) controls cell proliferation, growth, metabolism, and defense in plants. Sugar availability is the main signal for activation of TOR in plants, as it also is in mammals and yeast. Specific regulators of the TOR kinase pathway in plants are inorganic compounds in the form of major nutrients in the soils, and light inputs via their impact on autotrophic metabolism. The lack of TOR is embryo-lethal in plants, whilst dysregulation of TOR signaling causes major alterations in growth and development. TOR exerts control as a regulator of protein translation via the action of proteins such as S6K, RPS6, and TAP46. Phytohormones are central players in the downstream systemic physiological TOR effects. TOR has recently been attributed to have roles in the control of DNA methylation, in the abundance of mRNA splicing variants, and in the variety of regulatory lncRNAs and miRNAs. In this review, we summarize recent discoveries in the plant TOR signaling pathway in the context of our current knowledge of mammalian and yeast cells, and highlight the most important gaps in our understanding of plants that need to be addressed in the future.

Control of ABA Signaling and Crosstalk with Other Hormones by the Selective Degradation of Pathway Components

A rapid and appropriate genetic and metabolic acclimation, which is crucial for plants' survival in a changing environment, is maintained due to the coordinated action of plant hormones and cellular degradation mechanisms influencing proteostasis. The plant hormone abscisic acid (ABA) rapidly accumulates in plants in response to environmental stress and plays a pivotal role in the reaction to various stimuli. Increasing evidence demonstrates a significant role of autophagy in controlling ABA signaling. This field has been extensively investigated and new discoveries are constantly being provided. We present updated information on the components of the ABA signaling pathway, particularly on transcription factors modified by different E3 ligases. Then, we focus on the role of selective autophagy in ABA pathway control and review novel evidence on the involvement of autophagy in different parts of the ABA signaling pathway that are important for crosstalk with other hormones, particularly cytokinins and brassinosteroids.

ABSCISIC ACID INSENSITIVE5 Interacts With RIBOSOMAL S6 KINASE2 to Mediate ABA Responses During Seedling Growth in Arabidopsis

ABSCISIC ACID INSENSITIVE5 (ABI5) is an important regulator of abscisic acid (ABA) signaling pathway involved in regulating seed germination and postgerminative growth in Arabidopsis, which integrates various phytohormone pathways to balance plant growth and stress responses. However, the transcriptional regulatory mechanisms underlying ABI5 and its interacting proteins remain largely unknown. Here, we found that inhibition of AtTOR could increase ABA content by up-regulating the expression levels of ABA biosynthesis-related genes, and thus activated the expression of ABA-responsive genes. Pharmacological assay showed that abi5-1 mutant was insensitive to TOR inhibitor AZD8055, whereas AtABI5 overexpression lines were hypersensitive to AZD8055 in Arabidopsis. Biochemical interaction assays demonstrated that ABI5 physically interacted with the RIBOSOMAL S6 KINASE2 (S6K2) protein in plant cell. S6K2 positively regulated ABA responses during seedling growth and upregulated ABA-responsive genes expression. Furthermore, genetic and physiological analysis indicated that AtS6K2 overexpression lines enhanced resistance to drought treatment while AtS6K2 interference lines were sensitive to drought. These results indicated that AtABI5 interacted with AtS6K2 to positively modulate ABA responses during seedling growth and shed light on a underlying mechanism of the crosstalk between TOR and ABA signaling pathways in modulating seedling growth in Arabidopsis.

TOR mediates the autophagy response to altered nucleotide homeostasis in an RNase mutant

The Arabidopsis thaliana T2 family endoribonuclease RNS2 localizes to the vacuole and functions in rRNA degradation. Loss of RNS2 activity impairs rRNA turnover and leads to constitutive autophagy, a process for degradation of cellular components. Autophagy is normally activated during environmental stress and is important for stress tolerance and homeostasis. Here we show that restoration of cytosolic purine nucleotide levels rescues the constitutive autophagy phenotype of rns2-2 seedlings, whereas inhibition of purine synthesis induces autophagy in wild-type seedlings. rns2-2 seedlings have reduced activity of the target of rapamycin (TOR) kinase complex, a negative regulator of autophagy, and this phenotype is rescued by addition of inosine to increase purine levels. Activation of TOR in rns2-2 by exogenous auxin blocks the enhanced autophagy, indicating a possible involvement of the TOR signaling pathway in the activation of autophagy in the rns2-2 mutant. Our data suggest a model in which loss of rRNA degradation in rns2-2 leads to a reduction in cytoplasmic nucleotide concentrations, which in turn inhibits TOR activity, leading to activation of autophagy to restore homeostasis.

