Biology subjects

Thomine, S.

Publications and source records attributed to Thomine, S..

14 recordsLinked to original sources

bioRxiv2026

IRON DEFICIENCY RESHAPES THE POPLAR ROOT AND EXUDATE METABOLITE PROFILES AND DRIVES EXUDATE-MEDIATED IRON MOBILIZATION

Iron (Fe) deficiency under alkaline conditions limits Fe bioavailability and reshapes plant metabolism. We asked how Fe deficiency at pH 7.5 alters the metabolite profiles of roots and root exudates of Populus x canescens, and whether exudates mobilize Fe at high pH. Hydroponically grown plants were deprived of Fe for 20 and 27 days. Roots and exudates, collected in nutrient solution and in distilled water, were profiled by UHPLC-QTOF MS, and metabolites were annotated using MS/MS molecular networking (MetGem) and public spectral libraries. Fe deficiency caused significant global shifts in both root and exudate metabolomes. In roots, phenylpropanoids increased at 27 days (proanthocyanidins, neochlorogenic acid, naringenin), whereas the salicylate glycoside salicortin decreased, suggesting a redirection of phenylpropanoid flux. In nutrient-solution exudates, eight flavonoids, including quercitrin, accumulated strongly at 27 days, and catecholic coumarins such as fraxetin were detected in roots and exudates. Exudates from Fe-deficient plants increased Fe mobilization from Fe(III) oxides at pH 7.5, and quercitrin solubilized Fe as efficiently as fraxetin. Alkaline Fe deficiency thus reconfigures poplar root and exudate metabolomes, and exuded flavonoids, not only coumarins, may contribute to Fe mobilization at high pH.

plant biology↗

bioRxiv2025

Spatiotemporal Analysis Reveals Mechanisms Controlling Reactive Oxygen Species and Calcium Interplay Following Root Compression

Mechanical stimulation of the root triggers signal transduction involving Reactive Oxygen Species (ROS) and calcium, but their relationships are unclear. This study aims to clarify the temporal and spatial interrelations between calcium and ROS following a localized lateral compression of the root. We combined a microfluidic valve rootchip to apply controlled compression, with fluorescent probes and wide-field or confocal microscopy to monitor H2O2 and calcium dynamics in root tissues simultaneously. Pharmacological inhibitors were used to investigate the causal links between H2O2 and calcium responses. In response to compression, we observed transient H2O2 accumulation, with characteristics similar to the calcium response observed previously in the same microfluidic system. H2O2 and calcium response occurred in 3 kinetic phases: a fast calcium increase relying on mechanosensitive channels and external calcium entry, followed by a long-lasting H2O2 accumulation and a slow calcium increase depending on NADPH oxidase activity. H2O2 accumulated in all root tissues while calcium increases were confined to the root center. These results suggest that two mechanotransduction mechanisms are involved in root response to compression. One mechanism relies on plasma membrane mechanosensitive channels, triggering a fast calcium increase. Another independent mechanism, relying on FERONIA, induces H2O2 accumulation, which drives the slower secondary calcium increase.

plant biology↗

bioRxiv2025

The Rapid Mechanically Activated (RMA) channel transduces increases in plasma membrane tension into transient calcium influx

O_LIPlants respond to mechanical stimuli by a rapid increase in cytosolic calcium. The intensity and kinetics of the calcium changes define calcium signatures important for biological responses . In this study, we determine the properties of a calcium permeable force-gated channel localized at the plasma membrane called Rapid Mechanically Activated (RMA). C_LIO_LIUsing patch-clamp and pressure-clamp, we characterized the kinetics of activation and inactivation of RMA channel upon stimulation by pulses of pressure applied onto the plasma membrane. Combining repetitive pressure pulse protocols at different frequencies with modeling, we investigated the channels capacity to transduce high frequency mechanical stimuli. C_LIO_LIRMA channel rapidly activates in response to membrane tension, then it inactivates during prolonged stimulation. Upon repeated stimulations, RMA current amplitude decreases irreversibly indicating that undergoes adaptation. The channel kinetics may be modeled with four chemical states and the model predicts that it behaves as a pass band filter in the 10 Hz - 1 kHz range. C_LIO_LIIn conclusion, due to its activation/inactivation characteristics, RMA channel is a candidate to mediate cytosolic calcium signaling in response to mechano-stimulation. Its adaptation and filtering properties suggest its involvement in the transduction of high frequency mechanical stimulation such as those produced by insects vibrations. C_LI

