Biochem. J. (2015) 470, 1–14

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doi:10.1042/BJ20150505

REVIEW ARTICLE

TOR signalling in plants Daniel Rexin*†, Christian Meyer‡, Christophe Robaglia§ and Bruce Veit*1 *Forage Improvement, AgResearch, Private Bag 11008, Palmerston North 4442, New Zealand †Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand ‡Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech, Saclay Plant Sciences, F-78026 Versailles cedex, France §Laboratoire de Genetique et Biophysique des Plantes, CNRS-CEA-Aix Marseille Universit´e, UMR 7265 Biologie V´eg´etale et Microbiologie Environnementale, Facult´e des Sciences de Luminy, F-13009 Marseille, France

Although the eukaryotic TOR (target of rapamycin) kinase signalling pathway has emerged as a key player for integrating nutrient-, energy- and stress-related cues with growth and metabolic outputs, relatively little is known of how this ancient regulatory mechanism has been adapted in higher plants. Drawing comparisons with the substantial knowledge base around TOR kinase signalling in fungal and animal systems, functional aspects of this pathway in plants are reviewed. Both conserved and

divergent elements are discussed in relation to unique aspects associated with an autotrophic mode of nutrition and adaptive strategies for multicellular development exhibited by plants.

INTRODUCTION

plants whose growth and metabolism contrasts with that of other eukaryotes. Instead of purely consumption-based modes of nutrient and energy acquisition, plants feature a complex mixture of metabolic regulation. During seedling development, plants shift from animal-like heterotrophic utilization of seed reserves to an autotrophic light-driven metabolism made possible through the presence of the chloroplast. Vegetative growth presents further complexity, with reduced carbon and energy obtained through photosynthesis in green shoot tissues traded for inorganic mineral nutrients scavenged by roots. Cell growth and division feature complex, but incompletely understood, patterns of vesicle trafficking, with increases in cell size achieved through ongoing remodelling of a cellulose-based cell wall matrix coupled with turgor-driven expansion. To compensate for their lack of mobility, plants complement a high level of environmentally tuned physiological regulation with adaptive programmes of development. Complex and variable architectures are elaborated throughout the vegetative life of the plant through the activity of localized clusters of pluripotent cells known as meristems, with the fate of cells descended from these embryo-like tissues guided by a suite of signalling pathways that have no obvious animal equivalents. To provide context for a discussion of TOR signalling in plants, an overview of key findings from more intensively studied animal and fungal models is first provided. The functionality of key elements in plants is then considered with respect to both conserved and niche-specific growth and metabolic outputs.

Growth in living organisms is not a simple sum of available energy and nutrients, but instead represents a regulated output that supports complex survival and reproductive strategies.In eukaryotes, a key element for this regulation is TOR (target of rapamycin). Initially characterized as a growth-enabling protein kinase in single-celled yeast, TOR has since been found in all major eukaryote groups where it integrates growth and metabolism with combinations of cues relating to nutrients, energy and stress. This conserved activity and an array of associated elements suggest an ancient regulatory pathway that has been adapted to support a wide range of cellular and organismal growth strategies. Since the discovery of TOR more than 20 years ago, models for its functionality have progressed from it serving as a simple gatekeeper, enforcing nutrientdependent checkpoints on growth and cell division in single-celled yeast, to considerably more complex roles in multicellular species (Figure 1). Comparisons between animals and yeast highlight conserved elements both up- and down-stream of TOR that probably reflect ancestral roles of balancing cellular growth and metabolic homoeostasis, but also reveal additional players that integrate this set of core activities into multicellular programmes of development, many of which relate to cancer and metabolic disease. The present review focuses on TOR from the relatively unfamiliar, but potentially illuminating, perspective offered by

Key words: autotrophy, growth control, kinase, LST8, nutrition, plant signalling, plant, RAPTOR, signal transduction, target of rapamycin (TOR).

Abbreviations: AMPK, AMP-activated protein kinase; ATM, ataxia telangiectasia mutated; At, Arabidopsis thaliana ; 4E-BP, eIF4E-binding protein; eIF, eukaryotic initiation factor; FAT, FRAP/ATM/TRRAP2; FATC, C-terminal FAT; FKBP, FK506-binding protein; FRAP, FKBP–rapamycin-associated protein; FRB, FKBP12–rapamycin-binding domain; GPCR, G-protein-coupled receptor; HEAT, huntingtin/elongation factor 3/PP2A subunit/TOR1; LST8, lethal with sec-13 protein 8; Mip1, Mei2-interacting protein 1; mTOR, mammalian TOR; PA, phosphatidic acid; PDK, phosphoinositide-dependent kinase; PI3K, phosphoinositide 3-kinase; PIKK, phosphoinositide 3-kinase-related kinase; PLD, phospholipase D; PP2A, protein phosphatase 2A; PTEN, phosphatase and tensin homologue deleted on chromosome 10; PX, phox homology; RAG, Ras-related GTP-binding; RAPTOR, regulatory-associated protein of mTOR; RBR, RETINOBLASTOMA-RELATED; Rheb, Ras homologue enhanced in brain; RICTOR, rapamycin-insensitive companion of mTOR; RLK, receptor-like kinase; ROS, reactive oxygen species; RTK, receptor tyrosine kinase; S6K, ribosomal S6 kinase; Snf1, sucrose-non-fermenting 1; SnRK, Snf1-related kinase; TAP, 2A phosphatase-associated protein; TAV, transactivating/viroplasmin protein; TCTP, translationally controlled tumour protein; TOR, target of rapamycin; TORC, TOR complex; TRRAP, transformation/transcription domain-associated protein; TSC, tuberous sclerosis complex; ULK1, unc-51-like autophagy-activating kinase 1; Vps34, vacuolar protein sorting 34. 1 To whom correspondence should be addressed (email [email protected]).  c 2015 Authors; published by Portland Press Limited

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Figure 1 A graphic summary of the generic roles of TOR in co-ordinating cellular growth and metabolic outputs with extrinsic inputs

Largely unexplored features of upstream inputs are then surveyed in relation to both conserved and plant specific signal transduction pathways. More extensive background on TOR signalling is offered in a number of reviews, including several offering insights into plant-related aspects [1–9]. The emergence of TOR as a master integrator of growth and metabolism

Knowledge of TOR traces back to the mid-1970s with the characterization of a novel compound from Streptomyces hygroscopicus, a soil bacterium collected from Easter Island [10]. Named rapamycin, for the Polynesian name for Easter Island, Rapanui, this macrolide compound was first distinguished as an antifungal agent, but then later as a potent immunosuppressant and growth inhibitor. Insights into the cellular targets of rapamycin emerged later through analyses of yeast mutants resistant to its effects, with mutations compromising the interaction of rapamycin with a large protein that became known as target of rapamycin, or TOR [11–14]. Comparative studies group TOR into a family of serine/threonine kinases known as PIKKs (phosphoinositide 3-kinase-related kinases). Although the kinase domains of PIKKs share many conserved features and have overlapping responses to chemical inhibitors with that of their namesake, PI3K (phosphoinositide 3-kinase) [15], all members of this family show a preference towards protein rather than lipid substrates [16–18]. Orthologues of TOR [also referred to as FRAP for FKBP (FK506-binding protein)–rapamycin-associated protein, RAFT1 for rapamycin- and FK506-binding protein target 1, or RAPT1 for rapamycin target 1] are found in all major eukaryotic groups, including metazoans, mammals and plants, and can be recognized by a complex, but wellconserved, domain organization (Figure 2). A series of HEAT [named after huntingtin, elongation factor 3, a PP2A (protein phosphatase 2A) subunit and TOR1] repeats, which contain a ∼40-amino-acid sequence that forms two antiparallel α-helices, extend from the N-terminus and have been shown to mediate protein–protein interactions and membrane associations [19,20]. Downstream lie the ∼800 amino acids of the FAT domain [named after FRAP, ATM (ataxia telangiectasia mutated) and TRRAP2 (transformation/transcription domain-associated protein 2)] that consists of HEAT and TPR (tetratricopeptide repeat) repeats, and which, together with the FATC (C-terminal FAT) domains, contributes to protein interactions and kinase activation [21]. The FAT domain is followed by the FRB domain (for FKBP12– rapamycin-binding domain), which lies just upstream of the  c 2015 Authors; published by Portland Press Limited

kinase domain and is targeted by the inhibitory FKBP12– rapamycin complex. The conserved structural complexity of TOR kinase across eukaryotes suggests a well-entrenched functionality that is supported by a large body of genetic, biochemical and pharmacological evidence. In both fungi and animals, the highly specific inhibitory effects of rapamycin on TOR has revealed its role in channelling diverse signalling inputs into coherent growth responses. Early studies showed that many aspects of rapamycin-induced growth arrest mimic starvation responses, including G0 cell division arrest and down-regulation of protein synthesis [1,22]. Conversely, activation of TOR kinase by nutrients up-regulates the capacity for protein synthesis through phosphorylation of translation-related proteins, including S6K (ribosomal S6 kinase). This sensitivity of these and other responses to rapamycin has become a standard criterion for implicating TOR in complex signalling processes.

Modulation and targeting of TOR activity reflects its association in stable protein complexes

Although rapamycin initially seemed to offer a ‘silver bullet’ to selectively kill TOR activity to explore its functionality, subsequent analysis of TOR-deficient mutants in yeast revealed additional targets whose phosphorylation by TOR is resistant to rapamycin. This disparity later became understood with the discovery that TOR acts in two functionally distinct complexes: TORC1 and TORC2 [23,24]. The rapamycin-sensitive TORC1 is distinguished by the presence of RAPTOR (regulatory-associated protein of mTOR, where mTOR is mammalian TOR), which is thought to influence the activity of the kinase and its substrate specificity [25–29]. Similar to TOR, comparisons of the domain organization of RAPTOR proteins show a high degree of conservation across all major eukaryotic groups, including a RNC/C domain (for RAPTOR N-terminal conserved/putative caspase) and a series of HEAT and WD40 repeats (Figure 2). TORC2, by contrast, lacks RAPTOR, but contains other distinct accessory proteins, including RICTOR (rapamycin-insensitive companion of mTOR), which confers a distinct functionality on the complex [3,24]. TORC1 and TORC2 also feature a common element, LST8 (lethal with sec-13 protein 8), which like RAPTOR, has been described in all major eukaryotic groups [30–32] (Figure 2). Consisting primarily of seven WD40 repeat elements, the precise function of LST8 in TORC1 and TORC2 is not entirely clear. Recent structural studies of mammalian cellline-derived material suggest that LST8 may help to stabilize the organization of domains critical for full TOR kinase activity, and that the positioning of LST8 next to the FRB domain may effectively limit and/or facilitate access to the catalytic site of TOR [33]. This interpretation is in line with in vivo studies, where LST8 is required for nutrient- and RAPTOR-dependent activation of TOR [34,35]. Since their initial characterization in yeast, TORC1 and TORC2 have been shown to act in a largely conserved manner across fungal and animal species as regulatory switches that target specific growth-associated processes. TORC1 activity has been linked to regulation of protein synthesis, ribosome biogenesis, autophagy, lipid synthesis, mitochondrial metabolism and cell division [36]. By contrast, TORC2 outputs have been linked to actin cytoskeleton organization and cellular polarization [23,37,38]. Additional work has tied TORC2 activity to cell-cycle progression, anabolism and cell survival [39–42]. Studies in yeast also indicate partial redundancy between complexes for some functions [1,43].

TOR signalling in plants

Figure 2

Domain organization of TOR, RAPTOR and LST8 proteins in representative species

Figure 3

TOR expression during vegetative development

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(a) GUS activity in the leaf primordia of an Arabidopsis plant carrying an in-frame fusion of AtTOR with a GUS reporter gene. Strongest expression is seen in immature tissues with high rates of cell division. S, stem; L, leaf primordium; SAM, shoot apical meristem (image provided by R. Sormani). (b) Schematic diagram of a medial longitudinal cross-section of the shoot apical meristem showing a zone containing apical initials, with polarized patterns of cell division of their derivatives giving rise to leaf primordia and a layered tissue organization.

