Biology subjects

Fizames, C.

Publications and source records attributed to Fizames, C..

6 recordsLinked to original sources

bioRxiv2025

Establishment, maintenance and consequences of inter-individual transcriptional variability for a gene involved in nitrate nutrition in plants

Differences in phenotypes and gene expression are observed between genetically identical plants grown in the same environment. While we now have a good knowledge of the source and consequences of transcriptional differences observed between cells, in particular in unicellular organisms, it is still very scarce when it comes to variability between multicellular organisms. Using NRT2.1, a high affinity nitrate transporter gene, as a model for high inter-individual transcriptional variability, we showed that differences in expression between plants for that gene are established in young seedlings, maintained over time but not transmitted to the next generation. Our results also indicate that these differences in expression could have phenotypic consequences. Indeed, they can explain phenotypic variability for the root growth as well as the amount of nitrate imported by the NRT2.1 protein in the plant. Finally, we found an enrichment for genes involved in photosynthesis among the ones with an expression correlated with NRT2.1 in single seedlings. All in all, our study suggests that a global coordination of the genes involved in the carbon/nitrate balance in plants is established in young seedlings, with differences in this state between plants, and then maintained over time.

plant biology↗

bioRxiv2023

Natural genetic variation underlying the negative effect of elevated CO2 on ionome composition in Arabidopsis thaliana

The elevation of atmospheric CO2 leads to a decline in the plant mineral content, which might pose a significant threat to food security in the coming decades. To date, very few genes have been identified as having a role in the negative effect of elevated CO2 on plant mineral composition. Yet, several studies have shown a certain degree of diversity in the ionomes response to elevated CO2, associated with genotypic variation. This suggests the existence of genetic factors controlling the effect of CO2 on ionome composition. However, no large-scale studies have been carried out to date to explore the genetic diversity of the ionome responses to elevated CO2. Here, we used six hundred Arabidopsis thaliana accessions, representing geographical distributions ranging from worldwide to regional and local environments, to analyze the natural genetic variation underlying the negative effect of elevated CO2 on the ionome composition in plants. We show that the growth under elevated CO2 leads to a global and important decrease of the ionome content whatever the geographic distribution of the population. We also observed a high range of genetic diversity in the response of the ionome composition to elevated CO2, and we identified sub-populations, showing effects on their ionome ranging from the most pronounced to resilience or even to a benefit in response to elevated CO2. Using genome-wide association mapping on the response of each mineral element to elevated CO2 or on integrative traits, we identified a large set of QTLs and genes associated with the ionome response to elevated CO2. Finally, we demonstrate that the function of one of these genes is associated to the negative effect of elevated CO2 on the plant mineral composition. This resource will contribute to understand the genetic mechanisms underlying the negative effect of elevated CO2 on plant mineral nutrition, and could help towards the development of crops adapted to a high-CO2 world.

plant biology↗

bioRxiv2022

Arbuscular mycorrhizal fungus Rhizophagus irregularis expresses an outwardly Shaker-like channel involved in potassium nutrition of rice (Oryza sativa L.)

Potassium (K+) plays crucial roles in many physiological, molecular and cellular processes in plants. Direct uptake of this nutrient by root cells has been extensively investigated, however, indirect uptake of K+ mediated by the interactions of the roots with fungi in the frame of a mutualistic symbiosis, also called mycorrhizal nutrient uptake pathway, is much less known. We identified an ion channel in the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis. This channel exhibits the canonical features of Shaker-like channel shared in other living kingdoms and is named RiSKC3. Transcriptionally expressed in hyphae and in arbuscules of colonized rice roots, RiSKC3 has been shown to be located in the plasma membrane. Voltage-clamp functional characterization in Xenopus oocytes revealed that RiSKC3 is endowed with outwardly-rectifying voltage-gated activity with a high selectivity for potassium over sodium ions. RiSKC3 may have a role in the AM K+ pathway for rice nutrition in normal and salt stress conditions. The current working model proposes that K+ ions taken up by peripheral hyphae of R. irregularis are secreted towards the host root into periarbuscular space by RiSKC3. Significance StatementArbuscular mycorhizal fungus Rhizophagus irregularis expresses a Shaker-like channel, located in the plasma membrane, endowed with a strictly outwardly-rectifying voltage-gated activity with a high selectivity for potassium over sodium ions. The current working model proposes that K+ ions taken up by peripheral hyphae of R. irregularis are secreted towards the host root into periarbuscular space by this Shaker-like channel.