Target of rapamycin regulates potassium uptake in Arabidopsis and potato

Potassium (K) is an essential inorganic nutrient needed by plants for their growth and development. The conserved target of rapamycin (TOR) kinase, a well-known nutrition signaling integrator, has crucial roles in regulating growth and development in all eukaryotes. Emerging evidence suggests that TOR is a core regulator of nutrient absorption and utilization in plants. However, it is still unclear whether there is a causative link between the TOR pathway and potassium absorption. Here, we show that the expression of some potassium transporters and channels was regulated by TOR, and the suppression of TOR activity significantly affected potassium uptake in Arabidopsis and potato. Furthermore, we discovered that a Type 2A phosphatase-associated protein of 46 kDa (TAP46), a direct TOR downstream effector, could interact with CBL-interacting protein kinase 23 (CIPK23) in Arabidopsis and potato. In Arabidopsis, the K⁺ channel AKT1 conducting K⁺ uptake was significantly regulated by Calcineurin B-like Calcium Sensor Protein 1/9 (CBL1/9)-CIPK23 modules. We found that the cbl1cbl9, cipk23 (lks1-2 and lks1-3), and akt1 mutants were more hyposensitive to the TOR inhibitor than the wild-type, and the TOR inhibitor induced the downregulation of K⁺ uptake rate in the wild-type more than in these mutants. In addition, the overexpression of CIPK23 could effectively restore the defects in growth and potassium uptake induced by the TOR inhibitors. Thus, our work reveals a link between TOR signaling and CIPK23 and provides new insight into the regulation of potassium uptake in plants.

Target of Rapamycin Signaling in Plant Stress Responses

Target of Rapamycin (TOR) is an atypical Ser/Thr protein kinase that is evolutionally conserved among yeasts, plants, and mammals. In plants, TOR signaling functions as a central hub to integrate different kinds of nutrient, energy, hormone, and environmental signals. TOR thereby orchestrates every stage of plant life, from embryogenesis, meristem activation, root, and leaf growth to flowering, senescence, and life span determination. Besides its essential role in the control of plant growth and development, recent research has also shed light on its multifaceted roles in plant environmental stress responses. Here, we review recent findings on the involvement of TOR signaling in plant adaptation to nutrient deficiency and various abiotic stresses. We also discuss the mechanisms underlying how plants cope with such unfavorable conditions via TOR-abscisic acid crosstalk and TOR-mediated autophagy, both of which play crucial roles in plant stress responses. Until now, little was known about the upstream regulators and downstream effectors of TOR in plant stress responses. We propose that the Snf1-related protein kinase-TOR axis plays a role in sensing various stress signals, and predict the key downstream effectors based on recent high-throughput proteomic analyses.

TARGET OF RAPAMYCIN signaling plays a role in Arabidopsis growth promotion by Azospirillum brasilense Sp245

Azospirillum brasilense colonizes plant roots and improves productivity, but the molecular mechanisms behind its phytostimulation properties remain mostly unknown. Here, we uncover an important role of TARGET OF RAPAMYCIN (TOR) signaling on the response of Arabidopsis thaliana to A. brasilense Sp245. The effect of the bacterium on TOR expression was analyzed in the transgenic line TOR/tor-1, which carries a translational fusion with the GUS reporter protein, and the activity of TOR was assayed thought the phosphorylation of its downstream signaling target S6K protein. Besides, the role of TOR on plant growth in inoculated plants was assessed using the ATP-competitive inhibitor AZD-8055. A decrease in growth of the primary root correlates with an improved branching and absorptive capacity via lateral root and root hair proliferation 6 days after transplant to different concentrations of the bacterium (10³ or 10⁵ CFU/mL). Bacterization increased the expression of TOR in shoot and root apexes and promoted phosphorylation of S6K 3 days after transplant. The TOR inhibitor AZD-8055 (1 μM) inhibited plant growth and cell division in root meristems and in lateral root primordia, interfering with the phytostimulation by A. brasilense. In addition, the role of auxin produced by the bacterium to stimulate TOR expression was explored. Noteworthy, the A. brasilense mutant FAJ009, impaired in auxin production, was unable to elicit TOR signaling to the level observed for the wild-type strain, showing the importance of this phyhormone to stimulate TOR signaling. Together, our findings establish an important role of TOR signaling for the probiotic traits elicited by A. brasilense in A. thaliana.

Target of Rapamycin Regulates Genome Methylation Reprogramming to Control Plant Growth in Arabidopsis

DNA methylation is an indispensable epigenetic modification that dynamically regulates gene expression and genome stability during cell growth and development processes. The target of rapamycin (TOR) has emerged as a central regulator to regulate many fundamental cellular metabolic processes from protein synthesis to autophagy in all eukaryotic species. However, little is known about the functions of TOR in DNA methylation. In this study, the synergistic growth inhibition of Arabidopsis seedlings can be observed when DNA methylation inhibitor azacitidine was combined with TOR inhibitors. Global DNA methylation level was evaluated using whole-genome bisulfite sequencing (WGBS) under TOR inhibition. Hypomethylation level of whole genome DNA was observed in AZD-8055 (AZD), rapamycin (RAP) and AZD + RAP treated Arabidopsis seedlings. Based on functional annotation and KEGG pathway analysis of differentially methylated genes (DMGs), most of DMGs were enriched in carbon metabolism, biosynthesis of amino acids and other metabolic processes. Importantly, the suppression of TOR caused the change in DNA methylation of the genes associated with plant hormone signal transduction, indicating that TOR played an important role in modulating phytohormone signals in Arabidopsis. These observations are expected to shed light on the novel functions of TOR in DNA methylation and provide some new insights into how TOR regulates genome DNA methylation to control plant growth.

