Filling the gaps on root hair development under salt stress and phosphate starvation using current evidence coupled with a meta-analysis approach

Abstract

Introduction

Defining the environmental stressors and the plant cell target

Being immobile organisms, plants face several environmental obstacles that they must adapt to in order to live. They must actively regulate their growth and development in response to changes in their surroundings. Root hairs (RHs) are elongated single cells that originate from epidermal cells, and their primary roles include enhancing the surface area of contact between plant roots and soil, facilitating the absorption of nutrients and water, enhancing interaction with microorganisms, and providing stability to plants by anchoring them in the soil (Lopez et al. 2023). RH growth and morphogenesis are regarded to be environmental response integrators because of their significant susceptibility to environmental influences. RH formation and growth are influenced by several environmental elements, including nutrition, abiotic and biotic pressures, as well as cellular signals like calcium, reactive oxygen species, phytohormones, and cytoskeletal dynamics (Velasquez et al. 2016; Vissenberg et al. 2020). Plants in natural settings often encounter several abiotic challenges, including salt, osmotic, and nutritional starvation stresses. Nevertheless, the majority of studies on gene expression in stress reactions focus on analyzing a single particular stressor. It was demonstrated that the application of single stresses in combination elicits a distinct gene expression pattern that cannot be attributed only to the separate individual stress reactions (Sewelam et al. 2014; Rivero et al. 2022).

Salinity, nutritional deficiency, and overwatering are among the main factors that harm plant development (He et al. 2019). It has been estimated that 424 million hectares of topsoil (0 to 30 cm) and 833 million hectares of subsoil (30 to 100 cm) are impacted by high salinity. Moreover, nearly 33% of irrigated fields and 20% of all farmed land are saline (FAO 2022; Negacz et al. 2022). On the other hand, plants need phosphate (Pi), a finite, nonrenewable macronutrient essential for several cellular processes. Pi deficiency has a significant impact on plant development, including reduction in shoot growth and primary root elongation, enhanced growth of lateral roots and RHs growth, and accumulation of anthocyanins (Vance et al. 2003; Rubio et al., 2009). Over 40% of arable soils present Pi deficiency (Wang et al. 2021) and modern agriculture relies on Pi-containing fertilizers to fulfil the plant's requirement. However, only 10% to 20% of fertilizer-derived phosphate applied to soil is absorbed and used by crops. The rest becomes immobilized in the organic and inorganic fractions of the soil, which are unavailable to crop roots, while the other portion flows to rivers, ponds, and lakes, resulting in their pollution (Lambers et al. 2006; Kong et al. 2018). Due to these problems, sustainable agriculture requires fertilizer reduction, where understanding phosphate homeostasis is crucial (Cho et al. 2020). Pi is heterogeneous, concentrated in lower soil layers, and immobile, and plants have complex systems to absorb Pi from soil (Paz-Ares et al. 2022). Pi starvation response and regulation has been widely characterized in A. thaliana, Oryza sativa, and other plant species (Puga et al. 2017; Wang et al. 2021; Paz-Ares et al. 2022). It is important to highlight that most of these studies have been carried out in an in vitro system illuminated under white or different types of light. Due to different soils and uneven resource distribution, plants must alter their root systems to receive nutrients and water. Exposing roots to light may change these growth responses (Silva-Navas et al. 2019) since root illumination may reveal water and nutrient absorption depths within the soil. Silva-Navas et al. (2015) found that light may affect ethylene, ROS, and flavonol production, causing changes in root growth. Phosphorus deficit stimulates RH elongation (Bates and Lynch 1996), and exposing roots to light may change this growth response (Silva-Navas et al. 2016; 2019). Clearly, based on this evidence, systems for growing roots in dark need to be incorporated in the root biology research as a common practice.

