Joaquín Clúa

Root growth must continuously adjust to fluctuating nutrient availability, yet the mechanisms that quantitatively integrate environmental signals into developmental responses remain poorly understood. Distinct nutrient stresses, including ammonium toxicity and phosphate deficiency, inhibit primary root growth through iron-dependent processes, suggesting that iron acts as a central regulatory node. Here, we show that plants use an antagonistic module composed of CYBDOM ferrireductases and LPR ferroxidases to regulate apoplastic iron homeostasis and control root growth in a graded manner. Genetic perturbation of this module demonstrates that root growth inhibition scales quantitatively with iron accumulation, supporting a proportional control mechanism rather than a binary response. Loss of CYBDOM function causes excessive iron accumulation, elevated reactive oxygen species, and impaired meristem activity, whereas increased CYBDOM activity buffers iron deposition and confers resistance to stress. Mechanistically, iron-induced oxidative stress promotes HYP1 expression, which in turn limits further iron accumulation. Transcriptomic analyses distinguish ammonium-specific responses from Fe-associated transcriptional changes enriched in redox buffering and cell-wall remodeling. Finally, we show that this regulatory module is redeployed in distinct tissues under phosphate deficiency, indicating that plants reuse a conserved iron-based mechanism to coordinate growth across environmental contexts. Together, our findings establish genetically controlled Fe accumulation as a key determinant of developmental plasticity under nutrient stress.

Phosphorous and nitrogen are the main nutrients limiting plant growth in natural and agricultural systems. Plants typically uptake phosphorous in the form of inorganic phosphate, whereas the main nitrogen sources are nitrate and ammonium. Roots show a high degree of developmental plasticity in response to nutritional stresses, directly influencing plant fitness and stress resilience. In Arabidopsis thaliana , phosphate deficiency and high levels of ammonium in the media triggers a strong inhibition of the primary root growth. This developmental response is initiated by the accumulation of apoplastic iron in specific cell types, which triggers the inhibition of meristem maintenance and cell elongation. In this report, we show that DOMON domain-containing proteins are key molecular players controlling root development upon phosphate deficiency and ammonium toxicity via iron dynamics.

SUMMARY: Alternative transcription start sites (TSS) are widespread in eukaryotes and can alter the 5′ UTR length and coding potential of transcripts. Here we show that inorganic phosphate (Pi) availability regulates the usage of several alternative TSS in Arabidopsis (Arabidopsis thaliana). In comparison to phytohormone treatment, Pi had a pronounced and specific effect on the usage of many alternative TSS. By combining short‐read RNA sequencing with long‐read sequencing of full‐length mRNAs, we identified a set of 45 genes showing alternative TSS under Pi deficiency. Alternative TSS affected several processes, such as translation via the exclusion of upstream open reading frames present in the 5′ UTR of RETICULAN LIKE PROTEIN B1 mRNA, and subcellular localization via removal of the plastid transit peptide coding region from the mRNAs of HEME OXYGENASE 1 and SULFOQUINOVOSYLDIACYLGLYCEROL 2. Several alternative TSS also generated shorter transcripts lacking the coding potential for important domains. For example, the EVOLUTIONARILY CONSERVED C‐TERMINAL REGION 4 (ECT4) locus, which encodes an N⁶‐methyladenosine (m⁶A) reader, strongly expressed under Pi deficiency a short noncoding transcript (named ALT_ECT4) ~550 nt long with a TSS in the penultimate intron. The specific and robust induction of ALT_ECT4 production by Pi deficiency led to the identification of a role for m⁶A readers in primary root growth in response to low phosphate that is dependent on iron and is involved in modulating cell division in the root meristem. Our results identify alternative TSS usage as an important process in the plant response to Pi deficiency.

Arabidopsis primary root growth response to phosphate (Pi) deficiency is mainly controlled by changes in apoplastic iron (Fe). Upon Pi deficiency, apoplastic Fe deposition in the root apical meristem activates pathways leading to the arrest of meristem maintenance and inhibition of cell elongation. Here, we report that a member of the uncharacterized cytochrome b561 and DOMON domain (CYBDOM) protein family, named CRR, promotes iron reduction in an ascorbate-dependent manner and controls apoplastic iron deposition. Under low Pi, the crr mutant shows an enhanced reduction of primary root growth associated with increased apoplastic Fe in the root meristem and a reduction in meristematic cell division. Conversely, CRR overexpression abolishes apoplastic Fe deposition rendering primary root growth insensitive to low Pi. The crr single mutant and crr hyp1 double mutant, harboring a null allele in another member of the CYDOM family, shows increased tolerance to high-Fe stress upon germination and seedling growth. Conversely, CRR overexpression is associated with increased uptake and translocation of Fe to the shoot and results in plants highly sensitive to Fe excess. Our results identify a ferric reductase implicated in Fe homeostasis and developmental responses to abiotic stress, and reveal a biological role for CYBDOM proteins in plants.