plant biology↗

bioRxiv2025

Gain and loss of gene function shaped the nickel hyperaccumulation trait in Noccaea caerulescens

Nickel hyperaccumulation is an extreme adaptation to ultramafic soils observed in more than 500 plant species. However, our understanding of the molecular mechanisms underlying the evolution of this trait remains limited. To shed light on these mechanisms, we have generated a high-quality genome assembly of the metal hyperaccumulator Noccaea caerulescens. We then used this genome as reference to conduct comparative intraspecific and interspecific transcriptomic analyses using various accessions of N. caerulescens and the non-accumulating relative Microthlaspi perfoliatum, to identify genes associated with nickel hyperaccumulation. Our results suggest a correlation between nickel hyperaccumulation and a decrease in the expression of genes involved in defense responses and the regulation of membrane trafficking. Surprisingly, these analyses did not reveal a significant enrichment of genes involved in the regulation of metal homeostasis. However, we found that the expression levels of selected metal transporters, namely NcHMA3, NcHMA4 and NcIREG2, is consistently elevated in N. caerulescens accessions hyperaccumulating nickel. Furthermore, our analyses identified frameshift mutations in NcIRT1 associated with the loss of nickel hyperaccumulation in a few accessions. We further showed that the expression of a functional NcIRT1 in roots of the La Calamine accession increases nickel accumulation in shoots. Our results demonstrate that NcIRT1 participate in nickel hyperaccumulation in N. caerulescens. They also suggest that nickel hyperaccumulation is an ancient trait in N. caerulescens that has evolved from the high and constitutive expression of few metal transporters including NcIREG2 and that the trait was subsequently lost in a few accessions due to mutations in NcIRT1.

plant biology↗

bioRxiv2023

Local compression of the root in a microfluidic device triggers a calcium signal

Throughout their life, plant root are submitted to mechanical stresses due to pressure exerted by the soil. So far, few studies addressed root cell deformation and calcium signaling elicited by soil compression. In this study, we designed a microchip inspired by pneumatic microvalve concept in order to deliver a lateral pressure to the root of a plant expressing the RGECO1-mTurquoise calcium reporter. Lateral pressure applied on the root induced a moderate elastic deformation of root cortical cells and elicited a multicomponent calcium signal at the onset of the pressure pulse, followed by a second one at the release of the pressure. This indicates that straining rather than stressing of tissues is relevant to trigger the calcium signal. The calcium elevation was restricted to the tissue under pressure and did not propagate. Additionally, the calcium signals exhibited a remarkable attenuation upon repetitive stimulations. Highlights- A microvalve concept mimicking lateral soil pressure was developed. - Non-damaging lateral compression of the root induces an elastic deformation of cortical cells. - A multicomponent calcium signal is elicited at the onset of a pressure pulse and upon release of the pressure. - Straining rather than stressing of tissues is relevant to trigger the calcium signal. - The calcium signal is localized at the tissue under pressure and does not propagate. - Calcium signals exhibit a remarkable attenuation upon repetitive stimulations.

plant biology↗

bioRxiv2022

Proton exchange in the nitrate vacuolar transporter AtCLCa is required for growth and nitrogen use efficiency

