New Results

Arabidopsis inositol phosphate kinases, IPK1 and ITPK1, constitute a metabolic pathway in maintaining phosphate homeostasis

Hui-Fen Kuo, Yu-Ying Hsu, Wei-Chi Lin, Kai-Yu Chen, Teun Munnik, Charles A. Brearley, Tzyy-Jen Chiou
doi: https://doi.org/10.1101/270355

Summary

Emerging studies have implicated a close link between inositol phosphate (InsP) metabolism and cellular phosphate (Pi) homeostasis in eukaryotes; however, whether a common InsP species is deployed as an evolutionarily conserved metabolic messenger to mediate Pi signaling remains unknown. Here, using genetics and InsP profiling combined with Pi starvation response (PSR) analysis in Arabidopsis thaliana, we showed that the kinase activity of inositol pentakisphosphate 2-kinase (IPK1), an enzyme required for phytate (inositol hexakisphosphates; InsP6) synthesis, is indispensable for maintaining Pi homeostasis under Pi-replete conditions, and inositol 1,3,4-trisphosphate 5/6-kinase 1 (ITPK1) plays an equivalent role. Although both ipk1-1 and itpk1 mutants exhibited decreased levels of InsP6 and diphosphoinositol pentakisphosphate (PP-InsP5; InsP7), disruption of another ITPK family enzyme, ITPK4, which correspondingly caused depletion of InsP6 and InsP7, did not display similar Pi-related phenotypes, which precludes these InsP species as effectors. Notably, the level of D/L-Ins(3,4,5,6)P4 was concurrently elevated in both ipk1-1 and itpk1 mutants, which implies a potential role for InsP4 in regulating Pi homeostasis. However, the level of D/L-Ins(3,4,5,6)P4 is not responsive to Pi starvation that instead manifests a shoot-specific increase in InsP7 level. This study demonstrates a more nuanced picture of intersection of InsP metabolism and Pi homeostasis and PSR than has previously been elaborated, and additionally establishes intermediate steps to phytate biosynthesis in plant vegetative tissues.

Significance Statement Regulation of phosphate homeostasis and adaptive responses to phosphate limitation is critical for plant growth and crop yield. Accumulating studies implicate inositol phosphates as regulators of phosphate homeostasis in eukaryotes; however, the relationship between inositol phosphate metabolism and phosphate signaling in plants remain elusive. This study dissected the step where inositol phosphate metabolism intersects with phosphate homeostasis regulation and phosphate starvation responses.

Introduction

Elemental phosphorous (P) in its oxidized form, phosphate (PO43−; Pi), is essential to all life. As a component of nucleic acids, proteins, phospholipids and numerous intermediary metabolites, Pi is key to energy metabolism and signal transduction. Plants preferentially acquire P in the form of Pi from the rhizosphere, where Pi is often limiting owing to its sorption to soil particles and leaching (Holford, 1997). As an adaptation to fluctuating external Pi concentrations, plants have evolved intricate regulatory mechanisms to maintain cellular Pi homeostasis in vegetative tissue in order to coordinate growth, development, and reproduction, whereas in seeds, Pi is reserved in phytate (inositol hexakisphosphate, InsP6) that accumulates to several percentage dry weight (Raboy, 1997). In response to Pi deficiency, plants initiate a systematic response, termed the Pi-starvation response (PSR), which involves transcriptional, metabolic, and morphological reprogramming, to enhance Pi uptake, allocation, remobilization, and conservation (Rouached et al., 2010; Yang and Finnegan, 2010). Under Pi-replete or -replenishment conditions, plant cells relieve PSR and store excess Pi in the vacuole to avoid cellular toxicity as a result of cytosolic Pi surge (Müller et al., 2004; Lin et al., 2013; Liu et al., 2015; Liu et al., 2016). How plant cells perceive external and cellular Pi status to maintain Pi homeostasis remains elusive despite reports of multiple factors proposed to be signaling molecules, including sugar, phytohormones, microRNAs, InsPs and Pi per se (Martin et al., 2000; Franco-Zorrilla et al., 2005; Liu et al., 2005; Bari et al., 2006; Chiou et al., 2006; Chiou and Lin, 2011; Puga et al., 2014; Wang et al., 2014).

Inositol phosphates (InsPs) are metabolites of variable phosphorylation on a carbohydrate core, inositol, and are present in all eukaryotes. They are synthesized by evolutionarily conserved enzymes (Irvine and Schell, 2001) and play important roles in diverse cellular processes by functioning as structural and functional cofactors, regulators, and second messengers (Shears et al., 2012). According to the definition of a ‘signal’, being that of agonist-responsive change in concentration that is recognized by a defined receptor (Shears et al., 2012), only very few InsPs can be considered true signaling molecules, including Ins(1,4,5)P3 in the context of Ca2+ signaling (Berridge, 2009) and Ins(3,4,5,6)P4 as a regulator of the conductance of the Ca2+-activated chloride channels (Vajanaphanich et al., 1994; Shears et al., 2012). In plants, InsPs have been hypothesized to mediate signaling of multiple physiological processes, including stomatal closure, gravitropism, drought tolerance, and defense (Lemtiri-Chlieh et al., 2000; Lemtiri-Chlieh et al., 2003; Perera et al., 2006; Mosblech et al., 2008; Murphy et al., 2008; Perera et al., 2008; Laha et al., 2015); however, their roles as signaling messengers in most cases have not been assessed extensively.

The first elaboration of the involvement of InsPs in eukaryotic Pi homeostasis was revealed when a rabbit cDNA clone was shown to stimulate Pi uptake when ectopically expressed in Xenopus oocytes (Norbis et al., 1997). This so-called Pi uptake stimulator (PiUS) was identified to encode an InsP6 kinase (IP6K) that converts InsP6 to diphosphoinositol pentakisphosphates (PP-InsP5 or InsP7) (Norbis et al., 1997; Schell et al., 1999). In yeast, disruption of multiple enzymes responsible for biosynthesis of InsPs and diphosphoinositol phosphates (PP-InsPs) (e.g., Plc1p, Arg82p, and Kcs1p) led to constitutive activation of a Pi starvation-responsive phosphatase-coding gene, Pho5, under Pi-replete conditions (Auesukaree et al., 2005). Subsequent work showed that the synthesis of InsP7 by the other family of PP-InsP kinases (Vip1/PPIP5K), Vip1, is stimulated by Pi starvation (Lee et al., 2007) and InsP7 binds to Pho81, causing inhibition of the Pho80-Pho85 cyclin-cyclin–dependent kinase complex and unphosphorylation of the Pho4 transcription factor. The resulting reduction in phosphorylation of Pho4 localizes this protein to the nucleus, where it activates Pi starvation-inducible genes (Lee et al., 2007; Lee et al., 2008). The synthesis of PP-InsPs is also metabolically linked to the synthesis of the main intracellular Pi storage molecule, a linear chain of polyphosphate (polyP), and the yeast IP6K mutant, kcs1Δ, fails to accumulate polyP (Auesukaree et al., 2005; Lonetti et al., 2011).

Cellular adenylate energy is influenced by Pi availability and PP-InsP synthesis (Boer et al., 2010; Szijgyarto et al., 2011; Choi et al., 2017) and itself regulates the synthesis of PP-InsP (Voglmaier et al., 1996; Saiardi et al., 1999; Wundenberg et al., 2014). Together with the genetic and molecular evidence described previously, PP-InsPs have been proposed as metabolic messengers that mediate Pi signaling. This hypothesis is further supported by structural and biochemical analyses demonstrating that InsPs and PP-InsPs bind to an evolutionarily conserved SYG1/PHO81/XPR1 (SPX) domain present in proteins that play key roles in Pi sensing and transport, with PP-InsPs showing the highest binding affinity (at sub-micromolar concentrations for yeast and animal protein) (Secco et al., 2012; Secco et al., 2012; Wild et al., 2016). Disruption of InsP/PP-InsP binding sites in the SPX domain impaired yeast vacuolar transporter chaperone (VTC)-dependent polyP synthesis and failed to complement Pi-related phenotypes of the Arabidopsis phosphate 1 (pho1) mutant (Wild et al., 2016). Despite the wealth of current investigation, the evidence for PP-InsPs as evolutionally conserved messengers in eukaryotic Pi signaling is scattered, confounded by the absence of Pho80-Pho85-Pho81 homologs in other eukaryotic organisms and the contradictory responses of InsP7 levels to Pi starvation reported in yeast (Lee et al., 2007; Wild et al., 2016) as well as the presence of a Vip1-independent PHO signaling pathway (Choi et al., 2017).