SUMMARY: 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.

Accumulation of incompletely folded proteins in the endoplasmic reticulum (ER) leads to ER stress, activates ER protein degradation pathways, and upregulates genes involved in protein folding. This process is known as the unfolded protein response (UPR). The role of ER protein folding in plant responses to nutrient deficiencies is unclear. We analyzed Arabidopsis (Arabidopsis thaliana) mutants affected in ER protein quality control and established that both CALNEXIN (CNX) genes function in the primary root response to phosphate (Pi) deficiency. CNX1 and CNX2 are homologous ER lectins promoting protein folding of N-glycosylated proteins via the recognition of the GlcMan₉GlcNAc₂ glycan. Growth of cnx1-1 and cnx2-2 single mutants was similar to that of the wild type under high and low Pi conditions, but the cnx1-1 cnx2-2 double mutant showed decreased primary root growth under low Pi conditions due to reduced meristematic cell division. This phenotype was specific to Pi deficiency; the double mutant responded normally to osmotic and salt stress. Expression of CNX2 mutated in amino acids involved in binding the GlcMan₉GlcNAc₂ glycan failed to complement the cnx1-1 cnx2-2 mutant. The root growth phenotype was Fe-dependent and was associated with root apoplastic Fe accumulation. Two genes involved in Fe-dependent inhibition of primary root growth under Pi deficiency, the ferroxidase LOW PHOSPHATE 1 (LPR1) and P5-type ATPase PLEIOTROPIC DRUG RESISTANCE 2 (PDR2) were epistatic to CNX1/CNX2. Overexpressing PDR2 failed to complement the cnx1-1 cnx2-2 root phenotype. The cnx1-1 cnx2-2 mutant showed no evidence of UPR activation, indicating a limited effect on ER protein folding. CNX might process a set of N-glycosylated proteins specifically involved in the response to Pi deficiency.

Alternative transcription start sites (TSSs) are widespread in eukaryotes. In plants, light, development and tissue regulate selective usage of several TSSs, producing transcripts with distinct 5′UTR as well as shorter protein isoforms with distinct subcellular localization or activity. However, the function of non-coding transcripts generated by alternative TSSs is still largely unknown. We show that phosphate availability regulates numerous alternative TSSs, including a non-coding alternative TSS ( ALT _ECT4 ) associated with ECT4 , encoding a N ⁶ -methyladenosine (m ⁶ A) reader. We found that ECT4 harbors a cleavage-resistant miR826b target site at its 3’UTR, also present in ALT _ECT4 . In the absence of ALT _ECT4 , miR826b guides translation inhibition of ECT4 . Phosphate deficiency triggers specific and robust expression of ALT _ECT4 , counteracting miR826b inhibition of its targets, including ECT4 . The role of ALT _ECT4 as a miR826b antagonist shows that it acts in cis to regulate translation of the m ⁶ A reader ECT4, and this function might be shared among other non-coding transcripts generated by alternative TSS.

Legumes play an important role in the soil nitrogen availability via symbiotic nitrogen fixation (SNF). Phosphate (Pi) deficiency severely impacts SNF because of the high Pi requirement of symbiosis. Whereas PHT1 transporters are involved in Pi uptake into nodules, it is unknown how Pi is transferred from the plant infected cells to nitrogen-fixing bacteroids. We hypothesized that Medicago truncatula genes homologous to Arabidopsis PHO1, encoding a vascular apoplastic Pi exporter, are involved in Pi transfer to bacteroids. Among the seven MtPHO1 genes present in M. truncatula, we found that two genes, namely MtPHO1.1 and MtPHO1.2, were broadly expressed across the various nodule zones in addition to the root vascular system. Expressions of MtPHO1.1 and MtPHO1.2 in Nicotiana benthamiana mediated specific Pi export. Plants with nodule-specific downregulation of both MtPHO1.1 and MtPHO1.2 were generated by RNA interference (RNAi) to examine their roles in nodule Pi homeostasis. Nodules of RNAi plants had lower Pi content and a three-fold reduction in SNF, resulting in reduced shoot growth. Whereas the rate of ³³Pi uptake into nodules of RNAi plants was similar to control, transfer of ³³Pi from nodule cells into bacteroids was reduced and bacteroids activated their Pi-deficiency response. Our results implicate plant MtPHO1 genes in bacteroid Pi homeostasis and SNF via the transfer of Pi from nodule infected cells to bacteroids.