Beyond the darkness: recent lessons from etiolation and de-etiolation studies

The state of etiolation is generally defined by the presence of non-green plastids (etioplasts) in plant tissues that would normally contain chloroplasts. In the commonly used dark-grown seedling system, etiolation is coupled with a type of growth called skotomorphogenesis. Upon illumination, de-etiolation occurs, marked by the transition from etioplast to chloroplast, and, at the seedling level, a switch to photomorphogenic growth. Etiolation and de-etiolation systems are therefore important for understanding both the acquisition of photosynthetic capacity during chloroplast biogenesis and plant responses to light-the most relevant signal in the life and growth of the organism. In this review, we discuss recent discoveries (within the past 2-3 years) in the field of etiolation and de-etiolation, with a particular focus on post-transcriptional processes and ultrastructural changes. We further discuss ambiguities in definitions of the term 'etiolation', and benefits and biases of common etiolation/de-etiolation systems. Finally, we raise several open questions and future research possibilities.

StABI5 Involved in the Regulation of Chloroplast Development and Photosynthesis in Potato

Abscisic acid (ABA) insensitive 5 (ABI5)—a core transcription factor of the ABA signaling pathway—is a basic leucine zipper transcription factor that plays a key role in the regulation of seed germination and early seedling growth. ABI5 interacts with other phytohormone signals to regulate plant growth and development, and stress responses in Arabidopsis, but little is known about the functions of ABI5 in potatoes. Here, we find that StABI5 is involved in the regulation of chloroplast development and photosynthesis. Genetic analysis indicates that StABI5 overexpression transgenic potato lines accelerate dark-induced leaf yellowing and senescence. The chlorophyll contents of overexpressed StABI5 transgenic potato lines were significantly decreased in comparison to those of wild-type Desiree potatoes under dark conditions. Additionally, the RNA-sequencing (RNA-seq) analysis shows that many metabolic processes are changed in overexpressed StABI5 transgenic potatoes. Most of the genes involved in photosynthesis and carbon fixation are significantly down-regulated, especially the chlorophyll a-b binding protein, photosystem I, and photosystem II. These observations indicate that StABI5 negatively regulates chloroplast development and photosynthesis, and provides some insights into the functions of StABI5 in regard to potato growth.

Autophagy: An Intracellular Degradation Pathway Regulating Plant Survival and Stress Response

Autophagy is an intracellular process that facilitates the bulk degradation of cytoplasmic materials by the vacuole or lysosome in eukaryotes. This conserved process is achieved through the coordination of different autophagy-related genes (ATGs). Autophagy is essential for recycling cytoplasmic material and eliminating damaged or dysfunctional cell constituents, such as proteins, aggregates or even entire organelles. Plant autophagy is necessary for maintaining cellular homeostasis under normal conditions and is upregulated during abiotic and biotic stress to prolong cell life. In this review, we present recent advances on our understanding of the molecular mechanisms of autophagy in plants and how autophagy contributes to plant development and plants' adaptation to the environment.

Target of Rapamycin Regulates Genome Methylation Reprogramming to Control Plant Growth in Arabidopsis

DNA methylation is an indispensable epigenetic modification that dynamically regulates gene expression and genome stability during cell growth and development processes. The target of rapamycin (TOR) has emerged as a central regulator to regulate many fundamental cellular metabolic processes from protein synthesis to autophagy in all eukaryotic species. However, little is known about the functions of TOR in DNA methylation. In this study, the synergistic growth inhibition of Arabidopsis seedlings can be observed when DNA methylation inhibitor azacitidine was combined with TOR inhibitors. Global DNA methylation level was evaluated using whole-genome bisulfite sequencing (WGBS) under TOR inhibition. Hypomethylation level of whole genome DNA was observed in AZD-8055 (AZD), rapamycin (RAP) and AZD + RAP treated Arabidopsis seedlings. Based on functional annotation and KEGG pathway analysis of differentially methylated genes (DMGs), most of DMGs were enriched in carbon metabolism, biosynthesis of amino acids and other metabolic processes. Importantly, the suppression of TOR caused the change in DNA methylation of the genes associated with plant hormone signal transduction, indicating that TOR played an important role in modulating phytohormone signals in Arabidopsis. These observations are expected to shed light on the novel functions of TOR in DNA methylation and provide some new insights into how TOR regulates genome DNA methylation to control plant growth.

The Importance of TOR Kinase in Plant Development

TARGET OF RAPAMYCIN (TOR) kinase has been recognised as a key developmental regulator in both plants and animals. Despite their distinct developmental programmes, all eukaryotes studied possess a functional TOR kinase, which integrates environmental and nutrient signals to direct growth and development. This is particularly important in plants, as they are sessile and must sense and respond to external signals to coordinate multicellular growth appropriately. Thus, the investigation of TOR is essential for plant developmental studies in the context of the resources available for growth. Recently, links have been shown between TOR and plant development from embryogenesis through to senescence, however more investigation is crucial to fully elucidate TOR function in each developmental process.