In plants, a contemporary implication of InsP metabolism in regulation of Pi homeostasis comes from a study in which genetic disruption of the kinase responsible for InsP6 synthesis, inositol pentakisphosphate 2-kinase (IPK1), causes excessive Pi accumulation (Stevenson-Paulik et al., 2005) as a result of elevated Pi uptake/allocation activities and activation of a subset of Pi starvation-responsive genes (PSR genes) under Pi-replete conditions (Kuo et al., 2014). In addition to decreased InsP6 level, ipk1 mutation causes a significant change in InsP composition, including accumulation of lower phosphorylated InsP species (e.g., InsP3, InsP4 and InsP5) and decreased levels of PP-InsPs [InsP7 and InsP8 (bisdiphosphoinositol tetrakisphosphate)] (Stevenson-Paulik et al., 2005; Laha et al., 2015). The mechanism of IPK1 modulating Pi homeostasis and whether InsPs play a role in Pi-starvation signaling in plants is currently unknown.

As compared with the situation in other eukaryotic organisms, the investigation of biosynthesis of InsPs and their composition in the vegetative tissues of plants is necessarily more complicated than in other eukaryotes due to the presence of complex gene families of InsP biosynthesis enzymes. Mammalian InsP metabolism is dominated by receptor-coupled activation of phospholipase C (PLC) and subsequent metabolic conversion of Ins(1,4,5)P3 to multiple higher and lower InsPs (Irvine and Schell, 2001), but few plant studies offer detailed identification of InsP species in vegetative tissues due to the limited levels of labeling achieved with myo-[3H]inositol. Nevertheless, specific short-term non-equilibrium labeling with [32P]Pi has afforded a metabolic test capable of distinguishing the order in which phosphates are added to the inositol core (Stephens and Downes, 1990; Stephens and Irvine, 1990; Whiteford et al., 1997) and applied to vegetative tissues of plants that revealed a ‘lipid-independent’ pathway of InsP6 synthesis (Brearley and Hanke, 1993; Brearley et al., 1997).

Here, using reverse genetics and InsP profiling by [3H]inositol and [32P]Pi labelling, we show that maintenance of Pi homeostasis in plants under Pi-replete conditions depends on the kinase activity of IPK1 and an additional inositol 1,3,4-trisphosphate 5/6-kinase ITPK1. Profile comparison of InsPs between ipk1-1, itpk1, and another mutant defective in InsP6 synthesis, itpk4, reveals a correlation between elevated D/L-Ins(3,4,5,6)P4 [Ins(1,4,5,6)P4 and/or Ins(3,4,5,6)P4] level and activation of Pi uptake and PSR gene expression. However, the InsP profile in response to Pi starvation is distinct from that of the ipk1-1 and itpk1 mutants and marked a shoot-specific increase in InsP7 level accompanied by ATP increase. Our study reveals a complex relationship between InsP metabolism and Pi homeostasis in plants and identifies ITPK4 as a key enzyme in generating InsP4 precursors for phytate biosynthesis.

Results

Kinase activity of IPK1 is required for maintenance of Pi homeostasis

We previously demonstrated Pi overaccumulation in ipk1-1 mutants associated with activation of PSR genes involved in Pi uptake, allocation, remobilization, and signaling (Kuo et al., 2014). Because InsP kinases have been implicated in transcriptional regulation independent of their catalytic activities (Bosch and Saiardi, 2012; Xu et al., 2013; Xu et al., 2013), we examined whether regulation of Pi homeostasis by IPK1 is kinase-dependent. We constructed two forms of IPK1 bearing mutations in conserved kinase motifs (Stevenson-Paulik et al., 2005) (Figure S1A) at Lys168 (IPK1K168A) or Asp368 (IPK1D368A), both shown to cause loss of kinase activity in vitro (Gonzalez et al., 2010). The expression of wild-type (WT) IPK1 complemented low InsP6 content in ipk1-1 seeds, whereas InsP6 levels in seeds of transgenic lines expressing either of the two point-mutated forms of IPK1 remained as low as that in ipk1-1 seeds (Figure 1A). These point-mutated IPK1 forms were expressed both at the transcriptional and translational levels (Figures 1B and S1B), with subcellular protein localization in the cytosol and nucleus, similar to the WT IPK1 (Figure S1C). These results indicated that Lys168 and Asp368 are required for kinase activity of IPK1 in vivo.

Figure 1.
Figure 1. Characterization of kinase-inactive IPK1 transgenic plants.

(A) Relative InsP6 content (% of WT) in seeds of ipk1-1 mutants and homozygous transgenic lines expressing C-terminus YFP-tagged wild-type IPK1 (IPK1-YFP), IPK1K168A (IPK1K168A-YFP), or IPK1D368A (IPK1D368A-YFP) coding sequences in the ipk1-1 mutant background. Error bars, S.E. of n=3-12 independent experiments. (B) Relative expression (to WT) of PSR genes in roots, and (C) Pi content in shoots of 14-days after germination (DAG) seedlings. Asterisks indicate significant differences from WT (Student’s t-test; **, P < 0.005).

In contrast to WT IPK1, which was able to restore the Pi content of the ipk1-1 mutant to the WT level, both kinase-inactive IPK1 forms failed to complement excessive Pi accumulation and PSR gene activation in ipk1-1 (Figure 1B-C). Therefore, the kinase activity of IPK1 is required for regulation of Pi homeostasis. In addition to regulating Pi content, the kinase activity of IPK1 is also required for root system architecture (RSA), because neither of the kinase-inactive IPK1 proteins complemented the PSR-like RSA phenotypes (i.e., reduced primary root and enhanced lateral root growth) of ipk1-1 (Figure S1D).

Misregulation of Pi homeostasis in ipk1-1 is not caused by defective InsP6-mediated mRNA export

In yeast, InsP6 is required for mRNA export by activating the RNA-dependent ATPase activity of DEAD-box protein 5 (Dbp5p) in conjunction with GLFG lethal 1 (Gle1p), and mutations in ipk1 and gle1 resulted in mRNA retention in the nucleus and temperature-sensitive growth defects (York et al., 1999; Alcazar-Roman et al., 2006). A conserved mechanism was recently reported in Arabidopsis, and part of the growth defect of ipk1-1 is attributed to compromised mRNA export due to reduced level of InsP6 (Lee et al., 2015). To address whether defective mRNA export in the ipk1-1 mutant is a cause of the misregulation of Pi homeostasis, we examined Pi-related phenotypes of the mRNA export mutants reported (Lee et al., 2015). As shown in Figure S2, the loss-of-function mutation in the Dbp5 homologous gene LOW EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 4 (LOS4), and inducible GLE1 RNAi lines exhibited WT Pi content (Figure S2A-B) and PSR gene expression (Figure S2C). Furthermore, expression of variants of Gle1 (IS1 and IS2), which exhibit increased InsP6 sensitivity to LOS4 stimulation and improved growth defects of ipk1-1 (Lee et al., 2015), did not reduce Pi content or suppress PSR gene activation of the ipk1-1 mutant (Figure S2C-D). These results suggest that misregulation of Pi homeostasis in ipk1-1 is not caused by defective mRNA export due to reduced InsP6 level.

Genetic dissection of the roles for InsP and PP-InsP biosynthesis enzymes in Pi homeostasis regulation

The dependence of Pi homeostasis on the kinase activity of IPK1 suggested that the PSR activation signal is derived from InsP biosynthesis. To dissect which step(s) of InsP and PP-InsP biosynthesis controls this signal, we examined Pi-related phenotypes of mutants defective in several InsP and PP-InsP biosynthesis enzymes previously characterized in Arabidopsis, including myo-inositol-3-phosphate synthases (MIPS1-3) (Torabinejad and Gillaspy, 2006), Ins(1,4,5)P3 6-/3-kinases (inositol phosphate multikinases; IPK2α and IPK2β) (Stevenson-Paulik et al., 2002), Ins(1,3,4)P3 5-/6-kinase enzymes (inositol phosphate tris/tetrakisphosphate kinases; ITPK1-4) (Wilson and Majerus, 1997; Sweetman et al., 2007), PP-InsP synthesizing enzyme PPIP5K (VIP1/VIH2 and VIP2/VIH1) (Desai et al., 2014; Laha et al., 2015), and a mutant of an InsP6 transporter, multidrug resistance-associated protein 5 (MRP5) (Nagy et al., 2009). T-DNA insertional mutants were obtained and confirmed by RT-PCR to be null mutants (Table S1, Figure S3A-B).