In this Update, we summarized the current knowledge on Pi starvation and salt stress signaling pathways acting specifically on RHs. In addition, to uncover new molecular components, we use a meta-analysis approach to use available single-cell RNA-seq transcriptome information for RHs to elucidate the molecular connections between these 2 concurrent abiotic stressors. Gaining insight into the molecular mechanisms behind these 2 stress responses in a single plant cell can facilitate the development of highly adaptable roots in crops and promote sustainable agricultural practices. Since Pi deficiency and salinity have a huge impact on agricultural production, these issues require extensive experimental innovation and research for the development of more adaptable plants for global food sustainability.

Main transcriptional program that controls RH development

Only the root epidermal cells positioned above 2 cortical cells in cruciferous and other dicot plants have the ability to grow into RHs. The cells that develop RHs are known as hair cells or trichoblasts, whereas the cells that do not form RHs are termed non-hair cells or atrichoblasts. Detailed information on the epidermis cell-fate program between atrichoblasts and trichoblasts can be found in previous reviews (Bruex et al. 2012; Lin et al. 2015; Shibata and Sugimoto 2019). After the destiny of RH cells has been established in the epidermal cells, genes of the basic helix-loop-helix (bHLH) type that are located downstream of GLABRA2 (GL2) have significant functions in initiating and elongating these cells. The lack of GL2 in trichoblasts allows for the activation of RHD6 (and RSL1), leading to the commencement of RH development. This process is controlled by the interplay of many genes (Hwang et al. 2017). RHD6 and RSL1, which is the most similar known relative of RHD6, both code for class I RSL family transcription factors that are expressed only in H cells (Masucci and Schiefelbein 1994; Menand et al. 2007; Proust et al. 2016). RHD6 (and RSL1) in Arabidopsis stimulate the transcription of genes that encode additional bHLHs, such as RSL2 and RSL4, as well as ROOT HAIRLESS-LIKE 3 (LRL3)-LRLs in Lotus japonicus (Karas et al. 2009; Yi et al. 2010). RSL2 and RSL4 are members of the class II RSL family and operate as transcription factors. They have overlapping roles in regulating RH elongation, with RSL4 playing a more substantial role compared with RSL2 (Yi et al. 2010; Pires et al. 2013; Proust et al. 2016; Marzol et al. 2017). After the RHD6–RSLs, the activation and elongation of RH include the expression of hundreds of genes (Fig. 1, A and B) (Yi et al. 2010; Vijayakumar et al. 2016; Marzol et al. 2017). The only expression of RSL4 in atrichoblast cells is enough to generate abnormal RHs (Hwang et al. 2017); therefore, RHD6 (RSL1), RSL2, and RSL4 are essential components of the gene regulatory network that governs RH development (Lee and Cho 2013; Franciosini et al. 2017; Shibata et al. 2018, 2022). GL2 is mainly found in atrichoblast cells. A recent study discovered that GL2 positively regulates ZP1, which, in turn, has the ability to hinder the start and elongation of RHs in N cells by directly suppressing the expression of RHD6, RSL2, and RSL4 (Han et al. 2020). GL2-ZP1 serves as the last point of repression at the transcriptional level for initiating RH growth in H cells and preventing this process in N cells.

Figure 1.