TOR-DEPENDENT PROCESSES IN PLANTS

Compared with animals and yeast, relatively little work has been done on TOR signalling in plants. Early suggestions for the pathway in plants came from studies that described insulin-like signalling responses, including rapamycin-sensitive phosphorylation of S6K, one of the most prominent targets of mTOR [44,45]. However, until recently, similar inhibitor-based strategies had not been investigated in the widely used model plant Arabidopsis, in part because of its relative insensitivity to rapamycin. Instead, more gene-focused analyses have been encouraged by extensive genome-based resources, including full genome sequence, nearly saturated indexed collections of insertion mutants, facile strategies for overexpression and RNAi-based inhibition, as well as extensive transcriptomic datasets. More recently, strategies for chemical inhibition of TOR have been developed. By one approach, Arabidopsis is sensitized to rapamycin through expression of native or heterologous forms of FKBP12, which rapamycin depends on for its inhibitory ternary interaction with TOR [46–49]. In a second approach, specific inhibitors of mTOR that block the ATP-binding pocket of

the kinase domain have been shown to act as potent inhibitors of growth in plants, but their specificity for TOR relative to related kinases has not been fully characterized in plants [48,50,51]. Growth-related TOR outputs in plants

The first functional analysis of TOR in Arabidopsis offered support for a growth-related function in plants, showing that embryos homozygous for likely null insertion alleles of AtTOR (Arabidopsis thaliana TOR) arrest at an early stage of development [52]. It was shown further that expression of a TOR:GUS reporter translational fusion was focused in actively growing vegetative tissues, suggesting a role for TOR in regulating post-embryonic growth as well as a significant degree of posttranscriptional regulation, given a more ubiquitous distribution of TOR transcripts (Figure 3). Subsequent studies have confirmed this role, with decreased TOR activity achieved by RNAi or chemical inhibition leading to reduced rates of both vegetative shoot and root growth and reductions in cell size [47,48,53–56]. By contrast, artificially increased TOR transcript levels have the  c 2015 Authors; published by Portland Press Limited

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opposite effect [47,53], suggesting that, similar to animals and fungi, TOR activity rather than nutrient levels can be limiting for growth. Reduced TOR activity is also linked to altered cell wall biosynthesis, decreased root hair development, altered patterns of branching, and decreases in the number of dividing cells in meristematic tissues [48–50,56,57]. Mutations disrupting Arabidopsis ROL5, which encodes a small G-protein belonging to the Ras superfamily, are hypersensitive to rapamycin and have defective cell walls, further supporting a role for TOR in contributing to cell wall integrity [49]. Although these reports document changes in cellular growth processes that track TOR activity, no consistent changes in tissue organization have been described.

Metabolic regulation by TOR in plants

Similar to animals and fungi [58], the influence of TOR activity on growth in plants is accompanied by complex changes in metabolism, with TOR activity promoting production of metabolites for immediate growth versus storage forms for longer-term growth and reproductive strategies. Support for this type of activity is seen in the metabolite and transcriptional profiles of Arabidopsis in which RNAi or chemical inhibition of TOR or mutation of the TORC1 element LST8 leads to accumulation of starch, TCA (tricarboxylic acid) cycle intermediates and triacylglycerols, and associated changes in intermediate metabolism gene expression profiles [47,48,53,55,59]. Similar responses are also seen with rapamycin treatment in the single-celled green algal model Chlamydomonas [60]. In both models, accumulation of storage metabolites mimics growth arrest responses triggered by nitrogen limitation, suggesting a role for TOR in rerouting of carbon when low levels of other classes of nutrient preclude growth. Changes in TOR activity are also seen to affect nitrogen metabolism with altered levels of glutamine, nitrate and genes associated with its metabolism, although some conflicting results between experiments have been attributed to different carbon nutrient input levels [55]. Similarly, inactivation of the TAP42 (2A phosphataseassociated protein of 42 kDa) plant homologue TAP46, a PP2A-associated protein and a substrate of TOR, leads to activation of enzymes involved in nitrogen remobilization, such as glutamine synthase 1, and to the inhibition of enzymes involved in nitrate assimilation [61]. Large increases in the levels of free amino acids observed with decreased TOR activity have been linked to decreased rates of protein synthesis, but may also reflect increased protein recycling through derepression of autophagy. Decreases in stress-induced production of galactinol and raffinose, which have been proposed to act as scavengers for ROS (reactive oxygen species) produced in actively growing tissues, have also been observed with inhibition of TOR activity [7,47,59]. Although these types of TOR-mediated metabolic responses have been linked to lifespan extension in animals [62,63], their relevance to plants remains unclear. If the transition to reproductive development is considered a sign of aging in plants, delays in flowering seen in plants with reduced TOR activity [47] might suggest parallels with animal systems. It should be noted, however, that the transition to reproductive development in plants is subject to multiple inputs, including nutrient levels, temperature and stress, all of which act to decouple flowering from a strictly chronologically determined output [64]. Moreover, it could be argued that certain responses to TOR limitation, such as cellular senescence and remobilization of nutrients [53,65], constitute an accelerating aging phenotype, albeit one manifest at an organand tissue-specific level.  c 2015 Authors; published by Portland Press Limited

Figure 4 Representation of TOR signalling components in Homo sapiens, Schizosaccharomyces pombe, Saccharomyces cerevisiae, Chlamydomonas reinhardtii and Arabidopsis thaliana

MOLECULAR ASPECTS OF TOR FUNCTIONALITY

The rapid increase in the number of full genome sequences across a diverse range of eukaryotes has promoted comparative approaches towards understanding TOR signalling. For plants, these comparisons highlight a considerable degree of conservation with certain TOR signalling elements that have been functionally characterized in other eukaryotic models, but also draw attention to missing elements, whose absence must be reconciled with the unique evolutionary history and life strategies of plants (Figure 4). Graphics that compare the functionality of these elements are presented in Figures 5(a) and 5(b).

TORC1 elements TOR kinase

Similar to animals and fungi, the family of PIKKs in plants to which TOR belongs includes ATM, ATR (ataxia telangiectasia- and Rad3-related), TRRAP and SMG (suppressor of morphogenesis in genitalia), all of which share conserved FAT, PI3K and FATC domains [18,66] and, which like TOR, appear to moderate cellular responses to extrinsically determined factors, including stress. The FATC domain, whose integrity in TOR is essential in both fungi and mammals, appears dispensable in Arabidopsis, with no clear phenotype associated with its absence [57]. In this same study, more severely disrupted alleles that also lack the kinase domain could be rescued by

TOR signalling in plants

Figure 5

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Comparison of mammalian and plant TOR signalling pathways

(a) Mammalian pathway. (b) Plant pathway. Hypothetical links are indicated by dotted lines. For abbreviations, see the text.

transgenic expression of the kinase domain alone, suggesting the potential for autonomous kinase domain function, or intragenic complementation between partial proteins. Plants exhibit further distinctions in terms of the interaction of TOR to form complexes with accessory proteins. Despite the essential nature of TORC2 in animals and fungi, no equivalents for TORC2-specific proteins, such as RICTOR, are apparent in plant genome databases. Given the prominent role of TORC2 in supporting polarized growth in these other groups, its absence from plants could be linked to divergent strategies for driving cellular growth, which in plants feature distinct cytoskeletal dynamics and turgor-driven cell expansion. By contrast, TORC1 function in plants is well supported, with clear equivalents of RAPTOR evident [67,68] and evidence for interaction with canonical downstream targets [69]. If TOR does play a role in supporting polarized growth in plants, it might rely on mechanisms similar to those recently described in yeast in which cytoskeletal elements mediate regulation of TORC1 [70,71] or could alternatively rely on still unknown novel types of TOR complex, as suggested by recent precedents in protozoan models [72,73].

Raptor

Some evidence for specialization between duplicate forms of RAPTOR in Arabidopsis is seen in the gene pair AtRAPTOR3g and AtRAPTOR5g [67,68]. Moderate levels of AtRAPTOR3g transcripts can be detected across most vegetative tissues, with plants homozygous for disrupted forms showing a range of growth defects, including sporadic embryonic arrest, moderately decreased rates of vegetative growth, increased branching and delayed flowering. RAPTOR5g expression, by contrast, is more limited in vegetative tissues, with the highest levels in specific gametogenic and embryonic tissues. AtRAPTOR5g has no obvious loss-of-function phenotype by itself, but double mutants with

AtRAPTOR3g loss-of-function alleles grow very slowly (A. Larking, D. Rexin and B. Veit, unpublished work). If these double mutants represent null alleles for RAPTOR, they would indicate a capacity for TORC1-independent growth that can be contrasted with the animal and fungal systems, where TORC1 is essential for survival.

LST8

In addition to the TORC1-specific RAPTOR, plants harbour genes that encode LST8-like proteins, whose counterparts are found in both TORC1 and TORC2 of fungi and metazoans. Before its identification as a TORC component, LST8 was shown in yeast to support trafficking of amino acid permeases from the Golgi apparatus to the plasma membrane [30]. Further work showed that LST8 is essential for TOR-mediated RTG (repression of retrograde) signalling [31]. In response to mitochondrial stress, TOR-mediated phosphorylation of transcription factors Rtg1/3p and Gln3p is relaxed, leading to compensatory changes in carbon and nitrogen metabolism [31,32]. LST8-like proteins from both Arabidopsis [59] and the green alga Chlamydomonas [74] share the same well-conserved domain organization as seen in non-photosynthetic counterparts, can complement LST8-deficient yeast and show specific binding with TOR. Chlamydomonas LST8 and TOR are found together in high-molecular-mass membrane-associated complexes, with GFP-tagged LST8 localizing to motile endosome-like particles in Arabidopsis. Changes in growth and metabolism associated with deficiency of LST8 in Arabidopsis are complex. Similar to RAPTORdeficient plants, plants deficient for LST8 are viable, but grow more slowly, branch more frequently and display characteristic alterations in metabolite profiles. Unlike the RAPTOR-deficient plants, however, LST8-deficient plants show growth defects that are strongly exacerbated in long days, suggesting a specific  c 2015 Authors; published by Portland Press Limited

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role for LST8 in mediating metabolic adjustments to changes in photosynthetic inputs. The possibility that photoperioddependent phenotypes of LST8-deficient plants reflect a TORindependent activity of LST8 is suggested by precedents in Schizosaccharomyces pombe, where mutations in the LST8 counterpart lead to a suite of changes generally not tied to reductions in TOR activity, including diploidization, genome instability and decreased tubulin levels [75]. Alternatively, these light-dependent phenotypes might reflect a specific role for LST8 in supporting a link between the chloroplast outputs and TOR, analogous to its role in supporting retrograde signalling with the mitochondrion [31].