Reciprocal regulation of photosynthesis and mitochondrial respiration by TOR kinase in Chlamydomonas reinhardtii

While the role of TOR kinase in the chloroplast biogenesis and transcriptional regulation of photosynthesis is well documented in Arabidopsis, the functional relevance of this metabolic sensor kinase in chloroplast-mitochondria cross talk is unknown. Using Chlamydomonas reinhardtii as the model system, we demonstrate the role of TOR kinase in the regulation of chloroplast and mitochondrial functions: We show that TOR kinase inhibition impairs the maintenance of high ETR associated with PSII and low NPQ and inhibits efficient state transitions between PSII and PSI. While compromised photosynthetic functions are observed in TOR kinase inhibited cells, same conditions lead to augmentation in mitochondrial basal respiration rate by twofold and concomitantly a rise in ATP production. Interestingly, such upregulated mitochondrial functions in TOR-inhibited cells are mediated by fragmented mitochondria via upregulating COXIIb and downregulating Hxk1 and AOX1 protein levels. We propose that TOR kinase may act as a sensor that counter-regulates chloroplast versus mitochondrial functions in a normal C. reinhardtii cell.

TOR and SnRK1 signaling pathways in plant response to abiotic stresses: Do they always act according to the "yin-yang" model?

Plants are sessile photo-autotrophic organisms continuously exposed to a variety of environmental stresses. Monitoring the sugar level and energy status is essential, since this knowledge allows the integration of external and internal cues required for plant physiological and developmental plasticity. Most abiotic stresses induce severe metabolic alterations and entail a great energy cost, restricting plant growth and producing important crop losses. Therefore, balancing energy requirements with supplies is a major challenge for plants under unfavorable conditions. The conserved kinases target of rapamycin (TOR) and sucrose-non-fermenting-related protein kinase-1 (SnRK1) play central roles during plant growth and development, and in response to environmental stresses; these kinases affect cellular processes and metabolic reprogramming, which has physiological and phenotypic consequences. The "yin-yang" model postulates that TOR and SnRK1 act in opposite ways in the regulation of metabolic-driven processes. In this review, we describe and discuss the current knowledge about the complex and intricate regulation of TOR and SnRK1 under abiotic stresses. We especially focus on the physiological perspective that, under certain circumstances during the plant stress response, the TOR and SnRK1 kinases could be modulated differently from what is postulated by the "yin-yang" concept.

Mutation in the Arabidopsis regulatory-associated protein TOR 1B (RAPTOR1B) leads to decreased jasmonates levels in leaf tissue

The Target of Rapamycin (TOR) complex (TORC) regulates plant growth and development by modulation of metabolism in response to environmental cues. TORC contains in its core the TOR kinase and two interacting partners, namely; regulatory-associated partner of TOR (RAPTOR) and lethal with sec thirteen protein 8 (LST8). RAPTOR is described to act as a scaffold protein which recruits substrates for phosphorylation to the TOR kinase. In the current manuscript we show that mutation of Arabidopsis RAPTOR1B leads to significantly decreased levels of free jasmonic acid (JA), jasmonoyl-(L)-isoleucine (JA-Ile) as well as its biosynthetic precursor 12-oxo-phytodienoic acid (OPDA). Although raptor1b leaves showed decreased basic JA level compared to WT, the mutant responded substantially to wounding stress by producing the same amount of JA as WT. Furthermore, we could show that the chemical inhibition of TOR by AZD-8055 led to an opposite response. AZD-treated WT and raptor1b leaves accumulated high JA levels. These results strongly imply that the TOR signaling pathway is responding differentially to the inhibition of the TOR kinase as compared to the inhibition of the scaffold protein RAPTOR.

Targeting TOR signaling for enhanced lipid productivity in algae

Microalgae can produce large quantities of triacylglycerols (TAGs) and other neutral lipids that are suitable for making biofuels and as feedstocks for green chemistry. However, TAGs accumulate under stress conditions that also stop growth, leading to a trade-off between biomass production and TAG yield. Recently, in the model marine diatom Phaeodactylum tricornutum it was shown that inhibition of the target of rapamycin (TOR) kinase boosts lipid productivity by promoting TAG production without stopping growth. We believe that basic knowledge in this emerging field is required to develop innovative strategies to improve neutral lipid accumulation in oleaginous microalgae. In this minireview, we discuss current research on the TOR signaling pathway with a focus on its control on lipid homeostasis. We first provide an overview of the well characterized roles of TOR in mammalian lipogenesis, adipogenesis and lipolysis. We then present evidence of a role for TOR in controlling TAG accumulation in microalgae, and draw parallels between the situation in animals, plants and microalgae to propose a model of TOR signaling for TAG accumulation in microalgae.

TOR inhibitors: from mammalian outcomes to pharmacogenetics in plants and algae

Target of rapamycin (TOR) is a conserved eukaryotic phosphatidylinositol 3-kinase-related kinase that regulates growth and metabolism in response to environment in plants and algae. The study of the plant and algal TOR pathway has largely depended on TOR inhibitors first developed for non-photosynthetic eukaryotes. In animals and yeast, fundamental work on the TOR pathway has benefited from the allosteric TOR inhibitor rapamycin and more recently from ATP-competitive TOR inhibitors (asTORis) that circumvent the limitations of rapamycin. The asTORis, developed for medical application, inhibit TOR complex 1 (TORC1) more efficiently than rapamycin and also inhibit rapamycin-resistant TORCs. This review presents knowledge on TOR inhibitors from the mammalian field and underlines important considerations for plant and algal biologists. It discusses the use of rapamycin and asTORis in plants and algae and concludes with guidelines for physiological studies and genetic screens with TOR inhibitors.