Signaling pathways operating on RH growth when exposed to salt stress (left) and low Pi auxin-induced FER-dependent oxidation of TIR1/AFB2 (right). A) Under a low-phosphate (Pi) high-auxin environment, the RHs cells activate the pathway involving FERONIA receptor kinase (FER), LORELEI-LIKE GPI-ANCHORED PROTEIN 1 (LLG1), and RHO-type GTPase OF PLANTS 2 (ROP2). Then, ROP2-RESPIRATORY BURST OXIDASE HOMOLOG C (RBOHC) is responsible for the formation of a stable form of ROS, H₂O₂, and NO. ROS may have an effect on the synthesis of NO, despite the unclear origin of NO. ROS and NO cause oxidative changes as S-nitrosylation (SNO) on the Cys135/Cys511 residues in the AUXIN SIGNALING F-BOX 2 (AFB2) and the Cys140/Cys516 residues in the TRANSPORT INHIBITOR RESPONSE 1 (TIR1). These oxidative changes on AFB2/TIR affect the expression of auxin-responsive genes in the nucleus by enhancing the transport of TIR1/AFB2 from the cytoplasm to the nucleus. Oxidized TIR/AFB2 triggers the degradation of Aux/IAAs, by the action of the 26S proteasome, leading to the release of certain ARFs (e.g. ARF7/19). This process regulates RH gene expression, including the master regulator ROOT HAIR DEFECTIVE 6-LIKE 4 (RSL4) and downstream genes. B) Under high salt levels, the ABSCISIC ACID RESPONSIVE ELEMENT-BINDING FACTOR 1, 3, and 4 (ABF1, AFB3, AFB4) proteins from the bZIP family may physically bind to RHD6 and directly prevent it from activating transcription in RH cells. This results in a decrease in RH length and eventually improves the plant's ability to withstand salt stress. In addition to this transcriptional response, it has recently been shown that RH under salt stress conditions, are regulated by SALT OVERLY SENSITIVE 2 (SOS2), GUANOSINE NUCLEOTIDE DIPHOSPHATE DISSOCIATION INHIBITOR 1 (RhoGDI1), and ROP2. It was demonstrated that the kinase SOS2 phosphorylates RhoGDI1, a regulator of RH development, leading to a decrease in its stability. The modification of RhoGDI1 resulted in a specific modification of the polar positioning of ROP2, which impacted the beginning and elongation of RH development under salt stress. FER is also another component that perceives salt stress in the root epidermal cell surface. Finally, it is expected that PIN2 is affected by salt stress and induces its endocytosis, affecting the levels of auxin transport in the epidermis close to the initial site of RH development. Proposed common links between salt stress and auxin induction during Pi shortage are FER, ROP2 and PIN2. Produced with Biorender.com.

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Signaling pathways triggered by Pi starvation and salt stress that controls RH development

The responsiveness of RH length and density to the availability of nutrients, water, and microorganisms in the soil indicates that they may serve as indicators of soil conditions. The initial development of RHs are tightly controlled in response to the availability of nutrients, particularly inorganic phosphate (Pi) (recently summarized in Jia et al. 2022; Lopez et al. 2023). The length of RH increases by about 3 times under low-Pi settings compared with high-Pi conditions (Bates and Lynch 1996), and this is essential for enhancing its acquisition under limited conditions (Bates and Lynch 2000, 2001). On the other hand, it is known that salt stress drastically represses RH growth in the range of 75 to 125 mm NaCl (Liu et al. 2023), and this may trigger antagonist growth consequences under both low Pi and salt stresses at the same time. The molecular mechanisms of Pi starvation responses in roots have been extensively studied (Crombez et al. 2019; Paz-Ares et al. 2022). In short, the MYB family of transcription factors, PHOSPHATE STARVATION RESPONSE1 (PHR1) and PHL1 (PHR1-like) are key elements controlling Pi-responsive gene expression (Bustos et al. 2010; Ambawat et al. 2013). PHR1 and PHL1 can interact and recognize the same cis region, the PHR1 Binding Site (P1BS motif), in the promoter sequence of their target genes, which include phosphate stress inducible (PSI) and phosphate starvation response (PSR) genes (Rubio et al. 2001; Sobkowiak et al. 2012). PHR1 and PHL1 act redundantly and possibly cooperatively to regulate plant responses to Pi scarcity (Bustos et al. 2010; Wang et al. 2019). However, there are still gaps in our understanding of how these pathways act at the level of the RHs (Mangano et al. 2018; Pacheco et al. 2023). RSL4 (and RSL2) are the transcription factors that exhibit the highest response to low Pi as a conserved response in monocots and dicots (Bhosale et al. 2018; Giri et al. 2018). It is unclear if this RSLs induction is mediated by PHR1 and PHL1 specifically in RH cells.