DOWNSTREAM TARGETS AND PROCESSES OF TOR KINASE IN PLANTS Translational control

Similar to animals and fungi, plants undergo profound changes in their translational profiles [76] as part of growth and metabolic regulation, with TOR acting at several levels to regulate translational outputs. Increases in the capacity for protein synthesis that accompany the onset of anabolic growth processes are reflected in increases in rRNA levels that closely track levels of TOR activity [57]. Similar to what has been reported in yeast [77] and mammalian species [78], ChIP experiments suggest binding of the kinase domain of TOR with promoter regions of rRNA genes, though it is unclear whether this is a direct interaction. Additional changes in translational outputs in response to decreased TOR levels are also reflected in reduced loading of polysomes [51,53,79]. The best-supported examples of TOR-mediated translational control in plants are seen with S6K, which, like its animal counterparts, is a well-characterized substrate of TOR. The majority of studies on plant S6K have exploited Arabidopsis, which contains two closely related forms, AtS6K1 and AtS6K2. Early work demonstrated that the ribosomal protein S6 is efficiently phosphorylated by AtS6K [80] and that AtS6K2 could substitute for human p70S6K in human cell lines with respect to S6 phosphorylation [45]. Later work showed that, similar to the case in animals, S6K plays significant roles in mediating growth responses in plants, including those involving the growthpromoting hormones auxin and cytokinin [81–83]. Like many other members of the AGC kinase family to which it belongs, plant S6K is also a target for PDK1 (phosphoinositide-dependent kinase 1)-mediated phosphorylation [84] that contributes to full activation of S6K. Several studies have confirmed that chemical inhibition or knockdown of TOR gene activity leads to decreased S6K phosphorylation at defined sites equivalent to their animal counterparts [48,51,56,79,85]. Additional support for TORmediated phosphorylation of S6K is seen in studies demonstrating physical interactions between TOR, RAPTOR and S6K proteins in transient overexpression assays in Nicotiana benthamiana. Kinase activity of immunoprecipitated AtS6K is decreased by osmotic stress in a manner that is sensitive to RAPTOR and TOR stoichiometry [69], suggesting that TORC1-mediated signalling plays a role in this regulation. Studies in whole Arabidopsis plants reinforce this view, suggesting that TOR-dependent downregulation of S6K activity is integral to adaptive osmotic stress responses [53,69]. Similar to animal [86] and fungal [1] systems, TOR-activated S6K contributes to translation-mediated growth responses in plants by several mechanisms. In both animals [87] and plants  c 2015 Authors; published by Portland Press Limited

[48,69], TOR-activated S6K exhibits increased kinase activity towards ribosomal protein S6. Recent work in mouse models suggests that activated S6 contributes to growth through upregulating transcription of mRNAs for proteins that contribute to ribosome biogenesis [88]. In Arabidopsis, growth is tightly coupled to S6 levels [47,89]. TOR-activated S6K in plants has also been show to affect translation by promoting reinitiation of translation of mRNAs that contain multiple ORFs. Cauliflower mosaic virus-encoded TAV (transactivating/viroplasmin protein) promotes TOR-dependent activation of S6K, which in turn phosphorylates eIF3H (eukaryotic initiation factor 3H) to stabilize the association of the ribosome with mRNA upon transiting stop codons, thus enabling translational reinitiation at downstream ORFs that are essential for viral replication [79]. A subsequent study [51] suggests that this form of TOR-mediated translational control may also be relevant to a large number of plant mRNAs in which small ORFs (μORFs) lie upstream of the primary ORF [90,91].

Other post-transcriptional mechanisms

In animal models, two factors associated with newly processed RNAs, the splicing factor AS2/ASF and the exon junction complex-associated SKAR (S6K1 ALY-REF-like), both contribute to translational outputs in a TOR-dependent manner. Although equivalent forms of regulation remain undefined in plants, many associated elements are well-conserved [92]. Similarly, it is unclear whether plants have an equivalent of 4E-BP (eIF4E-binding protein), a well-defined target of mTOR, that, when phosphorylated, is released from eIF4E to upregulate m7 GTP cap-dependent translation initiation [93]. Plants nevertheless present clear examples of cap-dependent translation that is supported by elements shared with animals and fungi. The possible existence of widely diverged or convergent forms of 4E-BP in plants is suggested by precedents in yeast [94,95] as well as TOR-dependent phosphorylation of human 4E-BP when transfected into plant protoplasts [48]. Novel forms of TORC1-mediated regulation that are likely to have relevance in plants have emerged from analyses of factors that regulate the transition from mitotic to meiotic development in S. pombe, which offered the first functional analysis of a RAPTOR-like protein in eukaryotes, but also led to the identification of a novel class of targets for direct phosphorylation by TOR. Genetic screens for mutations that suppressed a dominant form of Mei2p, a meiosis-promoting RNA-binding protein, recovered truncated forms of Mip1 (Mei2-interacting protein 1) [29,96]. Previous studies had shown that Mei2p regulates meiosis via a novel mechanism that requires its physical interaction with Mip1 as well as specific non-coding polyadenylated transcripts [96–98]. Mip1 was also shown to be essential for mitotic growth, which subsequently became understood in terms of its equivalence to the TORC1 element RAPTOR. More recent analyses indicate that Mei2p is a direct substrate for phosphorylation by TOR, which targets Mei2p for ubiquitin-mediated turnover, thereby preventing the onset of determinant meiotic development in favour of continued mitotic growth [99]. Although no obvious counterparts for Mei2p are found in animals, plants harbour a diverse family of Mei2-like genes that contribute to both vegetative and reproductive development. One of these, first defined by the TERMINAL EAR1 gene of maize [100], but later characterized in other plants [101–105], is expressed in meristematic regions where it is thought to promote more indeterminate patterns of growth. A second distinct group of Mei2-like genes are expressed more widely during vegetative

TOR signalling in plants

and reproductive growth, and have been shown to contribute to both meiotic processes and the subsequent mitotic growth of resulting haploid gametophytes [106–108]. Physical interactions between AtRAPTOR3g and specific regions of the Mei2-like protein AML1 (Arabidopsis Mei2-like) have been shown in yeast two-hybrid studies [109].

Regulation of PP2A

Similar to other eukaryotes, regulation of protein phosphatase activity enables another set of TORC1-dependent outputs in plants. This mode of regulation was first described in yeast with the characterization of TAP42, which, when phosphorylated by TORC1, binds to PP2A to regulate its activity. Like yeast and animals, plants rely on PP2A to regulate a diverse range of processes involving serine/threonine-phosphorylation-dependent changes in protein activity [110]. Initial evidence that plants use a similar mechanism was obtained with two-hybrid screens against PP2A, which yielded a gene encoding a TAP42-like protein that was termed TAP46 [111]. RNAi-mediated knockdown of TAP46 produces a range of responses that mimic those obtained by inhibition of TOR activity, including reduced translation, autophagy and nitrogen remobilization [61]. These data, together with experiments showing TOR-dependent phosphorylation of TAP46 in vitro, support the view that the protein is a direct target of TORC1. It is unclear whether the association of TAP46 inhibits or activates PP2A, and whether TAP46 plays a role in targeting this activity to particular substrates, as has been suggested in yeast.

Autophagy

Genomic and functional analyses suggest that autophagy relies on mechanisms that are largely conserved across eukaryotes. In yeast and mammals, TOR is thought to inhibit autophagy by phosphorylation of ATG13, blocking its activation of ATG1, a kinase whose activity promotes formation of autophagosomes. More recently, a second TOR-regulatory input that restricts autophagy has been described in which ULK1 (unc-51-like autophagy-activating kinase 1), the mammalian equivalent of ATG1, is also phosphorylated by TOR [112– 114]. This modification of ULK1 effectively blocks an activating phosphorylation by AMPK (AMP-activated protein kinase). As activation of AMPK typically reflects reduced energy status, TOR mediated phosphorylation of ULK1 would provide a means for TOR to temper the activation of autophagy responses triggered by reduced energy levels. Functional counterparts to key autophagy elements have been described in both the single-celled alga Chlamydomonas as well as Arabidopsis [54,115,116], and results indicate that autophagosome formation is controlled in a similar manner via TOR and AMPK [117]. It was demonstrated further that TOR-dependent regulation of autophagy occurred either downstream or independently of ROS-related signalling inputs that are often associated with stress [54]. mRNA transcription

Although TOR activity is likely to influence transcriptional processes in plants by a variety of mechanisms, two novel and relatively direct mechanisms have been described with conserved features that suggest the possibility of animal equivalents. By one mechanism, S6K-mediated phosphorylation of the conserved RBR1 (RETINOBLASTOMA-RELATED 1) protein triggers its nuclear localization where it inhibits the activity of E2F transcription factors, and thus represses expression of cell-cycle-

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promoting genes [83]. This activity would provide a means to explain TOR-dependent increases in cell size promoted by nutrient-rich conditions. Studies point towards a novel and more direct mechanism by which TOR may regulate cell division via phosphorylation of E2Fa. Physiological experiments suggest that many aspects of growth triggered by glucose depend on TOR activity [56], with the transcriptional activation of specific cell division-related targets by E2Fa playing a key role [48]. Additional experiments suggest that E2Fa is a direct substrate of TOR, showing that it can be phosphorylated in vitro with TOR-containing immunoprecipitates, with analyses of non-phosphorylatable forms of E2Fa in planta suggesting that this TOR-mediated phosphorylation of E2Fa promotes cell proliferation. UPSTREAM REGULATORY INPUTS FOR TOR IN PLANTS

In contrast with clear-cut examples of growth-related output mechanisms for TOR that appear to be broadly conserved across eukaryotic groups, upstream inputs appear to be more varied. Some degree of conservation could be expected for mechanisms that emerged early in common single-celled ancestors for tuning TOR outputs in response to generic inputs such as energy, nutrient and stress. By contrast, less similarity would be expected for mechanisms that arose later to communicate taxon-specific inputs, including those supporting distinct modes of nutrient acquisition, as well as separately evolved programmes for multicellular development. Further differences would probably reflect distinct repertoires of potential signalling elements between newly diverged major eukaryotic taxa that might support emerging forms of regulation. From this perspective, comparisons highlight a number of distinctions between taxa in how TOR activity is regulated. Uncertain links for a conserved energy/stress-response module

Snf1 (sucrose-non-fermenting 1)/AMPK represents an ancient regulatory module that communicates cellular energy levels and associated forms of stress to downstream targets, including TOR [118]. In well-characterized fungal and animal systems, Snf1/AMPK kinases are activated by low ratios of ATP to ADP and AMP, leading to the regulation of a large number of downstream targets, including the repression of TOR. Plants have clear counterparts of Snf1/AMPK [119–121], e.g. SnRK1 (Snf1-related kinase 1), which have a conserved heterotrimeric organization, can complement yeast Snf1 and show related target specificities, but their link with TOR remains largely undefined [6]. Some type of SnRK1-mediated linkage between energy and TOR activity in plants would be consistent with the activation of TOR observed in response to light or sugar, with both blocked by inhibitors of mitochondrial ATP production [48]. In animals and many fungi, the SnRK1-mediated link between energy and TOR activity is partly indirect, mediated by the interaction of TSC1/2 (tuberous sclerosis complex 1/2) with Rheb (Ras homologue enhanced in brain) [122]. Phosphorylation of TSC1/2 by SNF1/AMPK in response to low energy stress upregulates the GTPase-activating activity of TSC1/2, which in turn converts a GTP-bound form of Rheb, a potent activator of TOR, to an inactive GDP-bound form. This indirect mode of regulation enables the integration of additional inputs, such as growth-factor-dependent phosphorylation of TSC1/2, which counteracts the AMPK-dependent repressive activity of TSC1/2 towards TOR. However, as plants lack any clear counterpart of TSC1/2 or Rheb, they may rely on other types of linkages such as  c 2015 Authors; published by Portland Press Limited

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that described in mammalian systems in which AMPK represses TOR activity directly through an inhibitory phosphorylation of RAPTOR [28]. A similar lack of clear functional counterparts of Rheb and TSC1/2 in budding yeast, but not fission yeast, suggests that the activation of TOR by Rheb represents part of a regulatory module that has co-evolved with TSC1/2 [123]. The possibility that other types of GTPase might provide a Rheb-like activity to activate TOR has also been suggested by the analysis of TCTP (translationally controlled tumour protein), a GEF (guanine-nucleotide-exchange factor) that is common to most eukaryotic groups and whose activities have been linked to TOR outputs. In Drosophila, experiments suggest that TCTP is necessary for Rheb-dependent TORC1 outputs [124]. However, subsequent studies have cast doubt on this model, showing a lack of functional interaction between TCTP and Rheb by several approaches [125,126]. In plants, which lack clear equivalents of Rheb, disruption or knockdowns of an Arabidopsis TCTP-like protein nevertheless show a range of growth-related phenotypes similar those reported for TOR-deficient plants [127]. More recent studies have extended these results, with complementation of function shown between Arabidopsis and Drosophila TCTPs [128]. Yeast two-hybrid analysis revealed specific binding of AtTCTP with a subclass of RAB GTPases, consistent with models in which non-Rheb GTPases may act in parallel or independently of Rheb to influence TOR activity.