A role for TOR signaling at every stage of plant life

From scientific advances in medical research to the plethora of anti-aging products available, our obsession with slowing the aging process and increasing life span is indisputable. A large research effort has been levied towards this perpetual search for the fountain of youth, yet the molecular mechanisms governing an organism's life span and the causes of aging are only beginning to emerge in animals and remain largely unanswered in plants. As one central pathway in eukaryotes controlling cell growth, development, and metabolism, the target of rapamycin (TOR) plays an evolutionarily conserved role in aging and the determination of life span. The modulation of TOR pathway components in a wide range of species, including the model plant Arabidopsis thaliana, has effects on life span. However, the mechanisms enabling some of the longest living species to endure, including trees that can live for millennia, have not been defined. Here, we introduce key TOR research from plant systems and discuss its implications in the plant life cycle and the broader field of life span research. TOR pathway functions in plant life cycle progression and life span determination are discussed, noting key differences from yeast and animal systems and the importance of 'omics' research for the continued progression of TOR signaling research.

The magic 'hammer' of TOR: the multiple faces of a single pathway in the metabolic regulation of plant growth and development

The target of rapamycin (TOR) pathway has emerged as a central hub synchronizing plant growth according to the nutrient/energy status and environmental inputs. Molecular mechanisms through which TOR promotes plant growth involve the positive regulation of transcription of cell proliferation-associated genes, mRNA translation initiation and ribosome biogenesis, to cite a few examples. Phytohormones, light, sugars, and sulfur have been found to broadly regulate TOR activity. TOR operates as a metabolic homeostat to fine-tune anabolic processes and efficiently enable plant growth under different circumstances. However, little is known about the multiple effectors that act up- and downstream of TOR. Here, we mainly discuss recent findings related to the TOR pathway in the context of plant metabolism and highlight areas of interest that need to be addressed to keep unravelling the intricate networks governing the regulation of TOR and its function in controlling biosynthetic growth.

Integration of nutrient, energy, light, and hormone signalling via TOR in plants

The multidomain target of rapamycin (TOR) is an atypical serine/threonine protein kinase resembling phosphatidylinositol lipid kinases, but retains high sequence identity and serves a remarkably conserved role as a master signalling integrator in yeasts, plants, and humans. TOR dynamically orchestrates cell metabolism, biogenesis, organ growth, and development transitions in response to nutrient, energy, hormone, and environmental cues. Here we review recent findings on the versatile and complex roles of TOR in transcriptome reprogramming, seedling, root, and shoot growth, and root hair production activated by sugar and energy signalling. We explore how co-ordination of TOR-mediated light and hormone signalling is involved in root and shoot apical meristem activation, proliferation of leaf primordia, cotyledon/leaf greening, and hypocotyl elongation. We also discuss the emerging TOR functions in response to sulfur assimilation and metabolism and consider potential molecular links and positive feedback loops between TOR, sugar, energy, and other essential macronutrients.

Mutations in the Arabidopsis ROL17/isopropylmalate synthase 1 locus alter amino acid content, modify the TOR network, and suppress the root hair cell development mutant lrx1

The growth and development of organisms must be tightly controlled and adjusted to nutrient availability and metabolic activities. The Target of Rapamycin (TOR) network is a major control mechanism in eukaryotes and influences processes such as translation, mitochondrial activity, production of reactive oxygen species, and the cytoskeleton. In Arabidopsis thaliana, inhibition of the TOR kinase causes changes in cell wall architecture and suppression of phenotypic defects of the cell wall formation mutant lrx1 (leucine-rich repeat extensin 1). The rol17 (repressor of lrx1 17) mutant was identified as a new suppressor of lrx1 that induces also a short root phenotype. The ROL17 locus encodes isopropylmalate synthase 1, a protein involved in leucine biosynthesis. Dependent on growth conditions, mutations in ROL17 do not necessarily alter the level of leucine, but always cause development of the rol17 mutant phenotypes, suggesting that the mutation does not only influence leucine biosynthesis. Changes in the metabolome of rol17 mutants are also found in plants with inhibited TOR kinase activity. Furthermore, rol17 mutants show reduced sensitivity to the TOR kinase inhibitor AZD-8055, indicating a modified TOR network. Together, these data suggest that suppression of lrx1 by rol17 is the result of an alteration of the TOR network.