Overall, once the root tip first detects low levels of Pi, it immediately upregulates TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (TAA1) and YUCCA genes (Bhosale et al. 2018; Giri et al. 2018), and this leads to an increase in auxin levels, some of which is transported to the upper part of the root throughout the epidermis layer (Casal and Estevez 2021). High levels of auxin in RH cells results in an elevation of REACTIVE OXYGEN SPECIES (ROS) (Mangano et al. 2017) and an increase in NITRIC OXIDE (NO) generation. Elevated levels of both ROS and NO induce the formation and growth of RH via an unidentified mechanism (in the case of NO) (Lombardo and Lamattina 2012; Mangano et al. 2017). Increased ROS is facilitated by RHO-type GTPase OF PLANTS (ROP) ROP2, and it is initiated by the activation of the NADPH oxidase C or RESPIRATORY BURST OXIDASE HOMOLOG C (RBOHC) (Duan et al. 2010). RBOHC generates superoxide ions (O₂⁻) on the apoplastic side, which are mostly transformed into hydrogen peroxide (H₂O₂) by the action of SUPEROXIDE DISMUTASES (SODs) or chemically. H₂O₂ is the stable form of ROS and partially relies on the activation of the Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) FERONIA (FER), together with its co-receptor LORELEI-LIKE-GPI-ANCHORED PROTEIN 1 (LLG1) and ROP2. The kinase domain of FER interacts with the ROP GUANINE NUCLEOTIDE-EXCHANGE FACTOR 1 (ROP-GEF1), and maybe with other ROP-GEFs (such as ROP-GEF4 or ROP-GEF10), to recruit and subsequently activate ROP2 and potentially additional ROPs (e.g. ROP4 and ROP6) (Denninger et al. 2019). A portion of the H₂O₂ generated enters the cytoplasm, perhaps facilitated by aquaporins of the PLASMA MEMBRANE INTRINSIC PROTEINS type (PIPs). Meanwhile, the remaining ROS may cause alterations in the cell wall crosslinking and relaxation (Pacheco et al. 2022). Recently, it was demonstrated that the transportation of TIR1/AFB2 to the nucleus relies on auxin-induced oxidation (Lu et al. 2024). These findings indicate that physiologically active ROS, H₂O₂ and NO have a significant impact on the positioning of TIR1/AFB2 proteins within the nucleus and cytoplasm in RHs (Fig. 1A). The FER–ROP2-RBOHC signaling pathway regulates this action and ROS-NO cause targeted oxidative modifications to the cysteine residues (Cys140/Cys516) in TIR1 and (Cys135/Cys511) in AFB2, leading to their translocation into the nucleus and initiating the transcriptional reprogramming to enhance RH growth (Lu et al. 2024). Previously, it was shown that the presence of the Cys140 mutation together with Cys480 in TIR1, under the influence of auxin-NO in roots, caused the interaction between TIR1 and AUXIN/INDOLE-3-ACETIC ACID 17 (IAA17) to be completely removed or greatly reduced (Terrile et al. 2012). This indicates that the process of S-nitrosylation, which involves the reversible binding of an NO molecule to a reactive cysteine (Cys) residue to form an S-nitrosothiol, is essential for the interaction between TIR1 and other proteins such as Aux/IAA proteins. This interaction facilitates the degradation of Aux/IAA proteins and subsequently promotes the activation of gene expression. However, it has not been directly proven for the RH growth (Terrile et al. 2012). The oxidized forms of TIR1 and AFB2 are crucial for enhancing the efficiency of TIR1/AFB2 in promoting transcriptional auxin responses in RH development.