Regulation of TOR activity by nutrients

Early work in yeast revealed rapamycin-sensitive TOR outputs for a diverse range of nutrient inputs, including carbon, nitrogen and phosphorus [1], but underlying mechanisms remain largely obscure, especially in plants. Unlike animals and many fungi where nutrients are acquired in more complex organic forms, plants rely largely on a tightly regulated uptake and assimilation of simple forms directly from the environment [129]. Through ATP and reducing power obtained from light, carbon dioxide absorbed from the atmosphere is converted into sugars that serve both as starting material for synthesis of biomolecules and as a mobile energy currency. Nitrogen is typically secured through active uptake of inorganic forms via roots. In favourable light environments, inorganic forms, such as nitrate, are transported to shoot tissues and then converted into glutamine with energy and reductant from light-harvesting reactions. When light is more limited, the assimilation and conversion of nitrogen into organic forms depends on energy provided by the regulated utilization of sugar and starch reserves. TOR-dependent growth in plants is tightly coupled to nitrogen availability, with the growth-promoting effects of inorganic nitrogen largely blocked by rapamycin [47]. Whether this TORdependent growth reflects a direct response to inorganic nitrogen rather than organic derivatives in plants is unclear. Unlike animals, both plants and yeasts can use inorganic nitrogen to synthesize organic forms such as amino acids. In yeast, the regulation of TOR activity in response to nitrogen signal plays a central role in controlling the assimilation of nitrogen in the form of ammonium [1], but equivalent TOR-dependent mechanisms in plants are not well defined. In both animals and yeast, activation of TOR can also be achieved by activation of RAG (Ras-related GTPbinding) proteins by organic forms of nitrogen. In mammalian models, the amino-acid-dependent binding of RAGs to RAPTOR promotes the localization of TORC1 to a lysosomal domain, where activation by Rheb is thought to occur [130]. In yeast, which contain vacuoles in place of lysosomes, a similar regulatory mechanism has been identified at the surface of yeast vacuoles [1],  c 2015 Authors; published by Portland Press Limited

but it remains unclear whether a similar regulatory mechanism is conserved in the green lineage. No obvious counterparts to RAG/GTR GTPases can be found in full genome sequences from plants (B. Veit, unpublished work). Like Rheb, RAG/GTR GTPases group within the Ras subfamily of the Ras GTPase superfamily, which appears absent from plants [131]. Localization requirements for TOR activation in plants that would offer further tests of a RAG/GTR-like mechanism are also not well defined. Alternative mechanisms defined in human cell culture and yeast models [132–134], in which amino acids activate TOR via the class III PI3K Vps34 (vacuolar protein sorting 34), also remain untested. Recent work in yeast has also highlighted a role for glutamine in supporting the sustained activation of TOR [135]. This type of mechanism could be viewed as an attractive model for nitrogen-dependent TOR regulation in plants given the pivotal role of glutamine in the assimilation of inorganic nitrogen via the GOGAT (glutamine oxoglutarate aminotransferase) pathway. With respect to carbon nutrition, recent work highlights an important role for sugar, showing that TOR-dependent growth in starch-depleted seedlings is tightly coupled to photosynthesis, and that TOR-dependent growth can be efficiently rescued in darkgrown seedlings by glucose [48]. Knockouts of HEXOKINASE1, a key element of sugar-sensing mechanisms in plants, have relatively little effect on TOR outputs. Instead, inhibitor studies suggest that growth responses are more indirect, requiring glycolysis and mitochondrial activity. This dependence might reflect the activation of TOR via a SnRK/AMPK-based mechanism that senses ATP derived from the oxidative metabolism of glucose. The link with mitochondrial outputs might also be explained by increased production of specific TCA cycle intermediates such as 2-oxoglutarate (α-ketoglutarate), which have been shown to influence TOR activity in animals and fungal systems [135,136]. This type of regulation might also have relevance to responses to nitrogen, where glutamine-dependent inputs into the TCA cycle would influence signalling to TOR [135].

Distinctions in lipid-dependent mechanisms for TOR activation

Analyses of TOR in animals and fungi have highlighted membrane-based activation mechanisms [15], but their relevance to plants remains unclear given distinct lexicons of lipid-based signalling molecules [137,138]. For animals, receptor-activated class I PI3Ks play key roles in the activation of TOR via production of PtdIns(3,4,5)P3 , which in turn leads to a membranebased activation of PDK. Plants, although lacking class I PI3Ks as well as detectable levels of PtdIns(3,4,5)P3 , do, however, exhibit gene activities that suggest possible alternative mechanisms for phospholipid-dependent activation of TOR. Counterparts of PTEN (phosphatase and tensin homologue deleted on chromosome 10), which in animals dampen PtdIns(3,4,5)P3 dependent responses through a PtdIns(3,4,5)P3 3-phosphatase activity [139] can be found in plants, but with activities against a distinct range of phosphoinositides. AtPTEN1, although displaying an in vitro phosphatase activity comparable with human PTEN, also exhibits an affinity for PtdIns3P. In vivo, specific expression of AtPTEN1 plays an essential role during pollen development [140], where its activity can be linked to autophagy and changes in the levels and localization of PtdIns3P [141]. Two other related proteins, AtPTEN2a and AtPTEN2b, have been shown to have a wider range of expression across tissues and activity against a broader range of substrates, including PtdIns3P, PtdIns(3,4)P2 and PtdIns(3,5)P2 , but not PtdIns(3,4,5)P3 [142]. The distinct phosphoinositide specificity

TOR signalling in plants

of plant PTENs compared with their animal counterparts is paralleled by differences in the binding and activation profiles of PDK, with plant forms binding a broader range of phosphoinositides as well as showing strong activation by PA (phosphatidic acid) as opposed to PtdIns(3,4,5)P3 [143,144]. Additional analyses have highlighted the potential relevance of these other phospholipid species to the regulation of TOR. Although both plants and fungi lack the class I PI3K for production of PtdIns(3,4,5)P3 , they carry the related, but more simply structured, class III PI3K Vps34, which catalyses the formation of PtdIns3P. Initially identified in yeast [145], Vps34 has the hallmarks of a more ancient form of PI3K, including a near ubiquitous distribution across eukaryotes and contributions to a number of endomembrane-focused processes ranging from vesicle trafficking to autophagy. Evidence that Vps34 may mediate regulation of TOR activity has emerged from cell culture and yeast models [132,146], although in Drosophila and certain human cell lines, this form of regulation may have been lost or is obscured by parallel signalling inputs. In plants, although no direct link between TOR and Vps34 has been demonstrated, knockdown phenotypes for both genes that relate to growth and metabolism align well [141,147–149]. An intriguing aspect of models for Vps34-mediated activation of TOR with particular relevance to plants relates to PA. Evidence from yeast and mammalian cell culture systems suggests that previously described roles of Vps34 for amino-acid-dependent activation of TOR may occur via the localized production of PA mediated by PLD (phospholipase D) [133,134,150]. PtdIns3P generated by Vps34 is proposed to anchor PLD to the lysosome surface via a PX (phox homology) lipid interaction domain. This membrane-bound PLD would offer a means to produce PA, which itself has been shown to activate TOR [151,152], through binding the FRB domain [153]. Additional work suggests an extension of this model in animal systems in which Rheb-dependent activation of TOR is mediated through Rheb-mediated activation of PLD [150,154]. Thus activation of TOR via a Vps34-dependent production of PA could be viewed as an ancestral mechanism, with Rheb-mediated regulation of PLD representing an additional mitogen/serum-sensitive regulatory module. In plants, a possible role for PA in mediated regulation of TOR in response to stress is beginning to emerge starting with regulated changes in PA levels triggered by several forms of stress. Towards understanding potential sources of PA, Arabidopsis contains at least 12 PLDs, with ten classed as C2-PLDs (Ca2 + dependent PLDs), which appear specific to plants, and two others, containing PH/PX-PLDs (pleckstrin homology/PX PLDs), that show affinities with the PLDs of mammals [155]. A functional analysis of one of the C2 class PLDs, PLDα3, suggests that its activation by hyperosmotic and salt stress enhances root growth and glucose sensitivity via PA-mediated activation of TOR [156]. Under these conditions, PLDα3-deficient plants accumulate less PA, have lower levels of AtTOR transcripts and phosphorylated S6K, whereas plants overexpressing PLDα3 have higher levels of AtTOR transcripts and phosphorylated S6K. Together, these observations support models in which that PA derived from PLD activity contributes to TOR regulation. Such a mechanism would provide an attractive model to link TOR activity to a diverse range of stress-and hormonerelated signalling outputs that rely on a diverse set of PLD genes found in plants. More recently, a further example of lipid-mediated regulation has emerged in yeast where TOR activity depends on a third species of phosphoinositide, PtdIns(3,5)P2 [157]. With both KOG1, the yeast equivalent of RAPTOR in TORC1, and its

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substrate S6K showing significant affinity for PtdIns(3,5)P2 , a model has been suggested for PtdIns(3,5)P2 promoting TORC1 co-localization with its activators and substrates. Although factors that control levels of PtdIns(3,5)P2 are not completely understood, its synthesis is thought to depend on both Vps34, and the phosphoinositide kinase Fab1p/PIKfyve, which together catalyse the sequential phosphorylation of a phosphoinositde precursor. Although no links between PtdIns(3,5)P2 and TOR signalling have been seen in plants, Arabidopsis lines with reduced FAB1 activity exhibit enlarged vacuoles and other membrane-trafficking defects that can be linked to pollen sterility and impaired responses to auxin [158–160].

Intercellular signalling inputs to TOR

Although plants exhibit some commonality with animals with respect to intracellular signal transduction pathways, significant differences are expected for how signals would be communicated across the plasma membrane and relayed to TOR. Surveys of plant genomes highlight the lack of RTKs (receptor tyrosine kinases) [161] and well-conserved seven-pass GPCRs (G-proteincoupled receptors) [162,163], which in animals play key roles in activating TOR through a variety of phosphorylation-dependent mechanisms. In their place, plants feature a unique repertoire of hormonal signal transduction pathways that have no clear equivalents among other eukaryotes [164]. By exploiting a versatile capacity for primary and secondary metabolism, plants fashion a wide range of small signalling molecules, from the relatively simple hydrocarbon ethylene to more complex hormones derived from amino acid, nucleotide, lipid, carotenoid, terpenoid and sterol precursors. Additional work has pointed to important roles of similarly diverse small peptide and RNA signalling molecules in mediating intercellular communication [165,166]. Receptor types for these signalling molecules are similarly varied. Auxin, gibberellin, jasmonate and strigolactone hormones rely on soluble receptors that target SCF (Skp, Cullin, F-box) complex-mediated regulation of turnover of proteins, many of which act as transcription factors to evoke hormone-associated responses. Membrane-associated receptors include bacterial twocomponent-like systems for ethylene and cytokinin, as well as RLK (receptor-like kinase)-type receptors for brassinosteroid and small peptides. RLKs are represented by hundreds of functionally diverse members in plants, compared with a handful of genes in animals, and which appear to be completely lacking in fungi [167]. The highly diversified families of RLKs [168] found in plants could be expected to play especially significant roles in communicating extracellular signals, given the lack of RTK and GPCR families and downstream class IA and IB PI3Ks that support analogous forms of communication in animals. Although the vast majority of RLKs have not been functionally characterized, recent work suggests that at least some RLKs may rely on heterotrimeric G-proteins as intracellular effectors, in contrast with animals and fungi where this linkage is restricted to interactions with GPCRs [169]. Relatively little is known of how these fundamental hormoneresponse pathways might interface with TOR-dependent outputs. Transcriptional reporters for early responses to the growthpromoting hormones auxin and cytokinin are unaffected by treatments that impair TOR-dependent growth responses, suggesting that TOR-dependent checkpoints lie downstream of early auxin responses. Early work has shown that the expression of a TOR:GUS translational fusion is enhanced by auxin treatment [4,170]. In a separate study, auxin has been shown to activate TOR  c 2015 Authors; published by Portland Press Limited

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as monitored by Torin-sensitive phosphorylation of S6K [51]. This up-regulation of S6K could be expected to reinforce auxin responses further, since many genes that encode auxin-response factor transcription factors contain μORFs whose inhibition of reinitiation is overcome by S6K-mediated phosphorylation of eIF3H, as described above.