Morphologically, none of the mutants displayed growth defects as severe as ipk1-1 (stunted growth and leaf necrosis), although mips1, itpk1 and mrp5-2 mutants were smaller than the WT (Figure 2A). The leaf epinasty and PSR-like RSA phenotypic characteristics of ipk1-1 mutants (Stevenson-Paulik et al., 2005; Kuo et al., 2014) were observed in itpk1 and mrp5-2 mutants (Figures 2A and S3C-D) (Kuo et al., 2014). Analysis of Pi content in the shoot tissues revealed that only itpk1 accumulated excessive Pi comparable to ipk1-1 (Figure 2B), and this phenotype persisted to the mature stage (Figure S3E). Mild but significantly elevated Pi content was observed in mrp5-2 seedlings but was no longer seen at the mature stage (Figures 2B and S3E). Consistent with the elevated Pi content, itpk1 exhibited elevated uptake of Pi activity comparable with that of ipk1-1, whereas all other mutants showed WT activities (Figure 2C-F). The excessive Pi accumulation in itpk1 mutants could be restored to the WT level by ectopic expression of a genomic construct of the ITPK1 sequence (Figure S4A), which confirms a role for ITPK1 in regulating Pi homeostasis.

Figure 2.
Figure 2. Characterization of mutants defective in InsP biosynthesis enzymes grown under Pi-replete condition.

(A) Morphology of 22-DAG plants grown in Pi-replete (1 mM) hydroponic medium. Scale bar, 1 cm. (B) Pi content in the shoots of 14-DAG seedlings grown on Pi-replete (1 mM) solid medium. Error bar, S.E. of n=4-21 independent experiments. (C-F) Pi uptake activities of 14-DAG seedlings under Pi-replete (250 μM) growth conditions. Error bars, S.E. of n=3-24 independent experiments. Uptake activities of genotypes in (A-C) were measured in overlapping sets of experiments and plotted separately for clear presentation. Asterisks denote significant differences from the WT (Student’s t-test; **, P < 0.005).

In addition to decreased InsP6 level, levels of InsP7 and InsP8 are also reduced in ipk1-1 mutants (Laha et al., 2015). We therefore examined whether PP-InsPs also play a role in the regulation of Pi homeostasis or PSR in plants. Two families of kinases, IP6K and Vip/PPIP5K, are involved in PP-InsP synthesis in eukaryotes (Wundenberg et al., 2014); however, only Vip1/PPIP5K homologs are identified in plants and shown to be responsible for InsP8 but not InsP7 synthesis in Arabidopsis (Mulugu et al., 2007; Desai et al., 2014; Laha et al., 2015). We analyzed mutants defective in each of the two Arabidopsis Vip1/PPIP5K homologs, AtVIP1/VIH2 and AtVIP2/VIH1, and observed slightly decreased Pi content in two alleles of atvip1 mutants (abbreviated as vip1-1 and vip1-2) with T-DNA disrupting the phosphatase-like domain but not in the alleles disrupted in the ATP-grasp kinase domain (vih2-3 and vih2-4) (Figure S3B) (Laha et al., 2015). Three atvip2 mutants (abbreviated as vip2-1, vip2-2 and vih1) did not show Pi-content phenotype, but vip1-2 vip2-1 double mutants exhibited lower Pi content comparable to the vip1-2 single mutant (Figures 2B and S3E), which suggests a dominant role for vip1 mutation in determining this phenotype. Despite the lower Pi content, Pi uptake and root-to-shoot allocation activity did not change in the vip1-1 or vip1-2 mutants (Figures 2F and S5A). Furthermore, the expression of PSR genes under Pi-replete conditions and the magnitude of PSR gene activation in response to Pi starvation in the vip1/vih2 and vip2/vih1 mutants were similar to that in the WT (Figure S5B-C). The cause of reduced Pi content observed in vip1 alleles defective in the phosphatase-like domain is unclear, but the contrasting Pi-related phenotypes between these vip1 alleles and ipk1-1 indicates that the decreased level of InsP8 in ipk1 mutants is not responsible for Pi homeostasis misregulation.

ITPK1 and IPK1 constitute a pathway involved in the maintenance of Pi homeostasis

The common phenotypes observed in itpk1 and ipk1-1 mutants (i.e., excessive Pi accumulation and elevated Pi uptake under Pi-replete growth conditions) suggest that ITPK1 and IPK1 are involved in the same pathway that regulates Pi homeostasis.

Consistently, a common set of representative PSR genes was upregulated in itpk1 and ipk1-1 mutants (Figure 3A), and overexpression of ITPK1 or IPK1 reduced shoot Pi content (Figure 3B). Correspondingly, ITPK1 overexpression significantly decreased Pi uptake activity, in contrast to the elevated uptake activity shown by itpk1 mutants (Figure 3C). In addition, several PSR genes were downregulated in ITPK1-overexpressing lines as compared with the WT (Figure 3A, e.g., PHT1;2, SPX1, AT4, IPS1 and PAP17). However, Pi-uptake activity and PSR gene expression did not differ significantly between IPK1-overexpression lines and the WT (Figure 3A-D).

Figure 3.
Figure 3. Phenotype similarities between itpk1, ipk1-1 mutants, and overexpression lines.

(A) Relative expression (to WT) of PSR genes in roots of 14-DAG itpk1, ipk1-1, IPK1-overexpression (OxIPK1) and ITPK1-overexpression (OxITPK1) lines grown under Pi-replete (1 mM) conditions (see Supporting Table S3 for qPCR raw data and S.E. of 3 independent experiments). Note that qPCR primers for ITPK1 are located 5’ to the T-DNA insertion site. (B) Pi content in shoots of 14-DAG T2 transgenic lines overexpressing ITPK1 or IPK1 compared to WT, itpk1 and ipk1-1 mutants grown under Pi-replete (250 μM) condition. Error bars, S.E. of n=6-12 independent experiments. (C and D) Pi uptake activities of 14-DAG seedlings grown under Pi-replete (250 μM Pi) condition. Error bars, S.E. of n=6-12 independent experiments. Asterisks denote significant differences from the WT (Student’s t-test; **, P < 0.005).

We drew additional support for the participation of ITPK1 and IPK1 in a common pathway regulating Pi homeostasis in terms of their tissue-specific expression patterns and subcellular localization. Promoter-GUS activity assay and RT-PCR analysis demonstrated co-expression of ITPK1 and IPK1 throughout development and in specific tissues and cell types, such as vasculature, trichomes and guard cells (Figure 4A-K). In addition, neither gene was transcriptionally responsive to Pi status (Figure 4L). The expression of ITPK1 native protein fused to yellow fluorescent protein (YFP), which restored Pi content of the itpk1 mutant to the WT level (Figure S4B), demonstrated co-localization of ITPK1 and IPK1 in the nucleus and cytoplasm (Figures 4M and S1C) (Kuo et al., 2014).

Figure 4.
Figure 4. Tissue-specific expression and protein subcellular localization of ITPK1 and IPK1, and phenotypes of itpk1, ipk1-1 and itpk1 ipk1-1 double mutants.