The primary regulatory mechanism at the nuclear level involves the direct activation of RSL4 (and possibly RSL2) by auxin, through several AUXIN RESPONSE FACTORS (ARFs). Subsequently, RSL4 activates the transcription of RBOHC and others, as well as several apoplastic peroxidases (PRXs). This process leads to the generation and establishment of an oscillating ROS homeostasis (Mangano et al. 2017). At the transcriptional level, auxin has the ability to directly control the expression of genes that come downstream RSL4, including those that encode RBOHC/J as well as several class III peroxidases (Fig. 1A) (Mangano et al. 2017; Marzol et al. 2022). The precise importance of direct (via ARFs) and indirect (through RSL4) auxin-regulated gene expression is still uncertain. There is also evidence indicating that jasmonic acid, strigolactones, and cytokinins have a beneficial effect on RH growth, whereas brassinosteroids and abscisic acid have a detrimental effect (recently revised in Vissenberg et al. 2020; Lopez et al. 2023). Additional hormones, including ethylene, cytokinin, and strigolactones, have been identified as playing a role in the connection between auxin and nutrition (Jia et al. 2022). The nutritional cues for roots and RHs, which undergo quick and dynamic changes in both temporal and spatial dimensions within the soil, are intricately connected to signaling pathways that promptly regulate cellular activities to adapt to a demanding environment. Plant RAPID ALKALINIZATION FACTORS (RALFs) are peptides that are secreted extracellularly and function as peptide-hormone signals. They bind to the extracellular regions of FER and other CrRLK1L members. RALF1 and RALF22 play essential roles in controlling the formation of RHs and facilitating the ability of roots to adjust to environmental changes. However, the precise signals that trigger their expression are yet unidentified (Zhu et al. 2020; Schoenaers et al. 2024). The connection between the peptide and receptor, namely RALF1-FER, initiates the activation of other downstream partners, such as ErbB3-binding protein 1 (EBP1), RPM1-induced protein kinase (RIPK), early translation factor eIF4E1, and Target of Rapamycin Complex 1 (TORC1), among others. The downstream components work together to control the RH growth among other processes in a synchronized way (Cheung 2024).