Nitrate is a major nutrient and osmoticum for plants. To deal with its fluctuating availability in soils, plants store it into vacuoles. AtCLCa, a 2NO3-/1H+ exchanger localized on the vacuole ensures this storage process. It belongs to the CLC family that includes exchangers and channels. A mutation in a glutamate residue conserved across CLC exchangers is likely responsible for the conversion of exchangers to channels. Here, we show that a clca mutant of this residue, E203, behaves as an anion channel in its native membrane. To investigate its physiological importance, we introduced the AtCLCaE203Apoint mutation in a clca KO mutant. We first showed that these AtCLCaE203A mutants display a growth deficit linked to water homeostasis disruption. Additionally, AtCLCaE203Aexpression is not able to complement the clca defect in nitrate accumulation and favors higher N-assimilation at the vegetative stage. Further analyses at post-flowering stages indicated that AtCLCaE203A results in an increase of N uptake allocation to seeds, leading to a higher nitrogen use efficiency compared to wild-type. Altogether, these results point out the critical function of the AtCLCa exchanger on the vacuole for plant metabolism and development.

plant biology↗

bioRxiv2022

Manganese excess and deficiency affects photosynthesis and metabolism in Marchantia polymorpha

Manganese is an essential metal for plant growth. The most important Mn-containing enzyme is the Mn4CaO5 cluster that catalyses water oxidation in Photosystem II. Mn deficiency primarily affects photosynthesis, while Mn excess is generally toxic. Mn excess and deficiency were studied in the liverwort Marchantia polymorpha, an emerging model ideally suited for analysis of metal stress since it accumulates rapidly toxic substances due to the absence of well-developed vascular and radicular systems and a reduced cuticle. We established growth conditions for Mn excess and deficiency, performed analysis of metal content in thalli and isolated chloroplasts and determined metabolites. Metabolome analysis revealed a strong accumulation of N-methylalanine upon exposure to Mn excess and a different response of Marchantia to heavy metal stress than that known for higher plants. We investigated photosynthetic performance by chlorophyll fluorescence at room temperature and at 77K, P700 absorption and by studying the susceptibility of thalli to photoinhibition. In vivo super-resolution fluorescence microscopy was used to visualize changes in the organization of the thylakoid membrane under Mn excess and deficiency. Non-optimal Mn concentrations changed the ratio of photosystem I to photosystem II and altered the organisation of thylakoid membranes. Mn deficiency seems to favour cyclic electron flow around photosystem I protecting thereby photosystem II against photoinhibition.

plant biology↗

bioRxiv2021

Duplication of NRAMP3 gene in poplars generated two homologous transporters with distinct functions

Transition metals are essential for a wealth of metabolic reactions, but their concentrations need to be tightly controlled across cells and cell compartments, as metal excess or imbalance has deleterious effects. Metal homeostasis is achieved by a combination of metal transport across membranes and metal binding to a variety of molecules. Gene duplication is a key process in evolution, as emergence of advantageous mutations on one of the copies can confer a new function. Here, we report that the poplar genome contains two paralogues encoding NRAMP3 metal transporters localized in tandem. All Populus species analyzed had two copies of NRAMP3, whereas only one could be identified in Salix species indicating that duplication occurred when the two genera separated. Both copies are under purifying selection and encode functional transporters, as shown by expression in the yeast heterologous expression system. However, genetic complementation revealed that only one of the paralogues has retained the original function in release of metals stored in the vacuole previously characterized in A. thaliana. Confocal imaging showed that the other copy has acquired a distinct localization to the Trans Golgi Network (TGN). Expression in poplar suggested that the copy of NRAMP3 localized on the TGN has a novel function in the control of cell-to-cell transport of manganese. This work provides a clear case of neo-functionalization through change in the subcellular localization of a metal transporter as well as evidence for the involvement of the secretory pathway in cell-to-cell transport of manganese.