FUNDING

CONCLUSION

REFERENCES

Functional analyses of TOR signalling in animals and fungal models, together with fully sequenced eukaryotic genomes, have presented a list of potential plant TOR signalling elements whose roles have only begun to be tested in well-developed genetic models such as Arabidopsis. Studies to date have validated roles for TORC1-mediated control of protein synthesis and turnover in response to nutritional and stress-related cues, supporting the ancestral character of this regulated output. More recent work in plants, however, has revealed novel facets of TOR-mediated regulation, including phosphorylation-mediated regulation of E2F and RBR transcription factors by TOR and S6K respectively, as well as novel forms of TOR-regulated translation reinitiation. In addition, recent work in fission yeast showing that the RNAbinding protein Mei2p is a direct target for TORC1-mediated phosphorylation suggests that the diversified family of Mei2-like genes in plants may play key roles in mediating TOR outputs. An intriguing, but poorly understood, aspect of TOR signalling in plants relates to how this ancient mechanism has been adapted to support unique strategies for nutrient acquisition and metabolism. With every green cell having the potential to make its own sugar via photosynthesis, it is perhaps not surprising that plants lack elements such as insulin receptors, which in animals serve to integrate TOR outputs with a centrally managed glucose economy. In their place, novel linkages with TOR in plants may help integrate their growth and metabolism with chloroplast-associated outputs. The uptake and assimilation of other nutrients, such as inorganic nitrogen, is likely to present further distinctions in how nutrient levels are coupled to TOR activity. The apparent absence of RAG/GTR systems described in animals and fungi draws attention to other, perhaps more basic, mechanisms that would draw on a more widely conserved set of players. Alternative mechanisms for TOR activation that rely on the more ubiquitous Vps34, PLDs and other agents for lipid modification offer promising candidates in this respect, and may also have relevance to a diverse set of extracellular inputs linked to growth and stress responses. Understanding how TOR activity is coupled to multicellular programmes of development in plants presents some of the most exciting challenges. As might be expected for independently evolved mechanisms selected to support fundamentally distinct growth strategies, many differences are seen between plants and animals, yet these are somehow coupled with TOR activity in plants to achieve coherent, but flexible, growth programmes, as well as adaptive patterns of metabolic regulation. With respect to cellular growth, the apparent lack of TORC2 in plants focuses attention on alternative mechanisms that plants might use to co-ordinate polarized growth processes. Whether these rely on TORC1, novel TOR complexes or largely TOR-independent forms of signalling remain key questions. Linkages between TOR with extracellular inputs, including growth- and stress-related signalling factors also remain poorly understood. Clearly, a more complete understanding of these elements promises new insights into this ancient signalling pathway that are relevant to plants, but may also reveal significant aspects that have gone unnoticed in other eukaryotic models.  c 2015 Authors; published by Portland Press Limited

This work was supported by funding from AgResearch, the Royal Society of New Zealand and Organisation for Economic Cooperation and Development (OECD) to B.V., and Direction des Sciences du Vivant-Commissariat a` l’Energie Atomique to C.R. and by grant ANR2011BSV6-01002 to C.R. and C.M.

1 Loewith, R. and Hall, M.N. (2011) Target of rapamycin (TOR) in nutrient signaling and growth control. Genetics 189, 1177–1201 CrossRef PubMed 2 Cornu, M., Albert, V. and Hall, M.N. (2013) mTOR in aging, metabolism, and cancer. Curr. Opin. Genet. Dev. 23, 53–62 CrossRef PubMed 3 Laplante, M. and Sabatini, D.M. (2012) mTOR signaling in growth control and disease. Cell 149, 274–293 CrossRef PubMed 4 Moreau, M., Sormani, R., Menand, B., Veit, B., Robaglia, C. and Meyer, C. (2010) The TOR complex and signaling pathway in plants. Enzymes 27, 285–302 5 John, F., Roffler, S., Wicker, T. and Ringli, C. (2011) Plant TOR signaling components. Plant Signal. Behav. 6, 1700–1705 CrossRef PubMed 6 Robaglia, C., Thomas, M. and Meyer, C. (2012) Sensing nutrient and energy status by SnRK1 and TOR kinases. Curr. Opin. Plant Biol. 15, 301–307 CrossRef PubMed 7 Dobrenel, T., Marchive, C., Azzopardi, M., Clement, G., Moreau, M., Sormani, R., Robaglia, C. and Meyer, C. (2013) Sugar metabolism and the plant target of rapamycin kinase: a sweet operaTOR? Front. Plant Sci. 4, 93 8 Bogre, L., Henriques, R. and Magyar, Z. (2013) TOR tour to auxin. EMBO J. 32, 1069–1071 CrossRef PubMed 9 Xiong, Y. and Sheen, J. (2014) The role of target of rapamycin signaling networks in plant growth and metabolism. Plant Physiol. 164, 499–512 CrossRef PubMed 10 Vezina, C., Kudelski, A. and Sehgal, S.N. (1975) Rapamycin (AY-22,989), a new antifungal antibiotic. I. Taxonomy of the producing streptomycete and isolation of the active principle. J. Antibiot. (Tokyo) 28, 721–726 CrossRef PubMed 11 Heitman, J., Movva, N.R. and Hall, M.N. (1991) Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. Science 253, 905–909 CrossRef PubMed 12 Kunz, J., Henriquez, R., Schneider, U., Deuter-Reinhard, M., Movva, N.R. and Hall, M.N. (1993) Target of rapamycin in yeast, TOR2, is an essential phosphatidylinositol kinase homolog required for G1 progression. Cell 73, 585–596 CrossRef PubMed 13 Stan, R., McLaughlin, M.M., Cafferkey, R., Johnson, R.K., Rosenberg, M. and Livi, G.P. (1994) Interaction between FKBP12–rapamycin and TOR involves a conserved serine residue. J. Biol. Chem. 269, 32027–32030 PubMed 14 Choi, J., Chen, J., Schreiber, S.L. and Clardy, J. (1996) Structure of the FKBP12–rapamycin complex interacting with the binding domain of human FRAP. Science 273, 239–242 CrossRef PubMed 15 Engelman, J.A., Luo, J. and Cantley, L.C. (2006) The evolution of phosphatidylinositol 3-kinases as regulators of growth and metabolism. Nat. Rev. Genet. 7, 606 CrossRef PubMed 16 Brunn, G.J., Hudson, C.C., Sekulic, A., Williams, J.M., Hosoi, H., Houghton, P.J., Lawrence, Jr, J.C. and Abraham, R.T. (1997) Phosphorylation of the translational repressor PHAS-I by the mammalian target of rapamycin. Science 277, 99–101 CrossRef PubMed 17 Burnett, P.E., Barrow, R.K., Cohen, N.A., Snyder, S.H. and Sabatini, D.M. (1998) RAFT1 phosphorylation of the translational regulators p70 S6 kinase and 4E-BP1. Proc. Natl. Acad. Sci. U.S.A. 95, 1432–1437 CrossRef PubMed 18 Templeton, G.W. and Moorhead, G.B. (2005) The phosphoinositide-3-OH-kinase-related kinases of Arabidopsis thaliana . EMBO Rep. 6, 723–728 CrossRef PubMed 19 Salih, E. (2005) Phosphoproteomics by mass spectrometry and classical protein chemistry approaches. Mass Spectrom. Rev. 24, 828–846 CrossRef PubMed 20 Kunz, J., Schneider, U., Howald, I., Schmidt, A. and Hall, M.N. (2000) HEAT repeats mediate plasma membrane localization of Tor2p in yeast. J. Biol. Chem. 275, 37011–37020 CrossRef PubMed 21 Hardt, M., Chantaravisoot, N. and Tamanoi, F. (2011) Activating mutations of TOR (target of rapamycin). Genes Cells 16, 141–151 CrossRef PubMed 22 Rohde, J., Heitman, J. and Cardenas, M.E. (2001) The TOR kinases link nutrient sensing to cell growth. J. Biol. Chem. 276, 9583–9586 CrossRef PubMed 23 Loewith, R., Jacinto, E., Wullschleger, S., Lorberg, A., Crespo, J.L., Bonenfant, D., Oppliger, W., Jenoe, P. and Hall, M.N. (2002) Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control. Mol. Cell 10, 457–468 CrossRef PubMed 24 Wullschleger, S., Loewith, R. and Hall, M.N. (2006) TOR signaling in growth and metabolism. Cell 124, 471–484 CrossRef PubMed

TOR signalling in plants 25 Hara, K., Maruki, Y., Long, X., Yoshino, K., Oshiro, N., Hidayat, S., Tokunaga, C., Avruch, J. and Yonezawa, K. (2002) Raptor, a binding partner of target of rapamycin (TOR), mediates TOR action. Cell 110, 177–189 CrossRef PubMed 26 Kim, D.H., Sarbassov, D.D., Ali, S.M., King, J.E., Latek, R.R., Erdjument-Bromage, H., Tempst, P. and Sabatini, D.M. (2002) mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery. Cell 110, 163–175 CrossRef PubMed 27 Nojima, H., Tokunaga, C., Eguchi, S., Oshiro, N., Hidayat, S., Yoshino, K., Hara, K., Tanaka, N., Avruch, J. and Yonezawa, K. (2003) The mammalian target of rapamycin (mTOR) partner, raptor, binds the mTOR substrates p70 S6 kinase and 4E-BP1 through their TOR signaling (TOS) motif. J. Biol. Chem. 278, 15461–15464 CrossRef PubMed 28 Gwinn, D.M., Shackelford, D.B., Egan, D.F., Mihaylova, M.M., Mery, A., Vasquez, D.S., Turk, B.E. and Shaw, R.J. (2008) AMPK phosphorylation of raptor mediates a metabolic checkpoint. Mol. Cell 30, 214–226 CrossRef PubMed 29 Shinozaki-Yabana, S., Watanabe, Y. and Yamamoto, M. (2000) Novel WD-repeat protein Mip1p facilitates function of the meiotic regulator Mei2p in fission yeast. Mol. Cell. Biol. 20, 1234–1242 CrossRef PubMed 30 Roberg, K.J., Bickel, S., Rowley, N. and Kaiser, C.A. (1997) Control of amino acid permease sorting in the late secretory pathway of Saccharomyces cerevisiae by SEC13, LST4, LST7 and LST8. Genetics 147, 1569–1584 PubMed 31 Liu, Z., Sekito, T., Epstein, C.B. and Butow, R.A. (2001) RTG-dependent mitochondria to nucleus signaling is negatively regulated by the seven WD-repeat protein Lst8p. EMBO J. 20, 7209–7219 CrossRef PubMed 32 Chen, E.J. and Kaiser, C.A. (2003) LST8 negatively regulates amino acid biosynthesis as a component of the TOR pathway. J. Cell Biol. 161, 333–347 CrossRef PubMed 33 Yang, H., Rudge, D.G., Koos, J.D., Vaidialingam, B., Yang, H.J. and Pavletich, N.P. (2013) mTOR kinase structure, mechanism and regulation. Nature 497, 217–223 CrossRef PubMed 34 Kim, D.H., Sarbassov, D.D., Ali, S.M., Latek, R.R., Guntur, K.V., Erdjument-Bromage, H., Tempst, P. and Sabatini, D.M. (2003) GβL, a positive regulator of the rapamycin-sensitive pathway required for the nutrient-sensitive interaction between raptor and mTOR. Mol. Cell 11, 895–904 CrossRef PubMed 35 Adami, A., Garcia-Alvarez, B., Arias-Palomo, E., Barford, D. and Llorca, O. (2007) Structure of TOR and its complex with KOG1. Mol. Cell 27, 509–516 CrossRef PubMed 36 Wang, X. and Proud, C.G. (2009) Nutrient control of TORC1, a cell-cycle regulator. Trends Cell Biol. 19, 260–267 CrossRef PubMed 37 Jacinto, E., Loewith, R., Schmidt, A., Lin, S., Ruegg, M.A., Hall, A. and Hall, M.N. (2004) Mammalian TOR complex 2 controls the actin cytoskeleton and is rapamycin insensitive. Nat. Cell Biol. 6, 1122–1128 CrossRef PubMed 38 Sarbassov, D.D., Ali, S.M., Kim, D.H., Guertin, D.A., Latek, R.R., Erdjument-Bromage, H., Tempst, P. and Sabatini, D.M. (2004) Rictor, a novel binding partner of mTOR, defines a rapamycin-insensitive and raptor-independent pathway that regulates the cytoskeleton. Curr. Biol. 14, 1296–1302 CrossRef PubMed 39 Sarbassov, D.D., Guertin, D.A., Ali, S.M. and Sabatini, D.M. (2005) Phosphorylation and regulation of Akt/PKB by the rictor–mTOR complex. Science 307, 1098–1101 CrossRef PubMed 40 Facchinetti, V., Ouyang, W., Wei, H., Soto, N., Lazorchak, A., Gould, C., Lowry, C., Newton, A.C., Mao, Y., Miao, R.Q. et al. (2008) The mammalian target of rapamycin complex 2 controls folding and stability of Akt and protein kinase C. EMBO J. 27, 1932–1943 CrossRef PubMed 41 Garcia-Martinez, J.M. and Alessi, D.R. (2008) mTOR complex 2 (mTORC2) controls hydrophobic motif phosphorylation and activation of serum- and glucocorticoid-induced protein kinase 1 (SGK1). Biochem. J. 416, 375–385 CrossRef PubMed 42 Ikenoue, T., Inoki, K., Yang, Q., Zhou, X. and Guan, K.L. (2008) Essential function of TORC2 in PKC and Akt turn motif phosphorylation, maturation and signalling. EMBO J. 27, 1919–1931 CrossRef PubMed 43 Aronova, S., Wedaman, K., Anderson, S., Yates, 3rd, J. and Powers, T. (2007) Probing the membrane environment of the TOR kinases reveals functional interactions between TORC1, actin, and membrane trafficking in Saccharomyces cerevisiae . Mol. Biol. Cell 18, 2779–2794 CrossRef PubMed 44 Dinkova, T.D., De La Cruz, H.R., Garc´ıa-Flores, C., Aguilar, R., Jim´enez-Garc´ıa, L.F. and De Jim´enez, E.S. (2007) Dissecting the TOR–S6K signal transduction pathway in maize seedlings: relevance on cell growth regulation. Physiol. Plant. 130, 1–10 CrossRef 45 Turck, F., Kozma, S.C., Thomas, G. and Nagy, F. (1998) A heat-sensitive Arabidopsis thaliana kinase substitutes for human p70s6k function in vivo . Mol. Cell. Biol. 18, 2038–2044 PubMed 46 Sormani, R., Yao, L., Menand, B., Ennar, N., Lecampion, C., Meyer, C. and Robaglia, C. (2007) Saccharomyces cerevisiae FKBP12 binds Arabidopsis thaliana TOR and its expression in plants leads to rapamycin susceptibility. BMC Plant Biol. 7, 26 CrossRef PubMed