The general response involves the SALT OVERLY SENSITIVE (SOS) pathway as an important and universally present signaling mechanism that enables plants to tolerate high levels of salt (Kawa and Testerink 2017). The complex is composed of the Ca²⁺ sensors SOS3 and SOS3-LIKE CALCIUM BINDING PROTEIN 8 (SCaBP8), the protein kinase SOS2, and the Na⁺/H⁺ antiporter SOS1 (Van Zelm et al. 2020). High levels of salt lead to an elevation in the concentration of Ca⁺² within the cytoplasm. This change is detected by SOS3 and SCaBP8, enabling them to interact with the main controller SOS2 and facilitate the movement of SOS2 to the plasma membrane. In that place, the enzymatic activity of SOS2 is stimulated, causing it to phosphorylate the Na⁺/H⁺ antiporter SOS1, and this activation leads to the movement of Na⁺ ions out of cells (Van Zelm et al. 2020). This general pathway has not been tested specifically for RHs. Under conditions of salt stress, the bZIP family proteins ABSCISIC ACID RESPONSIVE ELEMENT-BINDING FACTOR 1, 3, and 4 (ABF1, 3, 4) can physically interact with RHD6 and directly inhibit its transcriptional activation. This leads to a reduction in RH length and ultimately enhances the plant's resistance to salt stress (Jin et al. 2023). In addition, OBF BINDING PROTEIN 4 (OBP4), a DOF-type B transcription factor, is a negative regulator of RH growth via ABA, as induction of OBP4 reduces RH length and ABA treatment increases its expression levels (Rymen et al. 2017). On top of this transcriptional repression, recently is was demonstrated that RH under salt stress conditions are controlled by SALT OVERLY SENSITIVE 2 (SOS2), GUANOSINE NUCLEOTIDE DIPHOSPHATE DISSOCIATION INHIBITOR 1 (RhoGDI1), and ROP2 (Fig. 1B). It was shown that the kinase SOS2 triggered by salt stress phosphorylates RhoGDI1, a regulator of RH growth, resulting in a reduction in its stability. The alteration of RhoGDI1 led to a precise adjustment of the polar localization of ROP2 affecting the initiation and cell elongation of RH growth under salt stress. This illustrates the crucial role of SOS2-regulated RH formation in plant growth under conditions of salt stress. In addition, it was found that FER is necessary for root acclimatization under high salinity and that lack of FER-dependent signaling causes epidermal cells to burst, likely because cells cannot sense and compensate for cell wall weakening (Feng et al. 2018). FER senses salt stress-induced cell wall changes by linking the cell wall and plasma membrane (Dünser et al. 2019). Salt treatment can burst growing root epidermal cells in fer mutants, indicating cell wall weakness. It is proposed that FER might perceive changes in the cell wall composition through LEUCINE-RICH REPEAT EXTENSIN (LRXs) and RALFs (Feng et al. 2018; Dünser et al. 2019; Lan et al. 2023). Recently, it was shown that a complex of demethylated pectins interacts with RALF peptides and LRX proteins to control wall integrity in several plant cells (Moussu et al. 2023), including RHs (Schoenaers et al. 2024) enhancing resistance to salt stress (Zhao et al. 2018). It is tempting to hypothesize that FER and ROP2 are both connecting points between salt stress and auxin-induced Pi starvation in RHs. FER-ROP2 controls the levels of ROS and the subsequent transcriptional responses in RHs exposed to high auxin environments as well as in salt stress, where ROP2 is targeted in a polar manner to the plasma membrane. Another point of regulation on salt stress by roots, and possibly, with impact on RHs growth is the PIN2 localization. The activation of phospholipase D (PLD) by salt stress leads to an increase in clathrin-mediated endocytosis of PIN2 at the side of the root facing the greater salt concentration, reducing the amount of auxin being transported (Wang et al. 2019). This indicates that phosphatidic acid (PA) regulates the polar distribution of PIN and the polarity of auxin during halotropism in plants (Galvan-Ampudia and Testerink 2011; Galvan-Ampudia et al. 2013). This effect might also be important to regulate auxin levels to control RH growth under salt stress. In consequence, PIN2 could also be a shared component in both abiotic stresses that impact RH growth. Although our knowledge has greatly expanded on how RH grows under single abiotic stress, still there is an immense gap to be filled when a complex scenario has dual or higher order stresses. To date and based on current evidence, few regulatory connections have been established between salt stress and Pi starvation signaling pathways in RHs including the proposed FER, ROP2, and PIN2 (Fig. 1).

Salt and Pi starvation stresses have overlapping gene regulatory connections on RHs

Recent research has shown that numerous genes are differentially regulated in response to either Pi or salt changes. This underscores the intricate nature of the regulatory mechanisms that control such responses (Barragán-Rosillo et al 2021; Wu et al. 2021). As described above, Pi and salt have convergent effects on plant traits. Hence, such effects might be caused by the convergent impact of Pi and salt treatments on gene expression. To explore this hypothesis, we utilized existing RNA sequencing (RNA-seq) that highlights Pi-responsive or salt-responsive genes in Arabidopsis (Fig. 2). Transcriptomic data sets representing Pi-regulated under root illumination (Barragán-Rosillo et al. 2021) and darkness (Silva-Navas et al. 2019), salt-regulated (Wu et al 2021), and ABA-regulated (Song et al 2016) genes were collected. Although the role of auxin in phosphate acquisition is well known, abscisic acid (ABA) has emerged as a new participant in the phosphate homeostasis of plants. For example, ABA INSENSITIVE5 (ABI5) activates PHT1; 1 to facilitate Pi acquisition in Arabidopsis (Zhang et al. 2022). Additionally, ABA is a phytohormone that actively participates in the mitigation of salt stress (via osmotic or ionic stress) (Seok et al. 2017; Chang et al. 2019; Zou et al. 2022). Therefore, ABA is an interesting regulator to consider because these 2 stimuli converge in its function. Thus, a basic meta-analysis was conducted for this review by testing the magnitude of the overlap between genes reported to be responsive to Pi, salt, and ABA, a hormone that mediates in part the effects of salt stress on gene expression (Fig. 2B). Our meta-analysis indicates 17% (389 genes) and 18% (415 genes) of the 2,253 genes reported to be responsive to Pi under root illumination (Barragán-Rosillo et al 2021) are also regulated by salt or ABA, respectively (Fig. 2B), a greater overlap than what would be anticipated by random occurrence. Pi-regulated genes under darkness (Silva-Navas et al. 2019) also overlap significantly with salt and ABA-regulated genes. The size of the overlap of Pi-regulated genes in dark conditions is larger than Pi under light conditions with ABA-regulated genes (Fig. 2B), suggesting light affects the interaction between Pi and ABA. We investigate whether directionally, that is, induction or repression of gene expression, is common between Pi and ABA signals. Interestingly, genes induced by Pi overlap significantly only with ABA-induced genes (Fig. 2B). Although ABA-induced genes predominantly overlap with other ABA-induced genes, there is also some overlap with Pi-repressed genes, which suggests that multiple regulatory components are involved in the interaction between these 2 signals.