(A-J) Promoter activities of IPK1 and ITPK1 at different developmental stages. (A) 3-DAG; scale bar, 10 μm. (B) 5-DAG; scale bar, 1 mm. (C) 7-DAG; scale bar, 1 mm. (D) 14-DAG; scale bar, 1 cm. (E) Cross section of 14-DAG root; scale bar, 10 μm. (F) Guard cells of 14-DAG leaves; scale bar, 10 μm. (G) Trichome of 14-DAG leaves; scale bar, 0.1 mm. (H) 22-DAG floral tissues; scale bar, 0.5 cm. (I) 22-DAG flowers; scale bar, 0.5 mm. (J) Siliques; scale bar, 0.5 mm. (K and L) RT-PCR analysis of tissue-specific expression of ITPK1 and ITPK4 at different developmental stages (K) and in response to Pi status (L). S, shoot; R, root; LF, rosette leaves; FS, florescence stem; FL, flower; SL, silique; +P, 250 μM Pi; −P, 10 μM Pi. PCR amplification cycles for ITPK1, 32; ITPK4, 32; ACTIN2, 22. (M) Subcellular localization of C-terminus YFP-tagged IPK1 and ITPK1 protein in roots of 10-DAG ipk1-1 and itpk1 mutants, respectively; scale bar, 10 μm. Arrows, cytoplasm, arrowheads, nucleus. (N) Morphology of 25-DAG itpk1 ipk1-1 mutants grown under Pi-replete (250 μM) conditions. Insets show enlarged images of floral tissues (a), rosette leaves (b), roots (c), mature siliques (d) and aborted seeds (e). Scale bars are 1 cm, 1 mm and 100 μm for the whole plant, insets (a-d) and inset (e), respectively. (O) Tissue-specific Pi content and (P) relative expression of PSR genes of 16-DAG seedlings grown on Pi-replete (250 μM) solid medium. Error bar, S.E. of n=3-6 independent experiments. Asterisks denote significant differences from the WT (Student’s t-test; *, P < 0.05; **, P < 0.005).

We next examined the genetic interaction of ITPK1 and IPK1 with a genetic cross between ipk1-1 and itpk1 mutants. The ipk1-1 itpk1 double mutants exhibited more severe growth defects than single mutants (Figure 4N) and those that proceeded to the reproductive stage bore aborted seeds (Figure 4Nd and 4Ne]. Tissue Pi content was greater in ipk1-1 itpk1 double than single mutants, by 50% to 70%, which is likely attributed to the relative 50% to 80% reduction in fresh weight (Figure 4O). Notably, expression of PSR genes in ipk1-1 itpk1 double and single mutants was comparable (Figure 4P), which suggests IPK1 and ITPK1 function in a common regulatory pathway of Pi homeostasis.

A common elevation of D/L-Ins(3,4,5,6)P4 in itpk1 and ipk1-1 mutants

The observations that maintenance of Pi homoeostasis depends on (1) the kinase activity of IPK1, (2) an additional InsP kinase, ITPK1, and (3) the expression level of ITPK1 and IPK1 (i.e., contrary Pi-related phenotypes between mutants and overexpression lines), suggest the contribution of a stoichiometric alteration of InsP metabolites to Pi homeostasis regulation. To pinpoint the possible InsP molecules involved in such regulation, we compared InsP profiles of vegetative tissues of the relevant genotypes by in vivo labeling with [32P]Pi and/or myo-[3H]inositol and HPLC analysis. As shown in Figure 5A, Figure 5B, and myo-[3H]inositol-labeled chromatogram in Supporting Figure S6A, the itpk1 mutant shared a significant reduction in InsP6 (62 ± 2% WT) with the ipk1-1 mutant (17 ± 1% WT). To validate that reduced InsP6 level is not a cause of misregulated Pi homeostasis, with the normal Pi-related phenotypes exhibited by another low-InsP6 mutant mips1 (Murphy et al., 2008; Kuo et al., 2014), we analyzed the InsP profile of the mips1 mutant. Unexpectedly, mips1 mutants exhibited a WT level of InsP6 (Figures 5A-B and S6A). For comparison, we also performed profile analysis of other itpk mutants and found that two itpk4 mutants (itpk4-1 and itpk4-2; Table S1) showed a strong reduction in InsP6 level comparable to itpk1 and ipk1-1 mutants, by 50% and 80%, respectively (Figures 5A-B and S6A). Consistent with the previous report, itpk4 mutations also significantly reduced InsP6 level in seeds, to a similar extent as ipk1-1 (Figure S7A) (Stevenson-Paulik et al., 2005; Kim and Tai, 2011). The itpk4 mutants did not show striking morphological phenotypes (Figures 2A and S3C) or Pi-related phenotypes, such as altered Pi content (Figures 2B, S3E and S7B), Pi uptake (Figure 2E), or altered PSR gene expression (Figure S7C). RT-PCR and promoter-GUS analysis indicated that ITPK4 was expressed in the same vegetative tissues as ITPK1 and IPK1 (Figure S7D-L), which suggests that ITPK4 is likely involved in the same tissue-specific pool of InsP6 biosynthesis. In addition, YFP-tagged ITPK4, which complemented the seed-InsP6 phenotype of the itpk4-1 mutant (Figure S7A), like ITPK1 and IPK1, was also localized to the nuclei and cytoplasm (Figure S7M). Hence, reduced InsP6 level alone is insufficient to alter Pi homeostasis and ITPK4 is a key enzyme for InsP6 biosynthesis in both vegetative tissues and seeds.

Figure 5.
Figure 5. InsP profiles of various genotypes.

(A) HPLC analysis of roots extracts from 11-DAG seedlings of various genotypes labeled with [32P]Pi. InsP5a, Ins(1,2,4,5,6)P5 and/or Ins(2,3,4,5,6)P5 and/or Ins(1,2,3,4,6)P5 (these three isomers are not resolved on Partisphere SAX HPLC (Brearley and Hanke, 1996); InsP5b, Ins(1,3,4,5,6)P5; InsP4*, Ins(1,4,5,6)P4 and/or Ins(3,4,5,6)P4; InsP3, peaks with the chromatographic mobility of InsP3s. Insets show expanded chromatograms of more polar InsPs, obtained by counting 1-min fractions collected from the Flo-Detector eluted from retention time of 50 min onwards. The ordinate is scaled by the same factor for the different genotypes, representing a constant fraction of the largest (Pi) peak in each chromatogram. (B) Quantification of relative InsP6 content (% of total radioactivity per HPLC run recovered in the integrated InsP6 peak) in 11-DAG [32P]Pi-labeled seedlings. Error bar, S.E. of n=3-5 independent experiments. Double asterisks denote a significant difference from the WT (Student’s f-test, P < 0.005). (C) Identity of InsP4* in itpk1 mutant. An aliquot of extract of [32P]Pi-labeled itpk1 seedlings (11-DAG) was spiked with a hydrolysate of InsP6 and separated on a CarboPac PA200 column with post-column colourimetric detection of InsP peaks as described (Phillippy and Bland, 1988). Upper panel, [32P]-radioactivity counted inline on the Flo Detector. Note that InsP4 and InsP5 are below the level of detection on the Flo Detector, and therefore corresponding fractions (0.5 min) were collected for static counting (lower panel). Middle panel, UV trace obtained from this extract. Ins(1,4,5,6)P4/Ins(3,4,5,6)P4 is the latest eluting InsP4 on this column and elutes before Ins(1,2,3,4,6)P5. Lower panel, UV trace overlaid with [32P] counts of collected fractions. The retention time of the fractions in the upper and lower panel is corrected for the plumbing delay between the UV detector and the Flo Detector or the fraction collector. The broadness of the [32P] peaks (compared to the sharp UV peaks) is a consequence of band broadening after the UV detector (in the Flo Detector and the collected fractions). All the other InsP4 isomers elute before 20 min. InsP5[5-OH], Ins(1,2,3,4,6)P5; InsP5[4/6-OH], Ins(1,2,3,5,6)P5 and/or Ins(1,2,3,4,5)P5; InsP5[1/3-OH], Ins(1,2,4,5,6)Ps and/or Ins(2,3,4,5,6)P5; InsP5[2-OH], Ins(1,3,4,5,6)P5. Note that a single peak of InsP4 was detected in itpk1 in (A). (D) Isocratic separation and counting of collected fractions for analysis of InsP3 isomers. For better presentation, the chromatogram of each genotype was shifted by 200 CPM.

In accordance with decreased InsP6 level, InsP7 level was also decreased in the ipk1-1 mutant (Figure 5A) (Laha et al., 2015). Similarly, InsP7 level was decreased in itpk1 and itpk4 mutants (Figure 5A), and therefore we could not draw a correlation between the reduced InsP7 level and the Pi-related phenotypes observed in ipk1-1 and itpk1. The ipk1-1 mutant shows significant accumulation of Ins(1,3,4,5,6)P5 along with reduced InsP6 level (InsP5b in Figures 5A and S6A) (Stevenson-Paulik et al., 2005), but in contrast, there was no detectable accumulation in the corresponding InsP5 in the itpk1 mutant. This finding suggests that the elevated Ins(1,3,4,5,6)P5 level in the ipk1-1 mutant does not explain the misregulation of Pi homeostasis.