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47 Ren, M., Venglat, P., Qiu, S., Feng, L., Cao, Y., Wang, E., Xiang, D., Wang, J., Alexander, D., Chalivendra, S. et al. (2012) Target of rapamycin signaling regulates metabolism, growth, and life span in Arabidopsis. Plant Cell 24, 4850–4874 CrossRef PubMed 48 Xiong, Y., McCormack, M., Li, L., Hall, Q., Xiang, C. and Sheen, J. (2013) Glucose–TOR signalling reprograms the transcriptome and activates meristems. Nature 496, 181–186 CrossRef PubMed 49 Leiber, R.-M., John, F., Verhertbruggen, Y., Diet, A., Knox, J.P. and Ringli, C. (2010) The TOR pathway modulates the structure of cell walls in Arabidopsis. Plant Cell 22, 1898–1908 CrossRef PubMed 50 Montane, M.H. and Menand, B. (2013) ATP-competitive mTOR kinase inhibitors delay plant growth by triggering early differentiation of meristematic cells but no developmental patterning change. J. Exp. Bot. 64, 4361–4374 CrossRef PubMed 51 Schepetilnikov, M., Dimitrova, M., Mancera-Martinez, E., Geldreich, A., Keller, M. and Ryabova, L.A. (2013) TOR and S6K1 promote translation reinitiation of uORF-containing mRNAs via phosphorylation of eIF3h. EMBO J. 32, 1087–1102 CrossRef PubMed 52 Menand, B., Desnos, T., Nussaume, L., Berger, F., Bouchez, D., Meyer, C. and Robaglia, C. (2002) Expression and disruption of the Arabidopsis TOR (target of rapamycin) gene. Proc. Natl. Acad. Sci. U.S.A. 99, 6422–6427 CrossRef PubMed 53 Deprost, D., Yao, L., Sormani, R., Moreau, M., Leterreux, G., Nicolai, M., Bedu, M., Robaglia, C. and Meyer, C. (2007) The Arabidopsis TOR kinase links plant growth, yield, stress resistance and mRNA translation. EMBO Rep. 8, 864–870 CrossRef PubMed 54 Liu, Y. and Bassham, D.C. (2010) TOR is a negative regulator of autophagy in Arabidopsis thaliana . PLoS One 5, e11883 CrossRef PubMed 55 Caldana, C., Li, Y., Leisse, A., Zhang, Y., Bartholomaeus, L., Fernie, A.R., Willmitzer, L. and Giavalisco, P. (2013) Systemic analysis of inducible target of rapamycin mutants reveal a general metabolic switch controlling growth in Arabidopsis thaliana . Plant J. 73, 897–909 CrossRef PubMed 56 Xiong, Y. and Sheen, J. (2012) Rapamycin and glucose–target of rapamycin (TOR) protein signaling in plants. J. Biol. Chem. 287, 2836–2842 CrossRef PubMed 57 Ren, M., Qiu, S., Venglat, P., Xiang, D., Feng, L., Selvaraj, G. and Datla, R. (2011) Target of rapamycin regulates development and ribosomal RNA expression through kinase domain in Arabidopsis. Plant Physiol. 155, 1367–1382 CrossRef PubMed 58 De Virgilio, C. and Loewith, R. (2006) The TOR signalling network from yeast to man. Int. J. Biochem. Cell Biol. 38, 1476–1481 CrossRef PubMed 59 Moreau, M., Azzopardi, M., Clement, G., Dobrenel, T., Marchive, C., Renne, C., Martin-Magniette, M.L., Taconnat, L., Renou, J.P., Robaglia, C. and Meyer, C. (2012) Mutations in the Arabidopsis homolog of LST8/GβL, a partner of the target of rapamycin kinase, impair plant growth, flowering, and metabolic adaptation to long days. Plant Cell 24, 463–481 CrossRef PubMed 60 Lee, Y. and Fiehn, O. (2013) Metabolomic response of Chlamydomonas reinhardtii to the inhibition of target of rapamycin (TOR) by rapamycin. J. Microbiol. Biotechnol. 23, 923–931 CrossRef PubMed 61 Ahn, C.S., Han, J.-A., Lee, H.-S., Lee, S. and Pai, H.-S. (2011) The PP2A regulatory subunit Tap46, a component of the TOR signaling pathway, modulates growth and metabolism in plants. Plant Cell 23, 185–209 CrossRef PubMed 62 Gems, D. and Partridge, L. (2013) Genetics of longevity in model organisms: debates and paradigm shifts. Annu. Rev. Physiol. 75, 621–644 CrossRef PubMed 63 Kenyon, C.J. (2010) The genetics of ageing. Nature 464, 504–512 CrossRef PubMed 64 de Jong, M. and Leyser, O. (2012) Developmental plasticity in plants. Cold Spring Harb. Symp. Quant. Biol. 77, 63–73 CrossRef PubMed 65 Guiboileau, A., Sormani, R., Meyer, C. and Masclaux-Daubresse, C. (2010) Senescence and death of plant organs: nutrient recycling and developmental regulation. C.R. Biol. 333, 382–391 CrossRef PubMed 66 Lloyd, J.P. B. and Davies, B. (2013) SMG1 is an ancient nonsense-mediated mRNA decay effector. Plant J. 76, 800–810 CrossRef PubMed 67 Deprost, D., Truong, H.N., Robaglia, C. and Meyer, C. (2005) An Arabidopsis homolog of RAPTOR /KOG1 is essential for early embryo development. Biochem. Biophys. Res. Commun. 326, 844–850 CrossRef PubMed 68 Anderson, G.H., Veit, B. and Hanson, M.R. (2005) The Arabidopsis AtRaptor genes are essential for post-embryonic plant growth. BMC Biol. 3, 12 CrossRef PubMed 69 Mahfouz, M.M., Kim, S., Delauney, A.J. and Verma, D.P.S. (2006) Arabidopsis TARGET OF RAPAMYCIN interacts with RAPTOR, which regulates the activity of S6 kinase in response to osmotic stress signals. Plant Cell 18, 477–490 CrossRef PubMed 70 Goranov, A.I., Gulati, A., Dephoure, N., Takahara, T., Maeda, T., Gygi, S.P., Manalis, S. and Amon, A. (2013) Changes in cell morphology are coordinated with cell growth through the TORC1 pathway. Curr. Biol. 23, 1269–1279 CrossRef PubMed 71 Loewith, R. (2013) Growth control: function follows form. Curr. Biol. 23, R607–R609 CrossRef PubMed 72 Saldivia, M., Barquilla, A., Bart, J.M., Diaz-Gonzalez, R., Hall, M.N. and Navarro, M. (2013) Target of rapamycin (TOR) kinase in Trypanosoma brucei : an extended family. Biochem. Soc. Trans. 41, 934–938 CrossRef PubMed  c 2015 Authors; published by Portland Press Limited

