Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks

Background: FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is the central regulator of iron uptake in Arabidopsis thaliana roots. We performed transcriptome analyses of six day-old seedlings and roots of six week-old plants using wild type, a fit knock-out mutant and a FIT over-expression line grown under iron-sufficient or iron-deficient conditions. We compared genes regulated in a FIT-dependent manner depending on the developmental stage of the plants. We assembled a high likelihood dataset which we used to perform co-expression and functional analysis of the most stably iron deficiency-induced genes. Results: 448 genes were found FIT-regulated. Out of these, 34 genes were robustly FIT-regulated in root and seedling samples and included 13 novel FIT-dependent genes. Three hundred thirty-one genes showed differential regulation in response to the presence and absence of FIT only in the root samples, while this was the case for 83 genes in the seedling samples. We assembled a virtual dataset of iron-regulated genes based on a total of 14 transcriptomic analyses of iron-deficient and iron-sufficient wild-type plants to pinpoint the best marker genes for iron deficiency and analyzed this dataset in depth. Co-expression analysis of this dataset revealed 13 distinct regulons part of which predominantly contained functionally related genes. Conclusions: We could enlarge the list of FIT-dependent genes and discriminate between genes that are robustly FIT-regulated in roots and seedlings or only in one of those. FIT-regulated genes were mostly induced, few of them were repressed by FIT. With the analysis of a virtual dataset we could filter out and pinpoint new candidates among the most reliable marker genes for iron deficiency. Moreover, co-expression and functional analysis of this virtual dataset revealed iron deficiency-induced and functionally distinct regulons

Signalling and regulation pathways involved in cryptic effects induced by residual levels of pesticide degradation products on higher plants

International audienc

Signalling and regulation pathways involved in cryptic effects induced by residual levels of pesticide degradation products on higher plants

International audienc

Dissection of iron signaling and iron accumulation by overexpression of subgroup Ib bHLH039 protein

Iron is an essential growth determinant for plants, and plants acquire this micronutrient in amounts they need in their environment. Plants can increase iron uptake in response to a regulatory transcription factor cascade. Arabidopsis thaliana serves as model plant to identify and characterize iron regulation genes. Here, we show that overexpression of subgroup Ib bHLH transcription factor bHLH039 (39Ox) caused constitutive iron acquisition responses, which resulted in enhanced iron contents in leaves and seeds. Transcriptome analysis demonstrated that 39Ox plants displayed simultaneously gene expression patterns characteristic of iron deficiency and iron stress signaling. Thereby, we could dissect iron deficiency response regulation. The transcription factor FIT, which is required to regulate iron uptake, was essential for the 39Ox phenotype. We provide evidence that subgroup Ib transcription factors are involved in FIT transcriptional regulation. Our findings pose interesting questions to the feedback control of iron homeostasis

Drought response of nodulated roots in pea: from ecophysiological to transcriptomic analyses

International audienceIn the context of climate change, more frequent episodes of water stress are expected, which will negatively impact symbiotic N2 fixation and consequentely plant nitrogen nutrition, growth and productivity. This emphasizes the need to select drought tolerant pea genotypes. In this study, the physiological and transcriptional responses of both roots and nodules to a drought event, followed by a recovery period were investigated. The hybridization of a 40k pea microarray indicated that, as a result of drought, ~390 and ~380 genes were at least 2-fold differencially regulated in roots and nodules, respectively. After rewatering, most of these genes were regulated in an opposite manner to drought effect. This analysis allowed to identify common and specific metabolic regulatory processes involved in drought tolerance and recovery. The most highly deregulated genes in response to drought (including LEA family members, delta-1-pyrroline-5-carboxylate synthase, SWEET family members...) were subsequently analysed for their expression patterns in response to several drought events each followed by a recovery period. We will discuss the behavior of these genes in terms of kinetics and intensity of their expression. Acknowledgement: this study was supported by the Burgundy & Franche-Comté Region (FABER program), Terres Inovia, the FP7-ABSTRESS project and its grant FP7-613551, the FP7-LEGATO project and its grant agreement FP7-289562

Table S5. List of genes from the first synergistic group

List of genes in the first synergistic group. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe, "other affy ID" to some related affymetrix probes. LFC: Log2 fold change.pval BH= p-value obtained using a Benjamini Hochberg FDR test. CT=control condition. NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h

A transcriptomic approach identifies candidate genes for drought tolerance during the reproductive phase in pea

