Recent advances in unraveling the mystery of combined nutrient stress in plants.

Efficiently regulating growth to adapt to varying resource availability is crucial for organisms, including plants. In particular, the acquisition of essential nutrients is vital for plant development, as a shortage of just one nutrient can significantly decrease crop yield. However, plants constantly experience fluctuations in the presence of multiple essential mineral nutrients, leading to combined nutrient stress conditions. Unfortunately, our understanding of how plants perceive and respond to these multiple stresses remains limited. Unlocking this mystery could provide valuable insights and help enhance plant nutrition strategies. This review focuses specifically on the regulation of phosphorous homeostasis in plants, with a primary emphasis on recent studies that have shed light on the intricate interactions between phosphorous and other essential elements, such as nitrogen, iron, and zinc, as well as non-essential elements like aluminum and sodium. By summarizing and consolidating these findings, this review aims to contribute to a better understanding of how plants respond to and cope with combined nutrient stress.

Correlation between plant cell wall stiffening and root extension arrest phenotype in the combined abiotic stress of Fe and Al.

The plasticity and growth of plant cell walls (CWs) remain poorly understood at the molecular level. In this work, we used atomic force microscopy (AFM) to observe elastic responses of the root transition zone of 4-day-old Arabidopsis thaliana wild-type and almt1-mutant seedlings grown under Fe or Al stresses. Elastic parameters were deduced from force-distance curve measurements using the trimechanic-3PCS framework. The presence of single metal species Fe2+ or Al3+ at 10 µM exerts no noticeable effect on the root growth compared with the control conditions. On the contrary, a mix of both the metal ions produced a strong root-extension arrest concomitant with significant increase of CW stiffness. Raising the concentration of either Fe2+ or Al3+ to 20 µM, no root-extension arrest was observed; nevertheless, an increase in root stiffness occurred. In the presence of both the metal ions at 10 µM, root-extension arrest was not observed in the almt1 mutant, which substantially abolishes the ability to exude malate. Our results indicate that the combination of Fe2+ and Al3+ with exuded malate is crucial for both CW stiffening and root-extension arrest. However, stiffness increase induced by single Fe2+ or Al3+ is not sufficient for arresting root growth in our experimental conditions.

Arabidopsis casein kinase 2 triggers stem cell exhaustion under Al toxicity and phosphate deficiency through activating the DNA damage response pathway.

Aluminum (Al) toxicity and inorganic phosphate (Pi) limitation are widespread chronic abiotic and mutually enhancing stresses that profoundly affect crop yield. Both stresses strongly inhibit root growth, resulting from a progressive exhaustion of the stem cell niche. Here, we report on a casein kinase 2 (CK2) inhibitor identified by its capability to maintain a functional root stem cell niche in Arabidopsis thaliana under Al toxic conditions. CK2 operates through phosphorylation of the cell cycle checkpoint activator SUPPRESSOR OF GAMMA RADIATION1 (SOG1), priming its activity under DNA-damaging conditions. In addition to yielding Al tolerance, CK2 and SOG1 inactivation prevents meristem exhaustion under Pi starvation, revealing the existence of a low Pi-induced cell cycle checkpoint that depends on the DNA damage activator ATAXIA-TELANGIECTASIA MUTATED (ATM). Overall, our data reveal an important physiological role for the plant DNA damage response pathway under agriculturally limiting growth conditions, opening new avenues to cope with Pi limitation.

Root responses to aluminium and iron stresses require the SIZ1 SUMO ligase to modulate the STOP1 transcription factor.

STOP1, an Arabidopsis transcription factor favouring root growth tolerance against Al toxicity, acts in the response to iron under low Pi (-Pi). Previous studies have shown that Al and Fe regulate the stability and accumulation of STOP1 in roots, and that the STOP1 protein is sumoylated by an unknown E3 ligase. Here, using a forward genetics suppressor screen, we identified the E3 SUMO (small ubiquitin-like modifier) ligase SIZ1 as a modulator of STOP1 signalling. Mutations in SIZ1 increase the expression of ALMT1 (a direct target of STOP1) and root growth responses to Al and Fe stress in a STOP1-dependent manner. Moreover, loss-of-function mutations in SIZ1 enhance the abundance of STOP1 in the root tip. However, no sumoylated STOP1 protein was detected by Western blot analysis in our sumoylation assay in Escherichia coli, suggesting the presence of a more sophisticated mechanism. We conclude that the sumo ligase SIZ1 negatively regulates STOP1 signalling, at least in part by modulating STOP1 protein in the root tip. Our results will allow a better understanding of this signalling pathway.