evolutionary biology↗

bioRxiv2021

Copper microRNAs govern the formation of giant feeding cells induced by the root knot nematode Meloidogyne incognita in Arabidopsis thaliana

miR408 and miR398 are two conserved microRNAs which expression is activated by the SPL7 transcription factor in response to copper starvation. We identified these two microRNAs families as upregulated in Arabidopsis thaliana and Solanum lycopersicum roots infected by root-knot nematodes. These endoparasites induce the dedifferentiation of a few root cells and the reprogramming of their gene expression to generate giant feeding cells. By combining functional approaches, we deciphered the signaling cascade involving these microRNAs, their regulator and their targets. MIR408 expression was located within nematode-induced feeding cells in which it co-localised with SPL7 expression and was regulated by copper. Moreover, infection assays with mir408 and spl7 KO mutants or lines expressing targets rendered resistant to cleavage by miR398 demonstrated the essential role of the SPL7/MIR408/MIR398 module in the formation of giant feeding cells. Our findings reveals how perturbation of plant copper homeostasis, via the SPL7/MIR408/MIR398 module, governs the formation of nematode-induced feeding cells.

plant biology↗

bioRxiv2019

Transduction of mechanical cellular oscillation by the plasma-membrane mechanosensitive channel MSL10

Throughout their life, plants are submitted to recurrent cyclic mechanical loading due to wind. The resulting passive oscillation movements of stem and foliage is an important phenomenon for biological and ecological issues such as photosynthesis optimization 1-3 and thermal exchange 4. The induced motions at plant scale are well described and analyzed, with oscillations at typically 1 to 3 Hz in trees 5-10. However, the cellular perception and transduction of such recurring mechanical signals remains an open question. Multimeric protein complexes forming mechanosensitive (MS) channels embedded in the membrane provide an efficient system to rapidly convert mechanical tension into electrical signal 11. Here we show that the plasma membrane mechanosensitive channel MscS-LIKE 10 (MSL10) from the model plant Arabidopsis thaliana responds to pulsed membrane stretching with rapid activation and relaxation kinetics in the range of one second. Under sinusoidal membrane stretching MSL10 presents a greater activity than under static stimulation and behaves as a large bandpass oscillation \"follower\" without filtering the signal in the range of 0.3 to 3 Hz. With a localization in aerial organs naturally submitted to oscillations, our results suggest that the mechanosensitive channel MSL10 represents a molecular component of a universal system of oscillatory perception in plants.

plant biology↗

bioRxiv2019

Dynamic measurement of cytosolic pH and uncovers the role of the vacuolar transporter AtCLCa in the control of cytosolic pH.

Ion transporters are key players of cellular processes. The mechanistic properties of ion transporters have been well elucidated by biophysical methods. Meanwhile the understanding of their exact functions in the whole cell homeostasis is limited by the difficulty to monitor their activity in vivo. The development of biosensors to track subtle changes in intracellular parameters provides an invaluable key to tackle this challenging issue. Here, we adapted the use of a dual biosensor using guard cells as experimental model to visualize the impact on the cytosol of anion transport from intracellular compartments. To image the activity of AtCLCa, a vacuolar NO3-/H+ exchanger regulating stomata aperture in Arabidopsis thaliana, we expressed a genetically encoded biosensor, ClopHensor allowing monitoring the dynamics of cytosolic anion concentration and pH. We first show that ClopHensor is not only a Cl- but also a NO3- sensor. We were then able to unravel and quantify the variations of NO3- and pH in the cytosol. Our data show that AtCLCa activity modifies cytosolic pH and NO3-, demonstrating that the transport activity of a vacuolar exchanger has a profound impact on cytosolic homeostasis. We propose that a major function of this endomembrane transporter is to adjust cytosolic conditions to cellular needs. This opens a novel perspective on the function of intracellular transporters of the CLC family in eukaryotes: not only controlling the intra organelle lumen but also actively modifying cytosolic conditions.\n\nSignificanceIntracellular transporters are key actors in cell biological processes. Their disruption causes major physiological defects. The role of intracellular ion transporters is usually seen through an \"intra organelle\" lens, meanwhile their potential action on cytosolic ion homeostasis is still a black box. The case of a plant CLC is used as a model to uncover the missing link between the regulation of conditions inside the vacuole and inside the cytosol. The development of an original live imaging workflow to simultaneously measure pH and anion dynamics in the cytosol reveals the role of an Arabidopsis thaliana CLC, AtCLCa, in the modification of cytosolic pH. Our data highlight an unsuspected function of endomembrane transporters in the regulation of cytosolic pH.

