Transcriptomic response of Arabidopsis thaliana to the two rare earth elements lanthanum and ytterbium
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PROVIDER: PRJNA996115 | ENA |
REPOSITORIES: ENA
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Project description:The goal of this study is to compare the transcriptome (RNA-seq) modulations in the roots and shoots of Arabidopsis thaliana, as a plant model, exposed to two toxic concentrations of rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements, respectively.
2023-07-23 | GSE237657 | GEO
Project description:Purpose: The goals of this study is to compare the transcriptome (RNA-seq) modulations in Saccharomyces cerevisiae exposed to two rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements, respectively. Methods: mRNA were sequenced from Saccharomyces cerevisiae exposed to two different rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements respectively. The transcriptome of S. cerevisiae was analysed after being exposed for one hour to the EC10 (Effective concentration 10 %) and the EC50 (Effective concentration 50 %) of lanthanum (50 and 160 µM) and ytterbium (6 and 8 µM). The sequence reads were trimmed using Trimmomativ v0.36.1 and FastQC v0.67 used for quality check. Reads passing the quality check were mapped on the reference genome (S288C R64-2-1 of 2015-01-31 from https://www.yeastgenome.org/) of S. cerevisiae using TopHat v2.1.1. Reads that were mapped on the reference genome were quantified using HTSeq-count v0.6.1p1. Finally, differential gene expression analysis between treatments was carried out using DESeq2 v1.14.1. Differentially expressed genes between conditions were obtained and expressed as log2-fold change with adjusted p-values calculated via a Benjamini-Hochberg test. A cut-off adjusted p-value of < 0.01 was applied. Results: The transcription of genes related to several crucial pathways was modulated in response to both REEs, such as oxidative-reduction processes, DNA replication, and carbohydrate metabolism. REE-specific responses involving the cell wall and the pheromone signalling pathways were highlighted, while these were not reported for other metals. REE exposure also modified the expression and abundance of several ion transport systems, for which strong discrepancies were observed between the two contrasted REEs. Conclusions: Our results demonstrate the discrepancies in yeast response to different rare earth elements (light vs heavy rare earth elements). This results are valuable to prioritize key genes and proteins involved in REE detoxification mechanisms that would deserve further characterisation to better understand the REE toxicity on the environment and human health.
2021-06-01 | GSE175826 | GEO
Project description:Until recently, rare-earth elements (REEs) had been thought to be biologically inactive. This view changed with the discovery of the methanol dehydrogenase (Mdh) XoxF that strictly relies on REEs for its activity. Some methylotrophs only contain xoxF, while others, including the model phyllosphere colonizer Methylobacterium extorquens PA1, harbor this gene in addition to mxaFI encoding a Ca2+-dependent enzyme. Here we found that REEs induce the expression of xoxF in M. extorquens PA1, while repressing mxaFI, suggesting that XoxF is the preferred Mdh. Using reporter assays and a suppressor screen, we found that La3+ is sensed both in a XoxF-dependent and independent manner. Furthermore, we investigated the role of REEs during Arabidopsis thaliana colonization. Element analysis of the phyllosphere revealed the presence of several REEs at concentrations up to 10 μg per g dry weight. Complementary proteome analyses of M. extorquens PA1 revealed XoxF as a top induced protein in planta and resulted in the identification of a core set of La3+-regulated proteins under defined artificial media conditions. Among these, we identified a potential REE-binding protein that is encoded next to a gene for a TonB-dependent transporter. The latter was essential for REE-dependent growth on methanol indicating chelator-assisted uptake of REEs.
2019-01-21 | PXD011842 | Pride
Project description:Rare earth elements show antagonistic interactions as revealed by transcriptome profiling in Chlamydomonas reinhardtii.
| PRJNA735693 | ENA
Project description:Transcriptomic approach reveal distinct responses between light and heavy rare earth elements in Saccharomyces cerevisiae
| PRJNA734002 | ENA
Project description:Rare earth elements (REEs) are critical materials in electronics and clean technologies. With the diminishing of easily accessible minerals for mining, the REE recovery from waste is an alternative toward a circular economy. Present methods for REE recovery suffer from lengthy purifications, low extractability, and high wastewater streams. Here, we report an ultrafast electrothermal process (~3000°C, ~1 s) based on flash Joule heating (FJH) for activating wastes to improve REE extractability. FJH thermally degrades or reduces the hard-to-dissolve REE species to components with high thermodynamic solubility, leading to ~2× increase in leachability and high recovery yields using diluted acid (e.g., 0.1 M HCl). The activation strategy is feasible for various wastes including coal fly ash, bauxite residue, and electronic waste. The rapid FJH process is energy-efficient with a low electrical energy consumption of 600 kWh ton-1. The potential for this route to be rapidly scaled is outlined.
| S-EPMC8827657 | biostudies-literature
Project description:ACID MINE DRAINAGE TREATMENT AND RARE EARTH ELEMENTS PRECIPITATION IN A SULFATE-REDUCING SYSTEM COUPLED TO A MICROAEROPHILIC REACTOR FOR PARTIAL SULFIDE OXIDATION Metagenome
| PRJNA645222 | ENA
Project description:It has long been observed that rare earth elements (REEs) regulate multiple facets of plant growth and development. However, the underlying mechanisms remain largely unclear. Here, using electron microscopic autoradiography, we show the life cycle of a light REE (lanthanum) and a heavy REE (terbium) in horseradish leaf cells. Our data indicate that REEs were first anchored on the plasma membrane in the form of nanoscale particles, and then entered the cells by endocytosis. Consistently, REEs activated endocytosis in plant cells, which may be the cellular basis of REE actions in plants. Moreover, we discovered that a portion of REEs was successively released into the cytoplasm, self-assembled to form nanoscale clusters, and finally deposited in horseradish leaf cells. Taken together, our data reveal the life cycle of REEs and their cellular behaviors in plant cells, which shed light on the cellular mechanisms of REE actions in living organisms.
| S-EPMC4156694 | biostudies-literature
Project description:Purpose; Here we compare the transcriptomic effects of three REEs; Ce, Tm and Y, and a mixture of all three on Chlamydomonas reinhardtii in order to determine the degree of overlap of their effects. Methods; Transcriptome profiling (RNA-Seq) analysis performed on Chlamydomonas reinhardtii (wild-type strain, CC-125 aka 137c, Chlamydomonas resource center) exposed for 2 h to one of three soluble REEs (Ce, Tm, Y) salts at 0.5 μM or to an equimolar ternary mixture of these REEs. Illumina HiSeq (v.4) was used for the paired-end sequencing (2 × 100 base pairs) of 25 samples (5 replicates for each treatment: Ce; Tm; Y; Mix; Controls). For each sample, ca. 55 million of reads with their sequences, identification and quality scores were stored in two FastQ files. Results; Known functions of the differentially expressed genes support effects of REEs on protein processing in the endoplasmic reticulum, phosphate transport and the homeostasis of Fe and Ca. The only stress response detected related to protein misfolding in the endoplasmic reticulum. When the REEs were applied as a mixture, antagonistic effects were overwhelmingly observed with transcriptomic results suggesting that the REEs were initially competing with each other for bio-uptake. Conclusions; Our study represents the first detailed analysis of REE transcriptomic effects in a green microalga that is ubiquitous to fresh waters. Results generated by RNA-seq technology suggest that the approach of government agencies to regulate the REEs using biological effects data from single metal exposures may be a largely conservative approach.
2021-06-14 | GSE176268 | GEO