12

D. Rexin and others

73 Barquilla, A., Saldivia, M., Diaz, R., Bart, J.-M., Vidal, I., Calvo, E., Hall, M.N. and Navarro, M. (2012) Third target of rapamycin complex negatively regulates development of quiescence in Trypanosoma brucei . Proc. Natl. Acad. Sci. U.S.A. 109, 14399–14404 CrossRef PubMed 74 Diaz-Troya, S., Florencio, F.J. and Crespo, J.L. (2008) Target of rapamycin and LST8 proteins associate with membranes from the endoplasmic reticulum in the unicellular green alga Chlamydomonas reinhardtii . Eukaryot. Cell 7, 212–222 CrossRef PubMed 75 Ochotorena, I.L., Hirata, D., Kominami, K., Potashkin, J., Sahin, F., Wentz-Hunter, K., Gould, K.L., Sato, K., Yoshida, Y., Vardy, L. and Toda, T. (2001) Conserved Wat1/Pop3 WD-repeat protein of fission yeast secures genome stability through microtubule integrity and may be involved in mRNA maturation. J. Cell Sci. 114, 2911–2920 PubMed 76 Roy, B. and von Arnim, A.G. (2013) Translational regulation of cytoplasmic mRNAs. Arabidopsis Book 11, e0165 CrossRef 77 Martin, D.E., Powers, T. and Hall, M.N. (2006) Regulation of ribosome biogenesis: where is TOR? Cell Metab. 4, 259–260 CrossRef PubMed 78 Tsang, C.K., Liu, H. and Zheng, X.F. (2010) mTOR binds to the promoters of RNA polymerase I- and III-transcribed genes. Cell Cycle 9, 953–957 CrossRef PubMed 79 Schepetilnikov, M., Kobayashi, K., Geldreich, A., Caranta, C., Robaglia, C., Keller, M. and Ryabova, L.A. (2011) Viral factor TAV recruits TOR/S6K1 signalling to activate reinitiation after long ORF translation. EMBO J. 30, 1343–1356 CrossRef PubMed 80 Zhang, S.H., Broome, M.A., Lawton, M.A., Hunter, T. and Lamb, C.J. (1994) atpk1, a novel ribosomal protein kinase gene from Arabidopsis. II. Functional and biochemical analysis of the encoded protein. J. Biol. Chem. 269, 17593–17599 PubMed 81 Turck, F., Zilbermann, F., Kozma, S.C., Thomas, G. and Nagy, F. (2004) Phytohormones participate in an S6 kinase signal transduction pathway in Arabidopsis. Plant Physiol. 134, 1527–1535 CrossRef PubMed 82 Henriques, R., Magyar, Z. and Bogre, L. (2013) S6K1 and E2FB are in mutually antagonistic regulatory links controlling cell growth and proliferation in Arabidopsis. Plant Signal. Behav. 8, e24367 CrossRef PubMed 83 Henriques, R., Magyar, Z., Monardes, A., Khan, S., Zalejski, C., Orellana, J., Szabados, L., de la Torre, C., Koncz, C. and Bogre, L. (2010) Arabidopsis S6 kinase mutants display chromosome instability and altered RBR1–E2F pathway activity. EMBO J. 29, 2979–2993 CrossRef PubMed 84 Otterhag, L., Gustavsson, N., Alsterfjord, M., Pical, C., Lehrach, H., Gobom, J. and Sommarin, M. (2006) Arabidopsis PDK1: identification of sites important for activity and downstream phosphorylation of S6 kinase. Biochimie 88, 11–21 CrossRef PubMed 85 Reyes de la Cruz, H., Aguilar, R. and Sanchez de Jimenez, E. (2004) Functional characterization of a maize ribosomal S6 protein kinase (ZmS6K), a plant ortholog of metazoan p70(S6K). Biochemistry 43, 533–539 CrossRef PubMed 86 Ma, X.M. and Blenis, J. (2009) Molecular mechanisms of mTOR-mediated translational control. Nat. Rev. Mol. Cell Biol. 10, 307–318 CrossRef PubMed 87 Meyuhas, O. (2008) Physiological roles of ribosomal protein S6: one of its kind. Int. Rev. Cell Mol. Biol. 268, 1–37 PubMed 88 Chauvin, C., Koka, V., Nouschi, A., Mieulet, V., Hoareau-Aveilla, C., Dreazen, A., Cagnard, N., Carpentier, W., Kiss, T., Meyuhas, O. and Pende, M. (2014) Ribosomal protein S6 kinase activity controls the ribosome biogenesis transcriptional program. Oncogene 33, 474–483 CrossRef PubMed 89 Creff, A., Sormani, R. and Desnos, T. (2010) The two Arabidopsis RPS6 genes, encoding for cytoplasmic ribosomal proteins S6, are functionally equivalent. Plant Mol. Biol. 73, 533–546 CrossRef PubMed 90 Rosado, A., Li, R., van de Ven, W., Hsu, E. and Raikhel, N.V. (2012) Arabidopsis ribosomal proteins control developmental programs through translational regulation of auxin response factors. Proc. Natl. Acad. Sci. U.S.A. 109, 19537–19544 CrossRef PubMed 91 Zhou, F., Roy, B., Dunlap, J.R., Enganti, R. and von Arnim, A.G. (2014) Translational control of Arabidopsis meristem stability and organogenesis by the eukaryotic translation factor eIF3h. PLoS One 9, e95396 CrossRef PubMed 92 Ker´enyi, Z., M´erai, Z., Hiripi, L., Benkovics, A., Gyula, P., Lacomme, C., Barta, E., Nagy, F. and Silhavy, D. (2008) Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay. EMBO J. 27, 1585–1595 CrossRef PubMed 93 Richter, J.D. and Sonenberg, N. (2005) Regulation of cap-dependent translation by eIF4E inhibitory proteins. Nature 433, 477–480 CrossRef PubMed 94 Cridge, A.G., Castelli, L.M., Smirnova, J.B., Selley, J.N., Rowe, W., Hubbard, S.J., McCarthy, J.E., Ashe, M.P., Grant, C.M. and Pavitt, G.D. (2010) Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins. Nucleic Acids Res. 38, 8039–8050 CrossRef PubMed  c 2015 Authors; published by Portland Press Limited

95 Hughes, J.M., Ptushkina, M., Karim, M.M., Koloteva, N., von der Haar, T. and McCarthy, J.E. (1999) Translational repression by human 4E-BP1 in yeast specifically requires human eIF4E as target. J. Biol. Chem. 274, 3261–3264 CrossRef PubMed 96 Watanabe, Y. and Yamamoto, M. (1994) S. pombe mei2 + encodes an RNA-binding protein essential for premeiotic DNA synthesis and meiosis I, which cooperates with a novel RNA species meiRNA. Cell 78, 487–498 CrossRef PubMed 97 Harigaya, Y., Tanaka, H., Yamanaka, S., Tanaka, K., Watanabe, Y., Tsutsumi, C., Chikashige, Y., Hiraoka, Y., Yamashita, A. and Yamamoto, M. (2006) Selective elimination of messenger RNA prevents an incidence of untimely meiosis. Nature 442, 45 CrossRef PubMed 98 Shimada, T., Yamashita, A. and Yamamoto, M. (2003) The fission yeast meiotic regulator Mei2p forms a dot structure in the horse-tail nucleus in association with the sme2 locus on chromosome II. Mol. Biol. Cell 14, 2461–2469 CrossRef PubMed 99 Otsubo, Y., Yamashita, A., Ohno, H. and Yamamoto, M. (2014) S. pombe TORC1 activates the ubiquitin–proteasomal degradation of the meiotic regulator Mei2 in cooperation with Pat1 kinase. J. Cell Sci. 127, 2639–2646 CrossRef PubMed 100 Veit, B., Briggs, S.P., Schmidt, R.J., Yanofsky, M.F. and Hake, S. (1998) Regulation of leaf initiation by the TERMINAL EAR1 gene of maize. Nature 393, 166–168 CrossRef PubMed 101 Kawakatsu, T., Itoh, J., Miyoshi, K., Kurata, N., Alvarez, N., Veit, B. and Nagato, Y. (2006) PLASTOCHRON2 regulates leaf initiation and maturation in rice. Plant Cell 18, 612–625 CrossRef PubMed 102 Charon, C., Bruggeman, Q., Thareau, V. and Henry, Y. (2012) Gene duplication within the Green Lineage: the case of TEL genes. J. Exp. Bot. 63, 5061–5077 CrossRef PubMed 103 Paquet, N., Bernadet, M., Morin, H., Traas, J., Dron, M. and Charon, C. (2005) Expression patterns of TEL genes in Poaceae suggest a conserved association with cell differentiation. J. Exp. Bot. 56, 1605–1614 CrossRef PubMed 104 Charon, C., Vivancos, J., Mazubert, C., Paquet, N., Pilate, G. and Dron, M. (2009) Structure and vascular tissue expression of duplicated TERMINAL EAR1-like paralogues in poplar. Planta 231, 525–535 CrossRef PubMed 105 Anderson, G.H., Alvarez, N.D., Gilman, C., Jeffares, D.C., Trainor, V.C., Hanson, M.R. and Veit, B. (2004) Diversification of genes encoding mei2 -like RNA binding proteins in plants. Plant Mol. Biol. 54, 653–670 CrossRef PubMed 106 Kaur, J., Sebastian, J. and Siddiqi, I. (2006) The Arabidopsis -mei2 -like genes play a role in meiosis and vegetative growth in Arabidopsis. Plant Cell 18, 545–559 CrossRef PubMed 107 Hirayama, T., Ishida, C., Kuromori, T., Obata, S., Shimoda, C., Yamamoto, M., Shinozaki, K. and Ohto, C. (1997) Functional cloning of a cDNA encoding Mei2-like protein from Arabidopsis thaliana using a fission yeast pheromone receptor deficient mutant. FEBS Lett. 413, 16–20 CrossRef PubMed 108 Jeffares, D.C., Phillips, M.J., Moore, S. and Veit, B. (2004) A description of the Mei2 -like protein family; structure, phylogenetic distribution and biological context. Dev. Genes Evol. 214, 149–158 CrossRef PubMed 109 Anderson, G.H. and Hanson, M.R. (2005) The Arabidopsis Mei2 homologue AML1 binds ATRAPTOR1B, the plant homologue of a major regulator of eukaryotic cell growth. BMC Plant Biol. 5, 2 CrossRef PubMed 110 Uhrig, R.G., Labandera, A.-M. and Moorhead, G.B. (2013) Arabidopsis PPP family of serine/threonine protein phosphatases: many targets but few engines. Trends Plant Sci. 18, 505–513 CrossRef PubMed 111 Harris, D.M., Myrick, T.L. and Rundle, S.J. (1999) The Arabidopsis homolog of yeast TAP42 and mammalian α4 binds to the catalytic subunit of protein phosphatase 2a and is induced by chilling. Plant Physiol. 121, 609–618 CrossRef PubMed 112 Ganley, I.G., Lam du, H., Wang, J., Ding, X., Chen, S. and Jiang, X. (2009) ULK1·ATG13·FIP200 complex mediates mTOR signaling and is essential for autophagy. J. Biol. Chem. 284, 12297–12305 CrossRef PubMed 113 Hosokawa, N., Hara, T., Kaizuka, T., Kishi, C., Takamura, A., Miura, Y., Iemura, S., Natsume, T., Takehana, K., Yamada, N. et al. (2009) Nutrient-dependent mTORC1 association with the ULK1–Atg13–FIP200 complex required for autophagy. Mol. Biol. Cell 20, 1981–1991 CrossRef PubMed 114 Jung, C.H., Jun, C.B., Ro, S.H., Kim, Y.M., Otto, N.M., Cao, J., Kundu, M. and Kim, D.H. (2009) ULK–Atg13–FIP200 complexes mediate mTOR signaling to the autophagy machinery. Mol. Biol. Cell 20, 1992–2003 CrossRef PubMed 115 Perez-Perez, M.E., Florencio, F.J. and Crespo, J.L. (2010) Inhibition of target of rapamycin signaling and stress activate autophagy in Chlamydomonas reinhardtii . Plant Physiol. 152, 1874–1888 CrossRef PubMed 116 Avila-Ospina, L., Moison, M., Yoshimoto, K. and Masclaux-Daubresse, C. (2014) Autophagy, plant senescence, and nutrient recycling. J. Exp. Bot. 65, 3799–3811 CrossRef PubMed