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

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

Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation.

Root architecture varies widely between species; it even varies between ecotypes of the same species, despite strong conservation of the coding portion of their genomes. By contrast, noncoding RNAs evolve rapidly between ecotypes and may control their differential responses to the environment, since several long noncoding RNAs (lncRNAs) are known to quantitatively regulate gene expression. Roots from ecotypes Columbia and Landsberg erecta of Arabidopsis (Arabidopsis thaliana) respond differently to phosphate starvation. Here, we compared transcriptomes (mRNAs, lncRNAs, and small RNAs) of root tips from these two ecotypes during early phosphate starvation. We identified thousands of lncRNAs that were largely conserved at the DNA level in these ecotypes. In contrast to coding genes, many lncRNAs were specifically transcribed in one ecotype and/or differentially expressed between ecotypes independent of phosphate availability. We further characterized these ecotype-related lncRNAs and studied their link with small interfering RNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes, including antisense RNAs targeting key regulators of root-growth responses. Misregulation of several lincRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in ecotype Columbia. RNA-sequencing analysis following deregulation of lncRNA NPC48 revealed a potential link with root growth and transport functions. This exploration of the noncoding transcriptome identified ecotype-specific lncRNA-mediated regulation in root apexes. The noncoding genome may harbor further mechanisms involved in ecotype adaptation of roots to different soil environments.

Under phosphate starvation conditions, Fe and Al trigger accumulation of the transcription factor STOP1 in the nucleus of Arabidopsis root cells.

Low-phosphate (Pi) conditions are known to repress primary root growth of Arabidopsis at low pH and in an Fe-dependent manner. This growth arrest requires accumulation of the transcription factor STOP1 in the nucleus, where it activates the transcription of the malate transporter gene ALMT1; exuded malate is suspected to interact with extracellular Fe to inhibit root growth. In addition, ALS3 - an ABC-like transporter identified for its role in tolerance to toxic Al - represses nuclear accumulation of STOP1 and the expression of ALMT1. Until now it was unclear whether Pi deficiency itself or Fe activates the accumulation of STOP1 in the nucleus. Here, by using different growth media to dissociate the effects of Fe from Pi deficiency itself, we demonstrate that Fe is sufficient to trigger the accumulation of STOP1 in the nucleus, which, in turn, activates the expression of ALMT1. We also show that a low pH is necessary to stimulate the Fe-dependent accumulation of nuclear STOP1. Furthermore, pharmacological experiments indicate that Fe inhibits proteasomal degradation of STOP1. We also show that Al acts like Fe for nuclear accumulation of STOP1 and ALMT1 expression, and that the overaccumulation of STOP1 in the nucleus of the als3 mutant grown in low-Pi conditions could be abolished by Fe deficiency. Altogether, our results indicate that, under low-Pi conditions, Fe2/3+ and Al3+ act similarly to increase the stability of STOP1 and its accumulation in the nucleus where it activates the expression of ALMT1.

Genetic Dissection of Fe-Dependent Signaling in Root Developmental Responses to Phosphate Deficiency.

The inhibition of primary root (PR) growth is a major developmental response of Arabidopsis (Arabidopsis thaliana) to phosphate (Pi) deficiency. Previous studies have independently uncovered key roles of the LOW PHOSPHATE RESPONSE1 (LPR1) ferroxidase, the tonoplast-localized ALUMINUM SENSITIVE3 (ALS3)/SENSITIVE TO ALUMINUM RHIZOTOXICITY1 (STAR1) transporter complex, and the SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1; a transcription factor)-ALUMINUM-ACTIVATED MALATE TRANSPORTER1 (ALMT1; a malate transporter) regulatory module in mediating this response by controlling iron (Fe) homeostasis in roots, but how these three components interact to regulate PR growth under Pi deficiency remains unknown. Here, we dissected genetic relationships among these three key components and found that (1) STOP1, ALMT1, and LPR1 act downstream of ALS3/STAR1 in controlling PR growth under Pi deficiency; (2) ALS3/STAR1 inhibits the STOP1-ALMT1 pathway by repressing STOP1 protein accumulation in the nucleus; and (3) STOP1-ALMT1 and LPR1 control PR growth under Pi deficiency in an interdependent manner involving the promotion of malate-dependent Fe accumulation in roots. Furthermore, this malate-mediated Fe accumulation depends on external Pi availability. We also performed a detailed analysis of the dynamic changes in the tissue-specific Fe accumulation patterns in the root tips of plants exposed to Pi deficiency. The results indicate that the degree of inhibition of PR growth induced by Pi deficiency is not linked to the level of Fe accumulated in the root apical meristem or the elongation zone. Our work provides insights into the molecular mechanism that regulates the root developmental response to Pi deficiency.