A TOR-YAK1 signaling axis controls cell cycle, meristem activity and plant growth in Arabidopsis

TARGET OF RAPAMYCIN (TOR) is a conserved eukaryotic phosphatidylinositol-3-kinase-related kinase that plays a major role in regulating growth and metabolism in response to environment in plants. We performed a genetic screen for Arabidopsis ethylmethane sulfonate mutants resistant to the ATP-competitive TOR inhibitor AZD-8055 to identify new components of the plant TOR pathway. We found that loss-of-function mutants of the DYRK (dual specificity tyrosine phosphorylation regulated kinase)/YAK1 kinase are resistant to AZD-8055 and, reciprocally, that YAK1 overexpressors are hypersensitive to AZD-8055. Significantly, these phenotypes were conditional on TOR inhibition, positioning YAK1 activity downstream of TOR. We further show that the ATP-competitive DYRK1A inhibitor pINDY phenocopies YAK1 loss of function. Microscopy analysis revealed that YAK1 functions to repress meristem size and induce differentiation. We show that YAK1 represses cyclin expression in the different zones of the root meristem and that YAK1 is essential for TOR-dependent transcriptional regulation of the plant-specific SIAMESE-RELATED (SMR) cyclin-dependent kinase inhibitors in both meristematic and differentiating root cells. Thus, YAK1 is a major regulator of meristem activity and cell differentiation downstream of TOR.

Target of Rapamycin (TOR) Regulates the Expression of lncRNAs in Response to Abiotic Stresses in Cotton

TOR (Target of Rapamycin) kinase is an evolutionarily conserved protein kinase, which integrates stress-related cues with growth and metabolic outputs. Long non-coding RNAs (lncRNAs) play a vital role in the regulation of eukaryotic genes. However, little is known about TOR's function in regulating the expression of lncRNAs in plants. In this study, four putative homologous genes encoding the TOR protein were identified by utilizing the recently completed cotton genome. Pharmacological experiments with TOR inhibitor AZD8055 and on silencing GhTOR genes resulted in obvious cotton growth retardation, indicating the conserved role of TOR in plant growth. The expression pattern analyses in different tissues reveal that TOR may play a role in root development, and the transcript levels of TOR genes were changed under different stress conditions. Importantly, we found TOR may be a key player in regulating the expression of long non-coding RNAs (lncRNAs). A total of 10,315 lncRNAs were discovered in cotton seedlings, 90.7% of which were long intergenic ncRNAs. Moreover, we identified the differentially expressed lncRNAs, of which 296 were significantly upregulated and 105 were downregulated in TOR inactivated plants. GO and KEGG analyses of differentially expressed lncRNA neighboring genes reveal that these differentially expressed lncRNA-targeted genes are involved in many life processes, including stress response, glutathione, and ribosomes in cotton. A series of differentially expressed lncRNAs potentially involved in plant stress response was identified under TOR inhibition. Collectively, these results suggest that cotton TOR proteins may directly modulate the expression of putative stress-related lncRNAs and eventually play a potential role in the cotton stress response.

Inhibition of TOR Represses Nutrient Consumption, Which Improves Greening after Extended Periods of Etiolation

Upon illumination, etiolated seedlings experience a transition from heterotrophic to photoautotrophic growth. During this process, the tetrapyrrole biosynthesis pathway provides chlorophyll for photosynthesis. This pathway has to be tightly controlled to prevent the accumulation of photoreactive metabolites and to provide stoichiometric amounts of chlorophyll for its incorporation into photosynthetic protein complexes. Therefore, plants have evolved regulatory mechanisms to synchronize the biosynthesis of chlorophyll and chlorophyll-binding proteins. Two phytochrome-interacting factors (PIF1 and PIF3) and the DELLA proteins, which are controlled by the gibberellin pathway, are key regulators of this process. Here, we show that impairment of TARGET OF RAPAMYCIN (TOR) activity in Arabidopsis (Arabidopsis thaliana), either by mutation of the TOR complex component RAPTOR1B or by treatment with TOR inhibitors, leads to a significantly reduced accumulation of the photoreactive chlorophyll precursor protochlorophyllide in darkness but an increased greening rate of etiolated seedlings after exposure to light. Detailed profiling of metabolic, transcriptomic, and physiological parameters revealed that the TOR-repressed lines not only grow slower, they grow in a nutrient-saving mode, which allows them to resist longer periods of low nutrient availability. Our results also indicated that RAPTOR1B acts upstream of the gibberellin-DELLA pathway and its mutation complements the repressed greening phenotype of pif1 and pif3 after etiolation.

TOR signaling in plants: conservation and innovation

Target of rapamycin (TOR) is an evolutionarily conserved protein kinase that plays a central role in both plants and animals, despite their distinct developmental programs and survival strategies. Indeed, TOR integrates nutrient, energy, hormone, growth factor and environmental inputs to control proliferation, growth and metabolism in diverse multicellular organisms. Here, we compare the molecular composition, upstream regulators and downstream signaling relays of TOR complexes in plants and animals. We also explore and discuss the pivotal functions of TOR signaling in basic cellular processes, such as translation, cell division and stem/progenitor cell regulation during plant development.