Notably, the itpk1 mutant showed elevated level of an InsP4 species with identical chromatographic mobility to that in the ipk1-1 mutant, which is predominantly Ins(3,4,5,6)P4 (InsP4* in Figures 5A and S6A) (Stevenson-Paulik et al., 2005). The InsP4 species in the itpk1 mutant was further analysed by high-resolution HPLC separation and was co-eluted with D/L-Ins(3,4,5,6)P4 standard (D/L enantiomers are not separable by existing chromatographic technologies) (Figure 5C). In addition to the increase in InsP4 level, levels of earlier eluting InsP species were increased in both itpk1 and ipk1-1 mutants, which exhibited the chromatographic mobility of InsP3 (Figures 5A and S6A). Because there are 20 possible InsP3 isomers, being the most difficult InsP to resolve, isocratic HPLC analysis was performed under conditions designed for optimal resolution of these peaks (Wreggett and Irvine, 1989). As shown in Figure 5D, ipk1-1 and itpk1 mutations caused accumulation of distinct InsP3 isomers that were not detectable in the WT. Inclusion of an internal standard of myo-[3H]Ins(1,4,5)P3 revealed that these isomers are not Ins(1,4,5)P3, which was shown to present only a trivial fraction of InsP3 in plant tissues (Brearley and Hanke, 2000). We conclude that the only common change of InsP species associated with the Pi-related phenotypes of ipk1-1 and itpk1 is the elevated D/L-Ins(3,4,5,6)P4 level.

Pi starvation induced a shoot-specific increase of InsP7

To address whether itpk1 and ipk1-1 mutants exhibit an InsP profile that shares a common feature with Pi-starvation responses, we investigated the change in InsP profiles in shoots and roots of WT plants in response to different Pi-starvation regimes. InsP profiles were analyzed in seedlings subjected to 1- and 3-day Pi starvation, when cellular Pi concentrations were significantly reduced and PSR genes induced (Figure S8A-B). To avoid biased quantifications of InsPs caused by elevated Pi-uptake activities during Pi starvation, we performed a pulse-chase experiment with seedlings labeled with [32P]Pi before Pi starvation. Tissues were similarly radiolabeled in every pairwise ‘+P’ vs. ‘−P’ treatment, although more [32P] was allocated to shoots than roots (Figure 6A-B).

Figure 6.
Figure 6. Tissue-specific InsP profiles in response to 1- and 3-day Pi starvation.

(A) Chromatograms of HPLC analysis of [32P]Pi-labeled WT seedlings after 1- and 3-day Pi-replete (+P, 250 μM) or Pi-deficient (−P, 10 μM) treatments. 8-DAG seedlings were labeled with [32P]Pi under Pi-replete conditions for 3 days (“pulse“) before transfer to unlabeled media (“chase“). Insets show enlarged chromatograms of more polar InsPs, plotted from scintillation counts of 1-min fractions collected from retention time 50 min onwards. For clearer presentation, [32P] radioactivity signals of Pi starvation treatment (S-P and R-P) were shifted by 100 CPM. InsP5a, Ins(1,2,4,5,6)P5 and/or Ins(2,3,4,5,6)P5. (B) Total [32P]Pi recovered in metabolites of tissues after pulse-chase labeling determined by integration of peaks from in-line flow detection. Error bars, SE of three independently labeled populations of seedlings. (C) InsP6 level as percentage of total radioactivity across the gradient recovered in the integrated peak. (D) InsP7-to-InsP6 ratio determined from counting of fractions in inset (A). (E) InsP7 level as per mille total radioactivity derived from InsP7-to-InsP6 ratio [derived in (D)] multiplied by the InsP6 level in (C). (F) InsP4*-to-InsP6 ratio determined by scintillation counting of fractions as shown in Supporting Figure S9A. InsP4* shares common retention time with the elevated peak detected in the ipk1-1 and itpk1 mutants (Figure 5). (G) InsP4* level as per mille total radioactivity derived from InsP4*-to-InsP6 ratio (Figure S9A-D) multiplied by the InsP6 level in (C). Error bars in (B-G), S.E. of three independent labeling experiments. (H and I) Relative ATP and AMP level per mg fresh weight (FW) derived from normalization to the internal standard ribitol. Error bars, S.E. of n=9 and 7 independent experiments for the shoots and roots, respectively. Asterisks indicate significant differences from the WT (Student’s t-test; *, P < 0.05).

Overall, the chromatograms did not exhibit prominent profile changes in response to Pi starvation in either shoots or roots (Figures 6A and S9). Quantitative analysis indicated no significant change in InsP6 level in response to Pi starvation in shoots or roots (Figure 6C). Despite no significant change in InsP7 level in roots, shoots exhibited mild yet significant increase in InsP7-to-InsP6 ratio and InsP7 level in response to 1- and 3-day Pi starvation (Figure 6D-E). We were unable to assess the InsP8 level due to the detection limit in our analysis; however, depletion of InsP8 caused by vih2 mutation not affecting the Pi-starvation response implied that this InsP species does not mediate Pi signaling (Figure S5C). Notably, the increase in D/L-Ins(3,4,5,6)P4 level in itpk1 and ipk1-1 mutants was not observed in Pi-starved WT plants (Figures 6F-G and S9A-D), nor was the level of any InsP3 isomer, including Ins(1,4,5)P3, changed in response to Pi starvation (Figure S9E-F).

Because cellular adenylate energy is influenced by Pi availability (Boer et al., 2010; Alexova et al., 2017; Choi et al., 2017), and high energy phosphates delivered by ATP are required for pyrophosphorylation (Voglmaier et al., 1996), we examined whether phosphorylated adenine nucleotides are metabolically coordinated with the change in InsP7 level in response to Pi starvation by LC/MS analysis. ATP increased along with InsP7 level specifically in shoots during 1- and 3-day Pi starvation, whereas AMP level remained steady (Figure 6H-I), which resulted in a significant increase of ATP/AMP ratio (0.68 ± 0.1 and 1.1 ± 0.1 for 3-day ‘+P’ and ‘−P’ treatment, respectively, P=0.009). In conclusion, the changes in InsP profiles of WT seedlings in response to 1- and 3-day Pi starvation distinctly differ from those in itpk1 and ipk1-1 mutants, which suggests that the mechanism of the ITPK1 and IPK1 contribution to Pi homeostasis is distinct from the Pi-starvation response in WT plants.

Discussion

In this study, we demonstrated metabolism of distinct InsP species in correlation to Pi homeostasis and Pi limitation. Under Pi-replete conditions, the catalytic activity of IPK1 was required for maintenance of Pi homeostasis, providing the first evidence of the involvement of InsP metabolism, as opposed to other possible aspects of IPK1 protein function (Figures 1 and S1). This notion is further supported by the identification of an additional InsP-synthesizing enzyme, ITPK1, with a comparable role to IPK1 (Figures 2, 3, S3 and S4). The epistatic relationship of IPK1 and ITPK1 in suppressing PSR genes under Pi-replete conditions, together with their co-expression pattern throughout development and their subcellular co-localization (Figure 4), indicate that ITPK1 and IPK1 constitute an InsP metabolic pathway maintaining Pi homeostasis. InsP profiling revealed two distinct common features between ipk1-1 and itpk1 mutants: (1) decreases in InsP6 and InsP7 levels and (2) an increase in D/L-Ins(3,4,5,6)P4 level (Figures 5 and S6). In contrast, Pi starvation induced a distinct InsP profile from those with ipk1-1 and itpk1 mutations (Figure 6), which suggests that ipk1-1 and itpk1 mutations affect Pi homeostasis by a mechanism other than Pi-starvation signaling.

Decrease in InsP6, InsP7 or InsP8 level is not responsible for disturbed Pi homeostasis in ipk1-1 and itpk1 mutants

The fact that itpk4 mutants did not exhibit Pi-related phenotypes comparable to ipk1-1 and itpk1 mutants indicates that a decrease in InsP6 or InsP7 level did not cause the disturbed Pi homeostasis under Pi-replete conditions. The similar tissue/developmental expression pattern and subcellular localization of ITPK4 as ITPK1 and IPK1 suggest that these three enzymes control the same pool of vegetative InsP6 and InsP7 (Figure S7). While it is possible that radiolabeling does not entirely reflect metabolic (subcellular) pools of different InsP and PP-InsP metabolites, no other methods have been elaborated for measurement of these molecules in plants, never mind their subcellular fractionation. Although we were unable to determine the InsP8 level, vih2 mutants mediating InsP8 synthesis in planta (Laha et al., 2015) did not phenocopy ipk1-1 and itpk1 under Pi-replete conditions and exhibited normal Pi-starvation responses (Figures 2, S3 and S5), which suggests that InsP8 is unlikely involved in the regulation of Pi homeostasis.