plant biology↗

bioRxiv2022

Signaling pathways involved in the repression of root nitrate uptake by nitrate in Arabidopsis thaliana

In Arabidopsis thaliana, root high-affinity nitrate (NO3-) uptake depends mainly on NRT2.1, 2.4 and 2.5, which are repressed by high NO3- supply at the transcript level. For NRT2.1, this regulation is due to the action of (i) feedback downregulation by N metabolites and (ii) repression by NO3- itself mediated by the transceptor NRT1.1(NPF6.3). However, for NRT2.4 and NRT2.5 the signaling pathway(s) remain unknown along with the molecular elements involved. Here we show that unlike NRT2.1, NRT2.4 and NRT2.5 are not induced in a NO3- reductase mutant but are strongly upregulated following replacement of NO3- by ammonium (NH4+) as the N source. Moreover, increasing NO3- concentration in a mixed nutrient solution with constant NH4+ concentration results in a gradual repression of NRT2.4 and NRT2.5, which is suppressed in a nrt1.1 mutant. This indicates that NRT2.4 and NRT2.5 are subjected to repression by NRT1.1-mediated NO3- sensing, and not to feedback repression by reduced N metabolites. We further show that key regulators of NRT2s transporters, such as HHO1, HRS1, PP2C, LBD39, BT1 and BT2, are also regulated by NRT1.1-mediated NO3- sensing, and that several are involved in NO3- repression of NRT2.1, 2.4 and 2.5. Finally, we provide evidence that it is the phosphorylated form of NRT1.1 at the T101 residue, which is most active in triggering the NRT1.1-mediated NO3- regulation of all these genes. Altogether, these data led to propose a regulatory model for high-affinity NO3- uptake in Arabidopsis, highlighting several NO3- transduction cascades downstream the phosphorylated form of the NRT1.1 transceptor. One sentence summaryCharacterisation and identification of molecular elements involved in the signaling pathways repressing NRT2s transporters and root nitrate uptake in response to nitrate.

plant biology↗

bioRxiv2019

Genome-wide Analysis In Response to N and C Identifies New Regulators for root AtNRT2 Transporters

In Arabidopsis thaliana, the High-Affinity Transport System (HATS) for root NO3- uptake depends mainly on four NRT2 transporters, namely NRT2.1, NRT2.2, NRT2.4 and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways have been shown to control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 genes expression to the interaction of these signals has never been specifically investigated and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4 and NRT2.5 in response to N/C signals. Our systems analysis of the data highlighted the potential role of three putative transcription factors, TGA3, MYC1 and bHLH093. Functional analysis of mutants combined with yeast one hybrid experiments confirmed that all 3 transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals.\n\nOne sentence summaryIdentification of three transcription factors involved in the regulation of NRT2s transporters using a systems biology approach and NRT2.1 as target gene in response to combinations of N/C treatments

plant biology↗

bioRxiv2019

NRT2.1 phosphorylation prevents root high affinity nitrate uptake activity in Arabidopsis thaliana

In Arabidopsis thaliana, NRT2.1 codes for a main component of the root nitrate high-affinity transport system. Previous studies revealed that post-translational regulation of NRT2.1 plays an important role in the control of root nitrate uptake and that one mechanism could correspond to NRT2.1 C-terminus processing. To further investigate this hypothesis, we produced transgenic plants with truncated forms of NRT2.1. It revealed an essential sequence for NRT2.1 activity, located between the residues 494-513. Using a phospho-proteomic approach, we found that this sequence contains one phosphorylation site, at serine 501, which can inactivate NRT2.1 function when mimicking the constitutive phosphorylation of this residue in transgenic plants. This phenotype could neither be explained by changes in abundance of NRT2.1 and NAR2.1, a partner protein of NRT2.1, nor by a lack of interaction between these two proteins. Finally, the relative level of serine 501 phosphorylation was found to be modulated by nitrate in wildtype plants. Altogether, these observations allowed us to propose a model for a new and essential mechanism for the regulation of NRT2.1 activity.

plant biology↗