plant biology↗

bioRxiv2018

Wide cross-species RNA-Seq comparison reveals a highly conserved role for Ferroportins in nickel hyperaccumulation in plants

The Anthropocene epoch is associated with the spreading of metals in the environment increasing oxidative and genotoxic stress on living organisms1,2. Once regarded as a curiosity, plants hyperaccumulating metals are now envisioned as an opportunity to remediate metal contaminated soils. About 500 plant species adapted to metalliferous soils acquired the capacity to hyperaccumulate (>0.1% of dry weight) nickel in their shoot3. The phylogenetic distribution of these hyperaccumulators in 50 families suggest that this complex trait evolved multiple times independently from basic mechanisms involved in metal homeostasis. However, the exact nature of these mechanisms and whether they are shared between various lineages is not known. Here, using cross-species transcriptomic analyses in different plant families, we have identified convergent functions that may represent major nodes in the evolution of nickel hyperaccumulation. In particular, our data point out that constitutive high expression of IREG/Ferroportin transporters recurrently emerged as a mechanism involved in nickel hyperaccumulation.

plant biology↗

bioRxiv2018

Autophagy is essential for optimal Fe translocation to seeds in Arabidopsis

Micronutrient deficiencies affect a large part of the world population. They are mostly due to the consumption of grains with insufficient content of Fe or Zn. Both de novo uptake by roots and recycling from leaves may provide seeds with nutrients. Autophagy, which is a conserved mechanism for nutrient recycling in eukaryotes, was shown to be involved in nitrogen remobilization to seeds. Here, we have investigated the role of this mechanism in micronutrient translocation to seeds. We found that several Arabidopsis thaliana plants impaired in autophagy display defects in nutrient remobilization to seeds. In atg5-1 mutant, which is completely defective in autophagy, the efficiency of Fe translocation from vegetative organs to seeds was severely decreased even when Fe was provided during seed formation. Combining atg5-1 with sid2 mutation that counteracts premature senescence associated to autophagy deficiency and using 57Fe pulse labeling, we could propose a two-step mechanism in which iron taken up de novo during seed formation is first accumulated in vegetative organs and subsequently remobilized to seeds. Finally, we showed that translocations of zinc and manganese to seeds are also dependent on autophagy. Fine tuning autophagy during seed formation opens therefore new possibilities to improve micronutrient remobilization to seeds.

plant biology↗

bioRxiv2018

Vacuolar iron stores gated by NRAMP3 and NRAMP4 are the primary source of iron in germinating seeds

During seed germination, iron (Fe) stored in vacuoles is exported by the redundant NRAMP3 and NRAMP4 transporter proteins. A double nramp3 nramp4 mutant is unable to mobilize Fe stores and does not develop in the absence of external Fe. We used RNA sequencing to compare gene expression in nramp3 nramp4 and wild type during germination and early seedling development. Even though sufficient Fe was supplied, the Fe-responsive transcription factors bHLH38, 39, 100 and 101 and their downstream targets FRO2 and IRT1 mediating Fe uptake were strongly upregulated in the nramp3 nramp4 mutant. Activation of the Fe deficiency response was confirmed by increased ferric chelate reductase activity in the mutant. At early stages, genes important for chloroplast redox control (FSD1, SAPX), Fe homeostasis (FER1, SUFB) and chlorophyll metabolism (HEMA1, NYC1) were downregulated, indicating limited Fe availability in plastids. In contrast, expression of FRO3, encoding a ferric reductase involved in Fe import into the mitochondria, was maintained and Fe-dependent enzymes in the mitochondria were unaffected in nramp3 nramp4. Together these data show that a failure to mobilize Fe stores during germination triggered Fe deficiency responses and strongly affected plastids but not mitochondria.

plant biology↗