We have also ruled out that misregulated Pi homeostasis is a secondary consequence of mitigated InsP6-mediated mRNA export by demonstrating that mutations compromising or enhancing InsP6-Gle1-Los4 mRNA machinery neither caused comparable Pi-related phenotypes of ipk1-1 nor complemented ipk1-1 (Figure S2). The identification of two itpk4 alleles with similar reduction in InsP6 (and InsP7) level in ipk1-1 and itpk1, respectively, without showing Pi-related phenotypes, also argues against a role for InsP6-mediated mRNA export in regulating Pi homeostasis (Figures 2, 5 and S7). Of note, although growth retardation of ipk1-1 is attributed to defective InsP6-mediated mRNA export (Lee et al., 2015), itpk4 mutants did not exhibit growth defects comparable to ipk1-1 or itpk1 (Figure 2A). Thus, InsP6 reduction may not be the sole cause for the growth defect observed in the ipk1-1 and itpk1 mutants.

Correlation between the increased level of D/L-Ins(3,4,5,6)P4 and misregulation of Pi homeostasis in ipk1-1 and itpk1 mutants

Aside from the reduced levels of InsP6 and InsP7, the most significant common InsP profile change between itpk1 and ipk1-1 is the increased accumulation of the InsP4 species, shown to predominantly consist of Ins(3,4,5,6)P4 in the ipk1-1 mutant (Stevenson-Paulik et al., 2005). The isomeric identity of the InsP4 species in the itpk1 mutant remains to be determined, but human ITPK1 was found a reversible InsP 1-kinase/phosphatase that regulates the level of Ins(3,4,5,6)P4, an inhibitor of Ca2+-activated chloride channels in the plasma membrane (Vajanaphanich et al., 1994; Yang et al., 1999; Ho et al., 2002; Saiardi and Cockcroft, 2008). In tobacco, Ins(3,4,5,6)P4 is also linked to chloride transport, regulating growth and cell volume in pollen tubes (Zonia et al., 2002). We attempted to test the effect of Ins(1,4,5,6)P4 or Ins(3,4,5,6)P4 on Pi homeostasis of Arabidopsis seedlings by using membrane-permeant bioactivatable analogues of these two InsP isomers [Bt2-Ins(1,4,5,6)P4/PM and Bt2-Ins(3,4,5,6)P4/PM] (Vajanaphanich et al., 1994) but did not observe significant effects on tissue Pi accumulation or PSR gene expression. However, the effectiveness of intracellular delivery and metabolism of these InsP analogs on plant tissues remains to be assessed.

In addition to InsP4, InsP3 showed changes in ipk1-1 and itpk1 mutants (Figure 5D). In plants, Ins(1,4,5)P3 (assayed by a competitive InsP3-receptor binding assay) has been linked to several physiological responses, such as gravitropism, salt and drought stresses (Perera et al., 2001; Xiong et al., 2001; Perera et al., 2006; Perera et al., 2008). We demonstrated that neither ipk1-1 nor itpk1 mutation affected the levels of Ins(1,4,5)P3, as measured by radiolabelling approaches. Species that co-elute with this isomer are barely detectable in WT plants (Figure 5D) (Brearley and Hanke, 2000). Because the two mutants showed distinctive InsP3 profiles, and neither accumulated Ins(1,4,5)P3, we did not find any association between changes in specific InsP3 and Pi homeostasis.

Because InsP lipids, called polyphosphoinositides (PPIs), also play important roles in cellular signaling and InsP metabolism (Munnik and Vermeer, 2010; Munnik and Nielsen, 2011), we examined whether PPI levels were altered in ipk1-1 and itpk1 mutants and found elevated levels of phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] in both ipk1-1 and itpk1 (Figure S10A-B). We further examined Pi-related phenotypes in mutants or transgenic lines with elevated levels of PtdInsP2, i.e., phosphatidylinositol-phospholipase C2 (plc2), suppressor of actin 9 (sac9), and a PHOSPHATIDYLINOSITOL PHOSPHATE 5-KINASE 3 (PIP5K3)-overexpression line (Williams et al., 2005; Kusano et al., 2008; Stenzel et al., 2008; Kanehara et al., 2015). None of these lines were comparable to the ipk1-1 mutant (Figure S10C-D), which suggests that the increased PtdIns(4,5)P2 levels in ipk1-1 and itpk1 mutants are not likely attributable to the misregulated Pi homeostasis.

Pi starvation induced a change in InsP profile distinct from those caused by itpk1 and ipk1-1 mutations

Although ipk1-1 and itpk1 mutants exhibited characteristic phenotypes of Pi-starvation responses under Pi-replete conditions, their InsP profiles were distinct from those under Pi starvation, notably the contrasting levels of D/L-Ins(3,4,5,6)P4, InsP6 and InsP7 (Figures 5A, 6F-G and S9A-D). The level of D/L-Ins(3,4,5,6)P4 not being altered by Pi starvation suggests these InsP species are not involved in Pi-starvation signaling in WT plants. The disparate InsP profiles in response to Pi starvation versus that caused by ipk1-1 and itpk1 mutations imply two distinct Pi signaling pathways. In support of this notion, the Pi-starvation responses persisted in the ipk1-1 and itpk1 mutants, in which PSR genes remained inducible under Pi starvation (Figure S8C). We observed no distinct alteration of InsP profile in response to Pi starvation except for a significant increase in InsP7 level of unknown isomeric identity in the shoot of Pi-starved plants but not in the root (Figure 6D-E), where Pi-starvation responses also take place. Shoot tissues are more responsive to Pi starvation than are roots (Huang et al., 2008; Lin et al., 2008), which has led to a hypothesis that the shoot is the tissue where Pi starvation is sensed and the signal initiated (Hammond and White, 2008; Lin et al., 2008). Alternatively, because Pi starvation triggers differential transcriptional and metabolic responses between shoots and roots (Wu et al., 2003; Pant et al., 2015), the shoot-specific increase in InsP7 level may have tissue-specific physiological significance under Pi starvation conditions. It will be important to identify the kinase responsible for InsP7 synthesis in plants to address these speculations.

Adenylate energy has been shown to regulate PP-InsPs synthesis, with increased ATP/ADP ratio promoting mammalian IP6K kinase activity (Wundenberg et al., 2014). We observed that the shoot-specific increase in InsP7 level was associated with a shoot-specific increase in ATP and ATP/AMP ratio during 1- and 3-day Pi starvation (Figure 6H-I). Increases in ATP level in response to Pi starvation has been noted in barley leaves (Alexova et al., 2017), which contrasts with the decrease in ATP level during Pi starvation reported in yeast (Boer et al., 2010; Choi et al., 2017). Pi starvation-induced ATP decreases have been shown in other plant species (Duff et al., 1989; Rao et al., 1989), but concentration ratios of ATP to ADP (or AMP), which control kinetics of cellular metabolism (Pradet and Raymond, 1983), remained unchanged or was increased in those studies. Whether the elevated ATP/AMP ratio drives InsP7 accumulation in Pi-starved shoots awaits further characterization of the InsP7 synthesis enzyme. Of note, multiple enzymes involved in adenine nucleotide metabolism have been genetically identified to act upstream of the Pho80/Pho85/Pho81 complex as negative regulators of PHO signaling (Huang and Shea, 2005; Choi et al., 2017). Despite the inter-species difference in strategies for the Pi-starvation response, accumulating evidence has pointed to a close relationship between adenylate energy status and Pi signaling. PP-InsPs are proposed to be ‘metabolic messengers’ that mediate pyrophosphorylation of proteins involved in multiple cellular metabolism, including phosphorylation-based signal transduction pathways in yeast (Saiardi, 2012; Wu et al., 2016). Whether the shoot-specific Pi starvation-stimulated InsP7 observed in this study has a role in Pi signaling by such protein pyrophosphoryaltion remains speculative.