Figure 2.

Pi starvation and salt (Na⁺) stress produce similar effects on gene expression and Pi impact the expression of canonical ABA genes. A) Meta-analysis of selected RNA sequencing (RNA-seq) experiments was performed to test the magnitude of the overlap between genes reported to be responsive to Pi-scarcity (Pi), salt-treatment (Na⁺), and ABA treatment. Common Differentially Expressed Genes (DEGs) were identified in the overlaps between salt stress, Pi starvation, and Pi starvation with ABA. We generated a list of genes preferentially expressed in RHs (although not exclusive) according to published studies (Brady et al. 2007; Cao et al. 2019; Denyer et al. 2019; Jean-Baptiste et al. 2019; Ryu et al. 2019; Shulse et al. 2019; Zhang et al. 2019; Apelt et al. 2022). Such a list is enriched in Pi, salt, and ABA-responsive genes. B) (Right) Transcriptomic data sets representing Pi-regulated under light (Barragán-Rosillo et al 2021) and darkness (Silva-Navas et al. 2019), salt-regulated (Wu et al 2021), and ABA-regulated (Song et al 2016), genes were collected and analyzed. (Left) Comparison of Pi-induced, Pi-repressed (Barragán-Rosillo et al 2021) with ABA-induced and ABA-repressed genes (Song et al. 2016). The number of genes for each list is indicated in parentheses. The Genesect tool available at the VirtualPlant platform (Katari et al. 2010) was used to test the magnitude and significance of the intersection between the gene lists. The number of genes in the intersection is indicated in the center of the square for each comparison. Genesect is a test to determine if 2 gene lists overlap more or less than expected by chance. It runs 1,000 tests, randomly picking 2 gene lists from the Arabidopsis genome, matching the size of lists. It then checks how often the random lists overlap as much or more/less than the lists. The P value is the overlap count divided by 1,000 (*Monte-carlo P < 0.001). It also calculates a z-score based on a binomial distribution, showing how different the list's overlap is from the average of the 1,000 tests. The results were shown as a heatmap, where color intensity indicates the z-score for each comparison. Abbreviation: n.s., not significant. C) Gene expression changes of ABA canonical genes (Song et al. 2016) in response to Pi treatments (Barragán-Rosillo et al 2021). Induced and repressed genes by Pi are shown in red and blue, respectively.

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To elucidate the potential role of Pi, ABA, and salt interactions in the development of RHs, we added enriched single-cell data from various studies using diverse methodologies from fluorescence activated cell sorting protoplast GFP-tagged to single cell-RNA seq to pinpoint genes predominantly (although not exclusively) expressed in both trichoblasts and RHs (Brady et al. 2007; Cao et al. 2019; Denyer et al. 2019; Jean-Baptiste et al. 2019; Ryu et al. 2019; Shulse et al. 2019; Zhang et al. 2019; Apelt et al. 2022). Integrating findings from these publications allowed us to compile a comprehensive list of 1,644 RH-specific genes. Of these, 362 are responsive to salt, while 335 react to ABA, as shown in Fig. 2B. Specifically, 82 genes respond to both Pi (Barragán-Rosillo et al. 2021) and salt, and 78 genes are responsive to both Pi and ABA in RHs. This curated collection includes transcription factors as well as genes involved in signaling and metabolism (Supplementary Table S1), all of which may have a regulatory impact on the interplay between Pi and salt in RH development.