A chemical genetic strategy identify the PHOSTIN, a synthetic molecule that triggers phosphate starvation responses in Arabidopsis thaliana.

Plants display numerous strategies to cope with phosphate (Pi)-deficiency. Despite multiple genetic studies, the molecular mechanisms of low-Pi-signalling remain unknown. To validate the interest of chemical genetics to investigate this pathway we discovered and analysed the effects of PHOSTIN (PSN), a drug mimicking Pi-starvation in Arabidopsis. We assessed the effects of PSN and structural analogues on the induction of Pi-deficiency responses in mutants and wild-type and followed their accumulation in plants organs by high pressure liquid chromotography (HPLC) or mass-spectrophotometry. We show that PSN is cleaved in the growth medium, releasing its active motif (PSN11), which accumulates in plants roots. Despite the overaccumulation of Pi in the roots of treated plants, PSN11 elicits both local and systemic Pi-starvation effects. Nevertheless, albeit that the transcriptional activation of low-Pi genes by PSN11 is lost in the phr1;phl1 double mutant, neither PHO1 nor PHO2 are required for PSN11 effects. The range of local and systemic responses to Pi-starvation elicited, and their dependence on the PHR1/PHL1 function suggests that PSN11 affects an important and early step of Pi-starvation signalling. Its independence from PHO1 and PHO2 suggest the existence of unknown pathway(s), showing the usefulness of PSN and chemical genetics to bring new elements to this field.

Root tip contact with low-phosphate media reprograms plant root architecture.

Plant roots are able to sense soil nutrient availability. In order to acquire heterogeneously distributed water and minerals, they optimize their root architecture. One poorly understood plant response to soil phosphate (P(i)) deficiency is a reduction in primary root growth with an increase in the number and length of lateral roots. Here we show that physical contact of the Arabidopsis thaliana primary root tip with low-P(i) medium is necessary and sufficient to arrest root growth. We further show that loss-of-function mutations in Low Phosphate Root1 (LPR1) and its close paralog LPR2 strongly reduce this inhibition. LPR1 was previously mapped as a major quantitative trait locus (QTL); the molecular origin of this QTL is explained by the differential allelic expression of LPR1 in the root cap. These results provide strong evidence for the involvement of the root cap in sensing nutrient deficiency, responding to it, or both. LPR1 and LPR2 encode multicopper oxidases (MCOs), highlighting the essential role of MCOs for plant development.

Root architecture responses: in search of phosphate.

Soil phosphate represents the only source of phosphorus for plants and, consequently, is its entry into the trophic chain. This major component of nucleic acids, phospholipids, and energy currency of the cell (ATP) can limit plant growth because of its low mobility in soil. As a result, root responses to low phosphate favor the exploration of the shallower part of the soil, where phosphate tends to be more abundant, a strategy described as topsoil foraging. We will review the diverse developmental strategies that can be observed among plants by detailing the effect of phosphate deficiency on primary and lateral roots. We also discuss the formation of cluster roots: an advanced adaptive strategy to cope with low phosphate availability observed in a limited number of species. Finally, we will put this work into perspective for future research directions.

Identification of phosphatin, a drug alleviating phosphate starvation responses in Arabidopsis.

Inorganic phosphate (Pi) is present in most soils at suboptimal concentrations, strongly limiting plant development. Plants have the ability to sense and adapt to the surrounding ionic environment, and several genes involved in the response to Pi starvation have been identified. However, a global understanding of the regulatory mechanisms involved in this process is still elusive. Here, we have initiated a chemical genetics approach and isolated compounds that inhibit the response to Pi starvation in Arabidopsis (Arabidopsis thaliana). Molecules were screened for their ability to inhibit the expression of a Pi starvation marker gene (the high-affinity Pi transporter PHT1;4). A drug family named Phosphatin (PTN; Pi starvation inhibitor), whose members act as partial suppressors of Pi starvation responses, was thus identified. PTN addition also reduced various traits of Pi starvation, such as phospholipid/glycolipid conversion, and the accumulation of starch and anthocyanins. A transcriptomic assay revealed a broad impact of PTN on the expression of many genes regulated by low Pi availability. Despite the reduced amount of Pi transporters and resulting reduced Pi uptake capacity, no reduction of Pi content was observed. In addition, PTN improved plant growth; this reveals that the developmental restrictions induced by Pi starvation are not a consequence of metabolic limitation but a result of genetic regulation. This highlights the existence of signal transduction pathway(s) that limit plant development under the Pi starvation condition.

smFISH for Plants.