The PP2A-interactor TIP41 modulates ABA responses in Arabidopsis thaliana

Modulation of growth in response to environmental cues is a fundamental aspect of plant adaptation to abiotic stresses. TIP41 (TAP42 INTERACTING PROTEIN OF 41 kDa) is the Arabidopsis thaliana orthologue of proteins isolated in mammals and yeast that participate in the Target-of-Rapamycin (TOR) pathway, which modifies cell growth in response to nutrient status and environmental conditions. Here, we characterized the function of TIP41 in Arabidopsis. Expression analyses showed that TIP41 is constitutively expressed in vascular tissues, and is induced following long-term exposure to NaCl, polyethylene glycol and abscisic acid (ABA), suggesting a role of TIP41 in adaptation to abiotic stress. Visualization of a fusion protein with yellow fluorescent protein indicated that TIP41 is localized in the cytoplasm and the nucleus. Abolished expression of TIP41 results in smaller plants with a lower number of rosette leaves and lateral roots, and an increased sensitivity to treatments with chemical TOR inhibitors, indicating that TOR signalling is affected in these mutants. In addition, tip41 mutants are hypersensitive to ABA at germination and seedling stage, whereas over-expressing plants show higher tolerance. Several TOR- and ABA-responsive genes are differentially expressed in tip41, including iron homeostasis, senescence and ethylene-associated genes. In yeast and mammals, TIP41 provides a link between the TOR pathway and the protein phosphatase 2A (PP2A), which in plants participates in several ABA-mediated mechanisms. Here, we showed an interaction of TIP41 with the catalytic subunit of PP2A. Taken together, these results offer important insights into the function of Arabidopsis TIP41 in the modulation of plant growth and ABA responses.

The TOR Pathway Is Involved in Adventitious Root Formation in Arabidopsis and Potato

In the agriculture industry, adventitious root formation is a core issue of plants asexual propagation. However, the underlying molecular mechanism of adventitious root formation is far beyond understanding. In present study we found that target of rapamycin (TOR) signaling plays a key role in adventitious root formation in potato and Arabidopsis. The core components of TOR complex including TOR, RAPTOR, and LST8 are highly conserved in potato, but the seedlings of potato are insensitive to rapamycin, implying FK506 Binding Protein 12 KD (FKBP12) lost the function to bridge the interaction of rapamycin and TOR in potato. To dissect TOR signaling in potato, the rapamycin hypersensitive potato plants (BP12-OE) were engineered by introducing yeast FKBP12 (ScFKBP12) into potato. We found that rapamycin can significantly attenuate the capability of adventitious root formation in BP12-OE potatoes. KU63794 (KU, an active-site TOR inhibitor) combined with rapamycin can more significantly suppress adventitious root formation of BP12-OE potato than the single treatments, such as KU63794 or rapamycin, indicating its synergistic inhibitory effects on potato adventitious root formation. Furthermore, RNA-seq data showed that many genes associated with auxin signaling pathway were altered when BP12-OE potato seedlings were treated with rapamycin + KU, suggesting that TOR may play a major role in adventitious root formation via auxin signaling. The auxin receptor mutant tir1 was sensitive to TOR inhibitors and the double and quadruple mutants including tir1afb2, tir1afb3, and tir1afb1afb2afb3 displayed more sensitive to asTORis than single mutant tir1. Consistently, overexpression of AtTIR1 in Arabidopsis and potato can partially overcome the inhibitory effect of asTORis and promote adventitious root formation under asTORis treatments. These observations suggest that TOR signaling regulates adventitious root formation by mediating auxin signaling in Arabidopsis and potato.

The crosstalk between Target of Rapamycin (TOR) and Jasmonic Acid (JA) signaling existing in Arabidopsis and cotton

Target of rapamycin (TOR) acts as an important regulator of cell growth, development and stress responses in most examined diploid eukaryotes. However, little is known about TOR in tetraploid species such as cotton. Here, we show that TORC1-S6K-RPS6, the major signaling components, are conserved and further expanded in cotton genome. Though the cotton seedlings are insensitive to rapamycin, AZD8055, the second-generation inhibitor of TOR, can significantly suppress the growth in cotton. Global transcriptome analysis revealed that genes associated with jasmonic acid (JA) biosynthesis and transduction were significantly altered in AZD8055 treated cotton seedlings, suggesting the potential crosstalk between TOR and JA signaling. Pharmacological and genetic approaches have been employed to get further insights into the molecular mechanism of the crosstalk between TOR and JA. Combination of AZD8055 with methyl jasmonate can synergistically inhibit cotton growth, and additionally JA levels were significantly increased when cotton seedlings were subjected to AZD8055. JA biosynthetic and signaling mutants including jar1, coi1-2 and myc2-2 displayed TOR inhibitor-resistant phenotypes, whereas COI1 overexpression transgenic lines and jaz10 exhibited sensitivity to AZD8055. Consistently, cotton JAZ can partially rescue TOR-suppressed phenotypes in Arabidopsis. These evidences revealed that the crosstalk between TOR and JA pathway operates in cotton and Arabidopsis.

Shaping plant development through the SnRK1-TOR metabolic regulators

SnRK1 (Snf1-related protein kinase 1) and TOR (target of rapamycin) are evolutionarily conserved protein kinases that lie at the heart of energy sensing, playing central and antagonistic roles in the regulation of metabolism and gene expression. Increasing evidence links these metabolic regulators to numerous aspects of plant development, from germination to flowering and senescence. This prompts the hypothesis that SnRK1 and TOR modify developmental programs according to the metabolic status to adjust plant growth to a specific environment. The aim of this review is to provide support to this hypothesis and to incentivize further studies on this topic by summarizing the work that establishes a genetic connection between SnRK1-TOR and plant development.