Significant roles of ITPK family of enzymes in phytate biosynthesis in plant vegetative tissues

Mutation of IPK1 leads to substantively reduced InsP6 level in seeds (Stevenson-Paulik et al., 2005) and vegetative tissues (Stevenson-Paulik et al., 2005; Nagy et al., 2009). The concomitant accumulation of Ins(1,3,4,5,6)P5 in these tissues/organs (Stevenson-Paulik et al., 2005; Nagy et al., 2009) strongly indicates the dominant contribution of the Ins(1,3,4,5,6)P5 2-kinase activity of IPK1 to InsP6 synthesis. The coincident accumulation of Ins(3,4,5,6)P4 in vegetative tissues and seeds (Stevenson-Paulik et al., 2005) may be explained by mass action effects (Hanke et al., 2012), possibly indicating reversibility of the detected Ins(3,4,5,6)P4 1-kinase activity (Brearley and Hanke, 2000). The enzyme(s) responsible for producing Ins(3,4,5,6)P4 in plants are not well defined. In avian erythrocytes, Ins(3,4,5,6)P4 is the product of 5-phosphorylation of Ins(3,4,6)P3 and is itself the precursor of Ins(1,3,4,5,6)P5 (Stephens and Downes, 1990).

In nucleated mammalian cells, the origins of Ins(3,4,5,6)P4 have not been tested by the methods of Stephens and Downes (Stephens and Downes, 1990), but the single mammalian ITPK1 is a multifunctional kinase and phosphotransferase that interconverts Ins(3,4,5,6)P4 and Ins(1,3,4,5,6)P5 (Chamberlain et al., 2007). The existence in Arabidopsis of a gene family of four inositol tris/tetrakisphosphate kinases (ITPK1-4) complicates study of InsP metabolism. Our identification of significant contributions of ITPK1 and ITPK4 to InsP6 synthesis in vegetative tissues focuses attention on the contribution of these enzymes to not just InsP6 synthesis but also physiological processes regulated by the intermediate InsPs. ITPK1 mutation reduces labeling of InsP6 by 50%, with concomitant accumulation of D/L-Ins(3,4,5,6)P4, but because it does so without affecting Ins(1,3,4,5,6)P5 level (Figures 5A and S6A) suggests that ITPK1 does not likely act as an Ins(1,3,4,5,6)P5 1-phosphatase. ITPK1 may be acting at the level of InsP4-InsP5 interconversion. Remarkably, our studies show that ITPK4, which contributes to nearly 90% of vegetative InsP6, and more in seeds, has no effect on the Pi-starvation response. Our labeling studies showed no increased InsP4 accumulation in vegetative tissues (Figures 5A and S6A). This implies that most of the InsP4 precursors for InsP6 synthesis are generated by this enzyme and the contribution of ITPK4 may lie in its InsP3 kinase activity rather than its InsP4 isomerase/mutase activity (Sweetman et al., 2007).

Implication of InsP metabolism in regulating Pi homeostasis

Across eukaryotic kingdoms, the SPX domains of a large family of proteins involved in Pi sensing and transport have been shown to bind InsPs, thereby regulating SPX-protein activities and their interaction with other proteins (Wild et al., 2016). Although InsP6 and PP-InsPs at sub-micromolar concentration exhibited the highest binding affinity to the SPX domains, the lower InsP levels also exhibited physiologically relevant binding affinity at a micromolar range (Wild et al., 2016). Our study has pointed to a significant association between the level of D/L-Ins(3,4,5,6)P4 and maintenance of Pi homeostasis under Pi-replete conditions but not the Pi-starvation response. It remains speculative how increases in InsP4 level is associated with elevated Pi uptake and PSR-gene expression and the future identification of the enantiomerism of D/L-Ins(3,4,5,6)P4 in the itpk1 mutant and its interacting protein targets, such as by using InsP affinity screens (Wu et al., 2016), should provide further mechanistic insights. The confounding effects on PHO signaling of Kcs1p (negative) and Vip1p (positive) (Auesukaree et al., 2005; Lee et al., 2007), together with a Vip1-indepdent Pi-starvation signaling pathway (Choi et al., 2017), suggest the regulatory mechanisms that control Pi homeostasis likely involve multiple InsP and PP-InsP species. Different InsP and PP-InsP species may regulate Pi homeostasis via their competitive interaction with a spectrum of SPX-domain protein(s). For example, the binding of InsP6 and 5-InsP7 to OsSPX4/OsPHR2 yielded Kd of ~ 50 μM and 7 μM respectively (Wild et al., 2016), suggesting that competition between the more abundant InsP6 and less abundant PP-InsPs are relevant considerations in SPX function (Wild et al., 2016). Consequently, it will be important to consider the prevailing physiological concentration of potential InsP and PP-InsP competitors. Together with the diverse functions of SPX proteins at different levels of Pi homeostasis regulation (Secco et al., 2012; Azevedo and Saiardi, 2017) and our findings presented here, InsP7 may not be a general (or conserved) signal, and the role of other InsP intermediates in regulating Pi homeostasis need to be considered.

Experimental procedures

Plant materials and growth conditions

Arabidopsis thaliana mutant lines and their sources are listed in S1 Table; the wild-type line (WT) indicates Col-0 unless specified otherwise. Seeds were surface-sterilized, stratified at 4°C for 1-3 days, and germinated on agar medium of half-strength modified Hoagland nutrient solution containing 250 μM KH2PO4, 1% sucrose, and 0.8% Bacto agar (Aung et al., 2006). The Pi-replete (‘+P’) and Pi-deficient (‘−P’) media were supplemented with 250 μM (or 1 mM as specified) and 10 μM KH2PO4, respectively. For hydroponic growth, seedlings were germinated and grown on solid media for 10 days before being transferred to half-strength modified Hoagland nutrient solution with sucrose omitted. Plants were grown at 22 °C under a 16-h photoperiod with cool fluorescent white light at 100 to 150 μE m−2 s−1. For generating ipk1-1 itpk1 double mutants, both double mutants and isogenic WT progenies were recovered from the F2 population at an equivalent yet lower segregation rate (1%) than expected (6%). Because these two loci are located on different arms of chromosome 5, the reason for this segregation distortion is unknown.

Measurement of Pi content and Pi uptake activity

Total Pi content and Pi uptake activity were measured as described previously (Chiou et al., 2006). To measure the root-to-shoot Pi translocation activity, pulse-chase labeling was performed. 14-day after germination seedlings were first incubated in Pi-replete nutrient solution (half-strength modified Hoagland solution supplemented with 250 μM KH2PO4) containing 33[P]orthophosphate (Pi) for 3 h (‘pulse’ treatment), then transferred to Pi-replete nutrient solution without 33[P]Pi for indicated times (‘chase’ treatment). [33P] radioactivity in the plants tissues was measured as the Pi uptake assay and the root-to-shoot Pi translocation activity was measured by shoot-to-root ratio of 33P count.

Genotype analysis, transgene construction and plant transformation

Primers used for genotyping of T-DNA insertional lines were designed according to SIGnAL (http://signal.salk.edu/tdnaprimers.2.html) and are listed in Supporting Table S2. For constructing kinase-inactive IPK1, nucleotide substitutions were introduced in the primers (5’ phosphorylated; Supporting Table S2) used for PCR amplification by using a vector (pMDC32) containing the IPK1 CDS sequence driven by the 35S promoter as template. PCR product was ligated before transformation and sequences were confirmed before recombination into the Gateway destination vector pK7YWG2.0 (C’-YFP) (Karimi et al., 2007) via LR Clonase enzyme mix (Invitrogen). For complementation analysis, the genomic sequence of ITPK1, including 1 kb upstream of ATG start codon, was amplified by PCR (primers listed in Supporting Table S2) and cloned into pCR8/GW/TOPO (Invitrogen) followed by recombination into the Gateway destination vectors. pMDC99, pMDC32 (Curtis and Grossniklaus, 2003), and pK7YWG2.0 were chosen as destination vectors for complementation, promoter::GUS activity and YFP fluorescence analysis, respectively. All cloned constructs were validated by sequencing analysis before being introduced into Arabidopsis by the floral-dip transformation method (Clough and Bent, 1998).