Single-molecule fluorescence in situ hybridization (smFISH) is a powerful method for the visualization and quantification of individual RNA molecules within intact cells. With its ability to probe gene expression at the single cell and single-molecule level, the technique offers valuable insights into cellular processes and cell-to-cell heterogeneity. Although widely used in the animal field, its use in plants has been limited. Here, we present an experimental smFISH workflow that allows researchers to overcome hybridization and imaging challenges in plants, including sample preparation, probe hybridization, and signal detection. Overall, this protocol holds great promise for unraveling the intricacies of gene expression regulation and RNA dynamics at the single-molecule level in whole plants.

Measuring external primary cell wall elasticity of seedling roots using atomic force microscopy.

Stiffness plays a central action in plant cell extension. Here, we present a protocol to detect changes in stiffness on the external epidermal cell wall of living plant roots using atomic force microscopy (AFM). We provide generalized instructions for collecting force-distance curves and analysis of stiffness using contact-based mechanical model. With this protocol, and some initial training in AFM, a user is able to perform indentation experiments on 4- and 5-day-old Arabidopsis thaliana and determine stiffness properties. For complete details on the use and execution of this protocol, please refer to Godon et al.1.

ER-resident proteins PDR2 and LPR1 mediate the developmental response of root meristems to phosphate availability.

Inadequate availability of inorganic phosphate (Pi) in the rhizosphere is a common challenge to plants, which activate metabolic and developmental responses to maximize Pi acquisition. The sensory mechanisms that monitor environmental Pi status and regulate root growth via altered meristem activity are unknown. Here, we show that PHOSPHATE DEFICIENCY RESPONSE 2 (PDR2) encodes the single P(5)-type ATPase of Arabidopsis thaliana. PDR2 functions in the endoplasmic reticulum (ER) and is required for proper expression of SCARECROW (SCR), a key regulator of root patterning, and for stem-cell maintenance in Pi-deprived roots. We further show that the multicopper oxidase encoded by LOW PHOSPHATE ROOT 1 (LPR1) is targeted to the ER and that LPR1 and PDR2 interact genetically. Because the expression domains of both genes overlap in the stem-cell niche and distal root meristem, we propose that PDR2 and LPR1 function together in an ER-resident pathway that adjusts root meristem activity to external Pi. Our data indicate that the Pi-conditional root phenotype of pdr2 is not caused by increased Fe availability in low Pi; however, Fe homeostasis modifies the developmental response of root meristems to Pi availability.

Uncoupling Aluminum Toxicity From Aluminum Signals in the STOP1 Pathway.

Aluminum (Al) is a major limiting factor for crop production on acidic soils, inhibiting root growth and plant development. At acidic pH (pH < 5.5), Al3+ ions are the main form of Al present in the media. Al3+ ions have an increased solubility at pH < 5.5 and result in plant toxicity. At higher pH, the free Al3+ fraction decreases in the media, but whether plants can detect Al at these pHs remain unknown. To cope with Al stress, the SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1) transcription factor induces AL-ACTIVATED MALATE TRANSPORTER1 (ALMT1), a malate-exuding transporter as a strategy to chelate the toxic ions in the rhizosphere. Here, we uncoupled the Al signalling pathway that controls STOP1 from Al toxicity using wild type (WT) and two stop1 mutants carrying the pALMT1:GUS construct with an agar powder naturally containing low amounts of phosphate, iron (Fe), and Al. We combined gene expression [real-time PCR (RT-PCR) and the pALMT1:GUS reporter], confocal microscopy (pSTOP1:GFP-STOP1 reporter), and root growth measurement to assess the effects of Al and Fe on the STOP1-ALMT1 pathway in roots. Our results show that Al triggers STOP1 signaling at a concentration as little as 2 µM and can be detected at a pH above 6.0. We observed that at pH 5.7, 20 µM AlCl3 induces ALMT1 in WT but does not inhibit root growth in stop1 Al-hypersensitive mutants. Increasing AlCl3 concentration (>50 µM) at pH 5.7 results in the inhibition of the stop1 mutants primary root. Using the green fluorescent protein (GFP)-STOP1 and ALMT1 reporters, we show that the Al signal pathway can be uncoupled from the Al toxicity on the root. Furthermore, we observe that Al strengthens the Fe-mediated inhibition of primary root growth in WT, suggesting an interaction between Fe and Al on the STOP1-ALMT1 pathway.