Given the notable overlap between ABA and Pi-responsive genes, we delved into how Pi influences the expression of established ABA canonical genes (Song et al. 2016). Figure 2C illustrates the effect of Pi treatments on the expression of genes that play known roles in ABA signaling and metabolism. For instance, exposure to Pi upregulates the expression of PYL3, PYL9, and PYL10 receptors, which are key components of the ABA signaling pathway. The ABA hormone binds to these PYL receptors to trigger the downstream signaling cascade. Pi treatments also modify the expression of genes downstream of the PYL receptors, such as the kinases (SNRKs, CIPK) and phosphatases (AHG1, AIP1, ATHPP2C5), as well as ABA-responsive genes like LEA4 and COR78. Notably, the transcript levels of ABF2, a TF associated with salt tolerance (Kim et al. 2004), are elevated after Pi treatment. This suggests that Pi availability alters the expression of ABA pathway components, potentially affecting stress response mechanisms, including those for salt stress adaptation. Taken together, our analyses, taking advantage of the previously published transcriptomes, indicate that changes in salt and ABA signaling genes might result in shifts in Pi-responsive gene expression patterns in RHs. These comprehensive genomic studies underscore the significance of examining the interplay between Pi and salt signals. Pursuing this approach could provide profound insights into how plants fine-tune transcriptional regulation in response to both salt exposure and fluctuations in Pi levels.

Acknowledgments

We apologize to all the authors whom we could not cite due to space constraints.

Supplementary Data

The following material is available in the online version of this article.

Supplementary Table S1.

Funding

This work was funded by Agencia Nacional de Investigacion y Desarrollo (ANID) FONDECYT Postdoctorado grant 3220138 to M.I. and 3200833 to H.S.G., ANID FONDECYT 1210389 to J.M.A. and ANID FONDECYT 1200010 to J.M.E., ANID Millennium Science Initiative Program – Millennium Institute for Integrative Biology ICN17_022 to E.A.V., J.M.A., N.R.J., and J.M.E., ANID – Millennium Science Initiative Program NCN2021_010 to J.M.E. and ANPCyT Argentina PICT2021-0514 to J.M.E.

Data availability

The data underlying this article are available in the article and in its online supplementary material.

Dive Curated Terms

The following phenotypic, genotypic, and functional terms are of significance to the work described in this paper:

• ABF2 Gramene: AT1G45249

• ABF2 Araport: AT1G45249

• OBP4 Gramene: AT5G60850

• OBP4 Araport: AT5G60850

• SOS1 Gramene: AT2G01980

• SOS1 Araport: AT2G01980

• SOS3 Gramene: AT5G24270

• SOS3 Araport: AT5G24270

• AHG1 Gramene: AT5G51760

• AHG1 Araport: AT5G51760

• RALF1 Gramene: AT1G02900

• RALF1 Araport: AT1G02900

• FER Gramene: AT3G51550

• FER Araport: AT3G51550

• ROP2 Gramene: AT1G20090

• ROP2 Araport: AT1G20090

• TAA1 Gramene: At1g70560

• TAA1 Araport: At1g70560

• SOS2 Gramene: AT5G35410

• SOS2 Araport: AT5G35410

• RSL Gramene: ROOT HAIR DEFECTIVE-SIX LIKE

• RSL Araport: ROOT HAIR DEFECTIVE-SIX LIKE

• ROP4 Gramene: AT1G75840

• ROP4 Araport: AT1G75840

• ROP6 Gramene: AT4G35020

• ROP6 Araport: AT4G35020

References

Author notes