RNA isolation, RT-PCR, and qRT-PCR

Total RNA was isolated by using RNAzol reagent (Molecular Research Center) and cDNA was synthesized from 0.5 to 1 μg total RNA by using Moloney Murine Leukemia Virus Reverse Transcriptase (M-MLV RT, Invitrogen) and oligo(dT) primers. Sequences of primers used for RT-PCR and qRT-PCR are in Supporting Table S2. qRT-PCR involved use of the Power SYBR Green PCR Master Mix kit (Applied Biosystems) on a 7500 Real-Time PCR system as instructed. Gene expression was normalized by subtracting the Ct value of UBQ10 (ΔCt) from that of the gene studied and presented as 2−ΔCt. The expression relative to the WT (i.e., fold change relative to the WT) is presented as 2−ΔΔCt (where ΔΔCt =ΔCt-ΔCtWT). qPCR raw data is provided in Supporting Table S3.

GUS staining and fluorescence microscopy

GUS activity of transgenic T2 plants was detected as described (Lin et al., 2005), and the signal was observed under an Olympus SZX12 or a Zeiss AxioSkop microscope. Confocal microscopy images of the YFP signal were obtained by using a Zeiss LSM 510 META NLO DuoScan with LCI Plan-Neofluar x63/1.3 Immersion and Plan-Apochromat ×100/1.4 oil objectives. Excitation/emission wavelengths were 514 nm/520 to 550 nm for YFP.

InsP profiling of Arabidopsis seedlings and seeds

For InsP profile analysis of Arabidopsis vegetative tissue, seedlings (8-11 DAG) were labelled with myo-[2-3H]inositol (19.6 Ci mmol−1, Perkin Elmer NET114A00; 0.4 mCi mL−1 for 5 days) or [32P]Pi (8500-9120Ci mmol−1, Perkin Elmer NEX05300; 0.02 mCi mL−1 for 1-3 days accordingly) in half-strength Hoagland’s medium supplemented with Pi at levels specified in the text. InsP was extracted from the radiolabeled tissues, roots, shoots or whole seedlings as described (Azevedo and Saiardi, 2006). Extracts were resolved on a 250 × 4.6 mm Whatman Partisphere SAX WVS column fitted with guard cartridge of the same material at a flow rate of 1 mL min−1 with a gradient derived from buffer reservoirs containing A, water; B, 1.25M (NH4)2HPO4, adjusted to pH 3.8 with H3PO4, mixed according to the following gradient: time (min), %B; 0, 0; 5, 0; 65, 100; 75, 100. Isocratic separations of InsP3 species were performed at the same flow rate on the same column eluted with 20% buffer B. For myo-[3H]inositol labeling, fractions were collected every minute from retention time 0 to 30 min and every 0.5 min from 30 min onward, followed by scintillation counting (1:4 ratio column eluent to scintillation cocktail; Perkin-Elmer; ULTIMA-FLO AP). For [32P]Pi labeling, radioactivity was measured by Cherenkov counting on a Canberra Packard Radiomatic A515 Flow Detector fitted with a 0.5-mL flow cell with an integration interval of 0.1 min (Brearley et al., 1997).

myo-[3H]inositol and [32P]Pi exhibited different allocation between tissues in planta, with greater [3H] labeling of roots (Figure S6B), whereas [32P]Pi labeled shoots more strongly (Figure 6B). With the exception of experiments to compare the extent of labeling of InsP6 between a wide range of genotypes (Figure 5B), performed with whole seedlings, the shoot and root tissues were analyzed independently. Aside from stoichiometric differences of specific InsPs, the InsP profile was in general similar between these two tissues (Figures 6A and S6B).

For analysis of InsPs in seeds, 2 mg seed was homogenized in 500 μl of ice-cold 0.6 N HCl before centrifugation for 15 min to remove cell debris. Aliquots (20 μL) were injected onto a 3 mm i.d. × 200 mm Carbo Pac PA200 HPLC column (Dionex) fitted with a 3 mm × 50 mm guard column of the same material. The column was eluted at a flow rate of 0.4 mL/min with a gradient of methane sulfonic acid (Acros Organics) delivered from buffer reservoirs containing: A, water; B, 600 mM methane sulfonic acid according to the following schedule: time (minutes), % B; 0, 0; 25, 100; 38, 100; 39, 0; 49, 0. The column eluate was mixed by using a mixing tee with a solution of 0.1% w/v ferric nitrate in 2% w/v perchloric acid (Phillippy and Bland, 1988) delivered at a flow rate of 0.2 mL/min, before passage through a 194-uL volume knitted reaction coil (4 m × 0.25 mm i.d.) obtained from Biotech AB, Sweden. The column, mixing tee and reaction coil were held at 35°C. Peaks of InsP were detected at 290 nm with a Jasco UV-2077 Plus UV detector. Chromatographic data were integrated in ChromNav (Jasco) software. The position of elution of different stereoisomers of the different classes of InsPs was determined by the inclusion at regular intervals of a set of standards obtained by extended acid treatment of phytic acid (middle panel in Figure 5C).

ATP and AMP analysis

Adenylates from plant tissues were extracted as described (Cho et al., 2016). Tissues were homogenized in liquid nitrogen and re-suspended in 2.3% (v/v) TCA containing 200 μg/ml ribitol (250 μl per 100 mg tissue). Homogenates were centrifuged at 13,000 rpm at 4°C for 15 min, and supernatants were recovered and neutralized to pH 6.5-7 by KOH, followed by 30-min incubation on ice. Extracts were centrifuged at 13,000 rpm at 4°C for 15 min and the supernatants were collected for LC/MS quantification with an ultra-performance liquid chromatography (UPLC) system (ACQUITY UPLC, Waters, Millford, MA). The sample was separated with a ZIC-cHILIC column (3-μm particle size, 2.1 × 100 mm, Merck-Millipore). The UPLC system was coupled online to the Waters Xevo TQ-S triple quadruple mass spectrometer. Ribitol was used as internal standard. Characteristic MS transitions were monitored by the negative multiple reaction monitoring (MRM) mode for ATP (m/z, 506→159), AMP (m/z, 346→79), and ribitol (m/z, 151→71). Data acquisition and processing involved use of MassLynx v4.1 and TargetLynx software (Waters Corp.), with intensities of ATP and AMP normalized to ribitol.

Author Contributions

H.-F.K. and T.-J.C. conceived the project; H.-F.K., C.B. and T.-J.C. designed the experiments; H.-F.K., Y.-Y.H., W.-C.L., K.-Y.C., T.M. and C.B. performed the research; H.-F.K., C.B., T.M. and T.-J.C. interpreted the results; H.-F.K. and C.B. wrote the manuscript; H.-F.K., T.M., C.B. and T.-J.C. contributed to the final version of this article.

Acknowledgements

We thank Shu-Chen Shen (Confocal Microscope Facility, Scientific Instrument Center, Academia Sinica, Taiwan) for fluorescence microscopy imaging, Chen-Chuan Hsu (Plant Tech Core Facility, ABRC, Academia Sinica, Taiwan) for cross-section imaging of GUS staining in plants, ABRC Metabolomics Core for LC-MS measurement of ATP/AMP, Hsin-Yu Huang, Su-Fen Chiang and Hayley Whitfield (University of East Anglia, Norwich, United Kingdom) for technical support. vih and plc2 mutants were kindly given by Gabriel Schaff (University of Bonn, Germany) and Kazue Kanehara (Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan), respectively; mutants and transgenic lines of Gle1-Los4 mRNA export machinery were generously provided by Ho-Seok Lee and Hyun-Sook Pai (Department of Systems Biology, Yonsei University, Seoul, Korea). This work was supported by grants from the Ministry of Science and Technology of the Republic of China (MOST 104-2321-B-001-057 and MOST 105-2321-B-001-038 to T.-J. Chiou and postdoctoral fellowship to H.-F. Kuo), the BBSRC grants from the United Kingdom (BB/M022978/1 and BB/N002024/1 to C.A. Brearley), and the Netherlands Organization for Scientific Research (NWO 867.15.020 and 711.017.005 to T. Munnik).

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Posted February 24, 2018.
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Arabidopsis inositol phosphate kinases, IPK1 and ITPK1, constitute a metabolic pathway in maintaining phosphate homeostasis
Hui-Fen Kuo, Yu-Ying Hsu, Wei-Chi Lin, Kai-Yu Chen, Teun Munnik, Charles A. Brearley, Tzyy-Jen Chiou
bioRxiv 270355; doi: https://doi.org/10.1101/270355
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