TOR signalling in plants 117 Li, F. and Vierstra, R.D. (2012) Regulator and substrate: dual roles for the ATG1–ATG13 kinase complex during autophagic recycling in Arabidopsis. Autophagy 8, 982–984 CrossRef PubMed 118 Hardie, D.G., Ross, F.A. and Hawley, S.A. (2012) AMPK: a nutrient and energy sensor that maintains energy homeostasis. Nat. Rev. Mol. Cell Biol. 13, 251–262 CrossRef PubMed 119 Baena-Gonzalez, E. and Sheen, J. (2008) Convergent energy and stress signaling. Trends Plant Sci. 13, 474–482 CrossRef PubMed 120 Baena-Gonzalez, E., Rolland, F., Thevelein, J.M. and Sheen, J. (2007) A central integrator of transcription networks in plant stress and energy signalling. Nature 448, 938–942 CrossRef PubMed 121 Halford, N.G. and Hey, S.J. (2009) Snf1-related protein kinases (SnRKs) act within an intricate network that links metabolic and stress signalling in plants. Biochem. J. 419, 247–259 CrossRef PubMed 122 Huang, J. and Manning, B.D. (2008) The TSC1–TSC2 complex: a molecular switchboard controlling cell growth. Biochem. J. 412, 179–190 CrossRef PubMed 123 van Dam, T.J., Zwartkruis, F.J., Bos, J.L. and Snel, B. (2011) Evolution of the TOR pathway. J. Mol. Evol. 73, 209–220 CrossRef PubMed 124 Hsu, Y.C., Chern, J.J., Cai, Y., Liu, M. and Choi, K.W. (2007) Drosophila TCTP is essential for growth and proliferation through regulation of dRheb GTPase. Nature 445, 785–788 CrossRef PubMed 125 Rehmann, H., Bruning, M., Berghaus, C., Schwarten, M., Kohler, K., Stocker, H., Stoll, R., Zwartkruis, F.J. and Wittinghofer, A. (2008) Biochemical characterisation of TCTP questions its function as a guanine nucleotide exchange factor for Rheb. FEBS Lett. 582, 3005–3010 CrossRef PubMed 126 Wang, X., Fonseca, B.D., Tang, H., Liu, R., Elia, A., Clemens, M.J., Bommer, U.A. and Proud, C.G. (2008) Re-evaluating the roles of proposed modulators of mammalian target of rapamycin complex 1 (mTORC1) signaling. J. Biol. Chem. 283, 30482–30492 CrossRef PubMed 127 Berkowitz, O., Jost, R., Pollmann, S. and Masle, J. (2008) Characterization of TCTP, the translationally controlled tumor protein, from Arabidopsis thaliana . Plant Cell 20, 3430–3447 CrossRef PubMed 128 Brioudes, F., Thierry, A.M., Chambrier, P., Mollereau, B. and Bendahmane, M. (2010) Translationally controlled tumor protein is a conserved mitotic growth integrator in animals and plants. Proc. Natl. Acad. Sci. U.S.A. 107, 16384–16389 CrossRef PubMed 129 Nunes-Nesi, A., Fernie, A.R. and Stitt, M. (2010) Metabolic and signaling aspects underpinning the regulation of plant carbon nitrogen interactions. Mol. Plant 3, 973–996 CrossRef PubMed 130 Bar-Peled, L. and Sabatini, D.M. (2014) Regulation of mTORC1 by amino acids. Trends Cell Biol. 24, 400–406 CrossRef PubMed 131 Vernoud, V., Horton, A.C., Yang, Z. and Nielsen, E. (2003) Analysis of the small GTPase gene superfamily of Arabidopsis. Plant Physiol. 131, 1191–1208 CrossRef PubMed 132 Nobukuni, T., Joaquin, M., Roccio, M., Dann, S.G., Kim, S.Y., Gulati, P., Byfield, M.P., Backer, J.M., Natt, F., Bos, J.L. et al. (2005) Amino acids mediate mTOR/raptor signaling through activation of class 3 phosphatidylinositol 3OH-kinase. Proc. Natl. Acad. Sci. U.S.A. 102, 14238–14243 CrossRef PubMed 133 Yoon, M.S., Du, G., Backer, J.M., Frohman, M.A. and Chen, J. (2011) Class III PI-3-kinase activates phospholipase D in an amino acid-sensing mTORC1 pathway. J. Cell Biol. 195, 435–447 CrossRef PubMed 134 Xu, L., Salloum, D., Medlin, P.S., Saqcena, M., Yellen, P., Perrella, B. and Foster, D.A. (2011) Phospholipase D mediates nutrient input to mammalian target of rapamycin complex 1 (mTORC1). J. Biol. Chem. 286, 25477–25486 CrossRef PubMed 135 Stracka, D., Jozefczuk, S., Rudroff, F., Sauer, U. and Hall, M.N. (2014) Nitrogen source activates TOR (target of rapamycin) complex 1 via glutamine and independently of Gtr/Rag proteins. J. Biol. Chem. 289, 25010–25020 CrossRef PubMed 136 Duran, R.V. and Hall, M.N. (2012) Glutaminolysis feeds mTORC1. Cell Cycle 11, 4107–4108 CrossRef PubMed 137 van Leeuwen, W., Okresz, L., Bogre, L. and Munnik, T. (2004) Learning the lipid language of plant signalling. Trends Plant Sci. 9, 378–384 CrossRef PubMed 138 Xue, H.W., Chen, X. and Mei, Y. (2009) Function and regulation of phospholipid signalling in plants. Biochem. J. 421, 145–156 CrossRef PubMed 139 Hopkins, B.D., Hodakoski, C., Barrows, D., Mense, S.M. and Parsons, R.E. (2014) PTEN function: the long and the short of it. Trends Biochem. Sci. 39, 183–190 CrossRef PubMed 140 Gupta, R., Ting, J.T., Sokolov, L.N., Johnson, S.A. and Luan, S. (2002) A tumor suppressor homolog, AtPTEN1, is essential for pollen development in Arabidopsis. Plant Cell 14, 2495–2507 CrossRef PubMed

13

141 Zhang, Y., Li, S., Zhou, L.Z., Fox, E., Pao, J., Sun, W., Zhou, C. and McCormick, S. (2011) Overexpression of Arabidopsis thaliana PTEN caused accumulation of autophagic bodies in pollen tubes by disrupting phosphatidylinositol 3-phosphate dynamics. Plant J. 68, 1081–1092 CrossRef PubMed 142 Pribat, A., Sormani, R., Rousseau-Gueutin, M., Julkowska, M.M., Testerink, C., Joubes, J., Castroviejo, M., Laguerre, M., Meyer, C., Germain, V. and Rothan, C. (2012) A novel class of PTEN protein in Arabidopsis displays unusual phosphoinositide phosphatase activity and efficiently binds phosphatidic acid. Biochem. J. 441, 161–171 CrossRef PubMed 143 Deak, M., Casamayor, A., Currie, R.A., Downes, C.P. and Alessi, D.R. (1999) Characterisation of a plant 3-phosphoinositide-dependent protein kinase-1 homologue which contains a pleckstrin homology domain. FEBS Lett. 451, 220–226 CrossRef PubMed 144 Anthony, R.G., Henriques, R., Helfer, A., Meszaros, T., Rios, G., Testerink, C., Munnik, T., Deak, M., Koncz, C. and Bogre, L. (2004) A protein kinase target of a PDK1 signalling pathway is involved in root hair growth in Arabidopsis. EMBO J. 23, 572–581 CrossRef PubMed 145 Herman, P.K. and Emr, S.D. (1990) Characterization of VPS34 , a gene required for vacuolar protein sorting and vacuole segregation in Saccharomyces cerevisiae . Mol. Cell. Biol. 10, 6742–6754 PubMed 146 Backer, J.M. (2008) The regulation and function of Class III PI3Ks: novel roles for Vps34. Biochem. J. 410, 1–17 CrossRef PubMed 147 Welters, P., Takegawa, K., Emr, S.D. and Chrispeels, M.J. (1994) AtVPS34, a phosphatidylinositol 3-kinase of Arabidopsis thaliana , is an essential protein with homology to a calcium-dependent lipid binding domain. Proc. Natl. Acad. Sci. U.S.A. 91, 11398–11402 CrossRef PubMed 148 Lee, Y., Bak, G., Choi, Y., Chuang, W.I. and Cho, H.T. (2008) Roles of phosphatidylinositol 3-kinase in root hair growth. Plant Physiol. 147, 624–635 CrossRef PubMed 149 Leprince, A.S., Magalhaes, N., De Vos, D., Bordenave, M., Crilat, E., Clement, G., Meyer, C., Munnik, T. and Savoure, A. (2014) Involvement of phosphatidylinositol 3-kinase in the regulation of proline catabolism in Arabidopsis thaliana . Front. Plant Sci. 5, 772 PubMed 150 Sun, Y., Fang, Y., Yoon, M.S., Zhang, C., Roccio, M., Zwartkruis, F.J., Armstrong, M., Brown, H.A. and Chen, J. (2008) Phospholipase D1 is an effector of Rheb in the mTOR pathway. Proc. Natl. Acad. Sci. U.S.A. 105, 8286–8291 CrossRef PubMed 151 Fang, Y., Vilella-Bach, M., Bachmann, R., Flanigan, A. and Chen, J. (2001) Phosphatidic acid-mediated mitogenic activation of mTOR signaling. Science 294, 1942–1945 CrossRef PubMed 152 Foster, D.A. (2013) Phosphatidic acid and lipid-sensing by mTOR. Trends Endocrinol. Metab. 24, 272–278 CrossRef PubMed 153 Veverka, V., Crabbe, T., Bird, I., Lennie, G., Muskett, F.W., Taylor, R.J. and Carr, M.D. (2008) Structural characterization of the interaction of mTOR with phosphatidic acid and a novel class of inhibitor: compelling evidence for a central role of the FRB domain in small molecule-mediated regulation of mTOR. Oncogene 27, 585–595 CrossRef PubMed 154 Groenewoud, M.J. and Zwartkruis, F.J. (2013) Rheb and Rags come together at the lysosome to activate mTORC1. Biochem. Soc. Trans. 41, 951–955 CrossRef PubMed 155 Li, M., Hong, Y. and Wang, X. (2009) Phospholipase D- and phosphatidic acid-mediated signaling in plants. Biochim. Biophys. Acta 1791, 927–935 CrossRef PubMed 156 Hong, Y., Pan, X., Welti, R. and Wang, X. (2008) Phospholipase Dα3 is involved in the hyperosmotic response in Arabidopsis. Plant Cell 20, 803–816 CrossRef PubMed 157 Jin, N., Mao, K., Jin, Y., Tevzadze, G., Kauffman, E.J., Park, S., Bridges, D., Loewith, R., Saltiel, A.R., Klionsky, D.J. and Weisman, L.S. (2014) Roles for PI(3,5)P 2 in nutrient sensing through TORC1. Mol. Biol. Cell 25, 1171–1185 CrossRef PubMed 158 Hirano, T., Matsuzawa, T., Takegawa, K. and Sato, M.H. (2011) Loss-of-function and gain-of-function mutations in FAB1A/B impair endomembrane homeostasis, conferring pleiotropic developmental abnormalities in Arabidopsis. Plant Physiol. 155, 797–807 CrossRef PubMed 159 Whitley, P., Hinz, S. and Doughty, J. (2009) Arabidopsis FAB1/PIKfyve proteins are essential for development of viable pollen. Plant Physiol. 151, 1812–1822 CrossRef PubMed 160 Serrazina, S., Dias, F.V. and Malho, R. (2014) Characterization of FAB1 phosphatidylinositol kinases in Arabidopsis pollen tube growth and fertilization. New Phytol. 203, 784–793 CrossRef PubMed 161 Bevan, M. and Walsh, S. (2005) The Arabidopsis genome: a foundation for plant research. Genome Res. 15, 1632–1642 CrossRef PubMed  c 2015 Authors; published by Portland Press Limited

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D. Rexin and others

162 Urano, D. and Jones, A.M. (2013) “Round up the usual suspects”: a comment on nonexistent plant G protein-coupled receptors. Plant Physiol. 161, 1097–1102 CrossRef PubMed 163 Taddese, B., Upton, G.J.G., Bailey, G.R., Jordan, S.R. D., Abdulla, N.Y., Reeves, P.J. and Reynolds, C.A. (2014) Do plants contain G protein-coupled receptors? Plant Physiol. 164, 287–307 CrossRef PubMed 164 Vanstraelen, M. and Benkov´a, E. (2012) Hormonal interactions in the regulation of plant development. Annu. Rev. Cell Dev. Biol. 28, 463–487 CrossRef PubMed 165 Katsir, L., Davies, K.A., Bergmann, D.C. and Laux, T. (2011) Peptide signaling in plant development. Curr. Biol. 21, R356–R364 CrossRef PubMed 166 Sparks, E., Wachsman, G. and Benfey, P.N. (2013) Spatiotemporal signalling in plant development. Nat. Rev. Genet. 14, 631–644 CrossRef PubMed Received 28 April 2015/22 May 2015; accepted 8 June 2015 Published on the Internet 6 August 2015, doi:10.1042/BJ20150505

 c 2015 Authors; published by Portland Press Limited

167 Shiu, S.H., Karlowski, W.M., Pan, R., Tzeng, Y.H., Mayer, K.F. and Li, W.H. (2004) Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell 16, 1220–1234 CrossRef PubMed 168 Gish, L.A. and Clark, S.E. (2011) The RLK/Pelle family of kinases. Plant J. 66, 117–127 CrossRef PubMed 169 Bommert, P., Je, B.I., Goldshmidt, A. and Jackson, D. (2013) The maize Gα gene COMPACT PLANT2 functions in CLAVATA signalling to control shoot meristem size. Nature 502, 555–558 CrossRef PubMed 170 Menand, B. (2002) Etude par g´en´etique inverse du g`ene codant la prot´eine TARGET OF RAPAMYCIN d’Arabidopsis thaliana (AtTOR). Ph.D. Thesis, Universit´e Louis Pasteur, Strasbourg, France