Brassinosteriod Insensitive 2 (BIN2) acts as a downstream effector of the Target of Rapamycin (TOR) signaling pathway to regulate photoautotrophic growth in Arabidopsis

The components of the target of rapamycin (TOR) signaling pathway have been well characterized in heterotrophic organisms from yeast to humans. However, because of rapamycin insensitivity, embryonic lethality in tor null mutants and a lack of reliable ways of detecting TOR protein kinase in higher plants, the key players upstream and downstream of TOR remain largely unknown in plants. Using engineered rapamycin-sensitive Binding Protein 12-2 (BP12-2) plants, the present study showed that combined treatment with rapamycin and active-site TOR inhibitors (asTORis) results in synergistic inhibition of TOR activity and plant growth in Arabidopsis. Based on this system, we revealed that TOR signaling plays a crucial role in modulating the transition from heterotrophic to photoautotrophic growth in Arabidopsis. Ribosomal protein S6 kinase 2 (S6K2) was identified as a direct downstream target of TOR, and the growth of TOR-suppressed plants could be rescued by up-regulating S6K2. Systems, genetic, and biochemical analyses revealed that Brassinosteriod Insensitive 2 (BIN2) acts as a novel downstream effector of S6K2, and the phosphorylation of BIN2 depends on TOR-S6K2 signaling in Arabidopsis. By combining pharmacological with genetic and biochemical approaches, we determined that the TOR-S6K2-BIN2 signaling pathway plays important roles in regulating the photoautotrophic growth of Arabidopsis.

Target of Rapamycin Is a Key Player for Auxin Signaling Transduction in Arabidopsis

Target of rapamycin (TOR), a master sensor for growth factors and nutrition availability in eukaryotic species, is a specific target protein of rapamycin. Rapamycin inhibits TOR kinase activity viaFK506 binding protein 12 kDa (FKBP12) in all examined heterotrophic eukaryotic organisms. In Arabidopsis, several independent studies have shown that AtFKBP12 is non-functional under aerobic condition, but one study suggests that AtFKBP12 is functional during anaerobic growth. However, the functions of AtFKBP12 have never been examined in parallel under aerobic and anaerobic growth conditions so far. To this end, we cloned the FKBP12 gene of humans, yeast, and Arabidopsis, respectively. Transgenic plants were generated, and pharmacological examinations were performed in parallel with Arabidopsis under aerobic and anaerobic conditions. ScFKBP12 conferred plants with the strongest sensitivity to rapamycin, followed by HsFKBP12, whereas AtFKBP12 failed to generate rapamycin sensitivity under aerobic condition. Upon submergence, yeast and human FKBP12 can significantly block cotyledon greening while Arabidopsis FKBP12 only retards plant growth in the presence of rapamycin, suggesting that hypoxia stress could partially restore the functions of AtFKBP12 to bridge the interaction between rapamycin and TOR. To further determine if communication between TOR and auxin signaling exists in plants, yeast FKBP12 was introduced into DR5::GUS homozygous plants. The transgenic plants DR5/BP12 were then treated with rapamycin or KU63794 (a new inhibitor of TOR). GUS staining showed that the auxin content of root tips decreased compared to the control. DR5/BP12 plants lost sensitivity to auxin after treatment with rapamycin. Auxin-defective phenotypes, including short primary roots, fewer lateral roots, and loss of gravitropism, occurred in DR5/BP12 plants when seedlings were treated with rapamycin+KU63794. This indicated that the combination of rapamycin and KU63794 can significantly inhibit TOR and auxin signaling in DR5/BP12 plants. These studies demonstrate that TOR is essential for auxin signaling transduction in Arabidopsis.

The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6

Protein translation is an energy consuming process that has to be fine-tuned at both the cell and organism levels to match the availability of resources. The target of rapamycin kinase (TOR) is a key regulator of a large range of biological processes in response to environmental cues. In this study, we have investigated the effects of TOR inactivation on the expression and regulation of Arabidopsis ribosomal proteins at different levels of analysis, namely from transcriptomic to phosphoproteomic. TOR inactivation resulted in a coordinated down-regulation of the transcription and translation of nuclear-encoded mRNAs coding for plastidic ribosomal proteins, which could explain the chlorotic phenotype of the TOR silenced plants. We have identified in the 5' untranslated regions (UTRs) of this set of genes a conserved sequence related to the 5' terminal oligopyrimidine motif, which is known to confer translational regulation by the TOR kinase in other eukaryotes. Furthermore, the phosphoproteomic analysis of the ribosomal fraction following TOR inactivation revealed a lower phosphorylation of the conserved Ser240 residue in the C-terminal region of the 40S ribosomal protein S6 (RPS6). These results were confirmed by Western blot analysis using an antibody that specifically recognizes phosphorylated Ser240 in RPS6. Finally, this antibody was used to follow TOR activity in plants. Our results thus uncover a multi-level regulation of plant ribosomal genes and proteins by the TOR kinase.