Root branching responses to phosphate and nitrate.

Plant roots favour colonization of nutrient-rich zones in soil. Molecular genetic evidences demonstrate that roots sense and respond to local and global concentrations of inorganic phosphate and nitrate, in a fashion that depends on the shoot nutrient status. Recent investigations in Arabidopsis highlighted the role of the root tip in phosphate sensing and attributed to already known proteins (multicopper oxidases and nitrate transporters) new and unexpected functions in the root growth response to phosphate or nitrate.

The two Arabidopsis RPS6 genes, encoding for cytoplasmic ribosomal proteins S6, are functionally equivalent.

Many eukaryotic genomes have experienced ancient whole-genome duplication (WGD) followed by massive gene loss. These eliminations were not random since some gene families were preferentially retained as duplicates. The gene balance hypothesis suggests that those genes with dosage reduction can imbalance their interacting partners or complex, resulting in decreased fitness. In Arabidopsis, the cytoplasmic ribosomal proteins (RP) are encoded by gene families with at least two members. We have focused our study on the two RPS6 genes in an attempt to understand why they have been retained as duplicates. We demonstrate that RPS6 function is vital for the plant. We also show that reducing the level of RPS6 accumulation (in the knock-out rps6a or rps6b single mutants, or in the double heterozygous RPS6A/rps6a,RPS6B/rps6b), confers a slow growth phenotype (haplodeficiency). Importantly, we demonstrate that the functions of two RPS6 genes are redundant and interchangeable. Finally, like in most other described Arabidopsis rp mutants, we observed that a reduced RPS6 level slightly alters the dorsoventral leaf patterning. Our results support the idea that the Arabidopsis RPS6 gene duplicates were evolutionarily retained in order to maintain an expression level necessary to sustain the translational demand of the cell, in agreement with the gene balance hypothesis.

A receptor-like kinase mediates the response of Arabidopsis cells to the inhibition of cellulose synthesis.

BACKGROUND: A major challenge is to understand how the walls of expanding plant cells are correctly assembled and remodeled, often in the presence of wall-degrading micro-organisms. Plant cells, like yeast, react to cell-wall perturbations as shown by changes in gene expression, accumulation of ectopic lignin, and growth arrest caused by the inhibition of cellulose synthesis. RESULTS: We have identified a plasma-membrane-bound receptor-like kinase (THESEUS1), which is present in elongating cells. Mutations in THE1 and overexpression of a functional THE1-GFP fusion protein did not affect wild-type (WT) plants but respectively attenuated and enhanced growth inhibition and ectopic lignification in seedlings mutated in cellulose synthase CESA6 without influencing the cellulose deficiency. A T-DNA insertion mutant for THE1 also attenuated the growth defect and ectopic-lignin production in other but not all cellulose-deficient mutants. The deregulation of a small number of genes in cesA6 mutants depended on the presence of THE1. Some of these genes are involved in pathogen defense, in wall crosslinking, or in protecting the cell against reactive oxygen species. CONCLUSIONS: The results show that THE1 mediates the response of growing plant cells to the perturbation of cellulose synthesis and may act as a cell-wall-integrity sensor.

Identification of Chemical Inducers of the Phosphate-Starvation Signaling Pathway in A. thaliana Using Chemical Genetics.

In spite of its importance for agriculture and 30 years of genetic studies, the phosphate-starvation signaling pathway, that allows plants to detect, respond, and adapt to changes in the phosphate concentration of the rhizosphere, remains poorly known. Chemical genetics has been increasingly and successfully used as a complementary approach to genetics for the dissection of signaling pathways in diverse organisms. Screens can be designed to identify chemicals interfering specifically with a pathway of interest. We designed a screen that led to the discovery of the first chemical capable to induce specifically the phosphate-starvation signaling pathway in Arabidopsis thaliana. This procedure, described here, can be adapted for the discovery of inducers or repressors of other pathways.