BAPEAGEAPSIDrought is a major environmental factor limiting the productivity of crop plants. In pea drought stress occurring during the reproductive phase can greatly affect seed yield and quality. We investigated the response of pea plants (var. Caméor) subjected to water stress during the seed filling period, a phase when massive remobilization from the vegetative organs occurs to sustain seed high-nitrogen demand. Pea plants were subjected to drought stress at the beginning of the seedfilling period of the first two nodes for 8 days. Total and one-seed biomass decreased by 35% and 20% respectively by this limited water stress. Nitrogen allocation to the different plant compartments was also affected, with an increased N allocation to the leaves from the vegetative nodes and a decrease to the root and seed compartments. Transcriptomic changes in water-stressed leaves from the vegetative nodes were analysed by hybridization of a 40k pea micro-array : 178 genes were at least two fold up-regulated in water-stressed samples compared to well-watered samples, whereas 55 genes were downregulated. Among the most strongly up-regulated genes were those encoding a glutamine amidotransferase, a sucrose transporter from the SWEET family, a phosphoenolpyruvate carboxykinase and a carotenoid cleavage dioxygenase involved in strigolactone biosynthesis. Acknowledgement: this project was supported by the Burgundy Region (AGRALE6, FABER program) and the FP7 LEGATO project

TableS1_primers

Table S1: Primer pairs used for Q-PCR on the Medicago truncatula gene

Responses to Hypoxia and Endoplasmic Reticulum Stress Discriminate the Development of Vitreous and Floury Endosperms of Conventional Maize (Zea mays) Inbred Lines

Major nutritional and agronomical issues relating to maize (Zea mays) grains depend on the vitreousness/hardness of its endosperm. To identify the corresponding molecular and cellular mechanisms, most studies have been conducted on opaque/floury mutants, and recently on Quality Protein Maize, are version of an opaque2 mutation by modifier genes. These mutant lines are far from conventional maize crops. Therefore, a dent and a flint inbred line were chosen for analysis of the transcriptome, amino acid, and sugar metabolites of developing central and peripheral endosperm that is, the forth coming floury and vitreous regions of mature seeds, respectively. The results suggested that the formation of endosperm vitreousness is clearly associated with significant differences in the responses of the endosperm to hypoxia and endoplasmic reticulum stress. This occurs through a coordinated regulation of energy metabolism and storage protein (i.e., zein) biosynthesis during the grain-filling period. Indeed, genes involved in the glycolysis and tricarboxylic acid cycle are up-regulated in the periphery, while genes involved in alanine, sorbitol, and fermentative metabolisms are up-regulated in the endosperm center. This spatial metabolic regulation allows the production of ATP needed for the significant zein synthesis that occurs at the endosperm periphery; this finding agrees with the zein-decreasing gradient previously observed from the sub-aleurone layer to the endosperm center. The massive synthesis of proteins transiting through endoplasmic reticulum elicits the unfolded protein responses, as indicated by the splicing of bZip60 transcription factor. This splicing is relatively higher at the center of the endosperm than at its periphery. The biological responses associated with this developmental stress, which control the starch/protein balance, leading ultimately to the formation of the vitreous and floury regions of mature endosperm, are discussed

GOLLUM [FeFe]-hydrogenase-like proteins are essential for plant development in normoxic conditions and modulate energy metabolism

International audience[FeFe]-hydrogenase-like genes encode [Fe4S4]-containing proteins that are ubiquitous in eukaryotic cells. In humans, iron-only hydrogenase-like protein 1 (IOP1) represses hypoxia inducible factor-1 subunit (HIF1-) at normal atmospheric partial O-2 pressure (normoxia, 21kPa O-2). In yeasts, the nar1 mutant cannot grow at 21kPa O-2,O- but can develop at a lower O-2 pressure (2kPa O-2). We show here that plant [FeFe]-hydrogenase-like GOLLUM genes are essential for plant development and cell cycle progression. The mutant phenotypes of these plants are seen in normoxic conditions, but not under conditions of mild hypoxia (5kPa O-2). Transcriptomic and metabolomic experiments showed that the mutation enhances the expression of some hypoxia-induced genes under normal atmospheric O-2 conditions and changes the cellular content of metabolites related to energy metabolism. In conclusion, [FeFe]-hydrogenase-like proteins play a central role in eukaryotes including the adaptation of plants to the ambient O-2 partial pressure