Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA280603 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1957325.fastq.gz | Fastqsanger.gz | |||
| SRR1957326.fastq.gz | Fastqsanger.gz | |||
| SRR1957327.fastq.gz | Fastqsanger.gz |
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Project description:The biogenesis of iron-sulfur proteins in eukaryotes is an essential process involving the mitochondrial iron-sulfur cluster (ISC) assembly and export machineries and the cytosolic Fe/S protein assembly (CIA) apparatus. To define the integration of Fe/S protein biogenesis into cellular homeostasis, we compared the global transcriptional responses to defects in the three biogenesis systems in S. cerevisiae using DNA microarrays. Microarray analyses were carried out with regulatable yeast mutants in which representatives of each of the three biosynthetic systems could be depleted. In particular, we used the mutants Gal-YAH1, Gal-ATM1 and Gal-NBP35.
2007-12-14 | E-MEXP-1215 | biostudies-arrayexpress
Project description:Toxoplasma gondii is a parasitic protist that is the agent of toxoplasmosis. It is capable of infecting a wide variety of vertebrates, including humans. The infection is mainly asymptomatic in immunocompetent patients, but in case of immunosuppression or for the congenital form of toxoplasmosis it can lead to severe pathologies with a possible fatal outcome. Like for other eukaryotes, many key cellular functions in T. gondii involve proteins containing an iron-sulfur cluster as a cofactor. Cytosolic and nuclear iron-sulfur proteins depend on a specific pathway for assembling their iron-sulfur cofactor. We have investigated the T. gondii homolog of the HCF101 protein, initially characterized in plants as a chloroplast-based iron-sulfur transfer protein, by co-immunoprecipitating associated protein partners and identifying them by mass spectrometry. It confirmed that T. gondii HCF101 is not involved in plastid-based iron-sulfur metabolism, but in the biogenesis of cytosolic and nuclear iron-sulfur proteins instead.
2025-01-24 | PXD051551 | Pride
Project description:Toxoplasma gondii is a parasitic protist that is the agent of toxoplasmosis. It is capable of infecting a wide variety of vertebrates, including humans. The infection is mainly asymptomatic in immunocompetent patients, but in case of immunosuppression or for the congenital form of toxoplasmosis it can lead to severe pathologies with a possible fatal outcome. Like for other eukaryotes, many key cellular functions in T. gondii involve proteins containing an iron-sulfur cluster as a cofactor. Cytosolic and nuclear iron-sulfur proteins depend on a specific pathway for assembling their iron-sulfur cofactor. We have investigated the T. gondii homolog of the HCF101 protein, initially characterized in plants as a chloroplast-based iron-sulfur transfer protein, by generating a specific mutant on which we performed a quantitative proteomic analysis to get insights into its function in the parasites. We discovered that T. gondii HCF101 is not involved in plastid-based iron-sulfur metabolism, but in the biogenesis of cytosolic and nuclear iron-sulfur proteins instead. Control TATi ΔKu80 dataset is similar to the one provided in PRIDE entry PXD048386
2025-01-24 | PXD051549 | Pride
Project description:Thiol-containing metabolites are central to cellular redox homeostasis1. Among these, cysteine functions as a proteogenic amino acid, supports redox balance and iron–sulfur cluster biogenesis, and, when depleted, triggers ferroptosis2. Cells nevertheless maintain cysteine at low levels, reflecting its intrinsic toxicity, but the mechanisms by which excess cysteine causes cell death remain unclear3. Here, we performed a genome-wide CRISPR screen and identified mitochondrial iron transporters as essential mediators of cysteine toxicity. Limiting mitochondrial iron availability suppresses cysteine-induced cell death and prevents impairment of iron–sulfur cluster proteins and respiration. Mechanistically, cysteine mobilizes iron from ferritin, expands cytosolic iron pool, and drives mitochondrial iron accumulation. Enhancing glutathione reductase activity specifically within mitochondria restores redox balance downstream of iron accumulation and protects cells by maintaining iron–sulfur cluster integrity. Our findings suggest that maintaining low cysteine levels safeguards mitochondrial iron homeostasis, and that excess cysteine triggers a distinct mitochondrial iron-dependent cell death under conditions of thiol imbalance.
2026-08-14 | PXD082300 | Pride
Project description:Thiol-containing metabolites are central to cellular redox homeostasis1. Among these, cysteine functions as a proteogenic amino acid, supports redox balance and iron–sulfur cluster biogenesis, and, when depleted, triggers ferroptosis2. Cells nevertheless maintain cysteine at low levels, reflecting its intrinsic toxicity, but the mechanisms by which excess cysteine causes cell death remain unclear3. Here, we performed a genome-wide CRISPR screen and identified mitochondrial iron transporters as essential mediators of cysteine toxicity. Limiting mitochondrial iron availability suppresses cysteine-induced cell death and prevents impairment of iron–sulfur cluster proteins and respiration. Mechanistically, cysteine mobilizes iron from ferritin, expands cytosolic iron pool, and drives mitochondrial iron accumulation. Enhancing glutathione reductase activity specifically within mitochondria restores redox balance downstream of iron accumulation and protects cells by maintaining iron–sulfur cluster integrity. Our findings suggest that maintaining low cysteine levels safeguards mitochondrial iron homeostasis, and that excess cysteine triggers a distinct mitochondrial iron-dependent cell death under conditions of thiol imbalance.
2026-08-14 | PXD082345 | Pride
Project description:Toxoplasma gondii is a parasitic protist that is the agent of toxoplasmosis. It is capable of infecting a wide variety of vertebrates, including humans. The infection is mainly asymptomatic in immunocompetent patients, but in case of immunosuppression or for the congenital form of toxoplasmosis it can lead to severe pathologies with a possible fatal outcome. Like for other eukaryotes, many key cellular functions in T. gondii involve proteins containing an iron-sulfur cluster as a cofactor. Cytosolic and nuclear iron-sulfur proteins depend on a specific pathway for assembling their iron-sulfur cofactor. It was demonstrated in other eukaryotes (ie in the budding yeast model) that a sulfur-containing precursor originating from the mitochondrion and transported through the ABCB7 transporter is essential for building cytosolic iron-sulfur clusters. We have investigated the T. gondii homolog of the ABCB7 transporter by generating a specific mutant on which we performed a quantitative proteomic analysis to get insights into its involvement in the biogenesis of cytosolic and nuclear iron-sulfur proteins.
2024-08-09 | PXD048386 | Pride
Project description:Aspartyl-tRNA synthetase 2 (Dars2) is involved in the regulation of mitochondrial protein synthesis and tissue-specific mitochondrial unfolded protein response (UPRmt). The role of Dars2 in the self-renewal and differentiation of hematopoietic stem cells (HSCs) is unknown. Here we show that knockout (KO) of Dars2 significantly impairs the maintenance of HSCs and progenitor cells (HSPCs) without involving its tRNA synthetase activity. Dars2 KO results in significantly reduced expression of Srsf2/3/6 and impairs multiple events of mRNA alternative splicing (AS). Dars2 directly localizes to Srsf3 labeled spliceosomes in HSPCs and regulates the stability of Srsf3. Dars2-deficient HSPCs exhibit aberrant AS of mTOR and Slc22a17. Dars2 KO greatly suppresses the levels of labile ferrous iron and iron-sulfur cluster containing proteins, which dampens mitochondrial metabolic activity and DNA damage repair pathway in HSPCs. Our study reveals that Dars2 plays an unprecedented role in the iron-sulfur metabolism and maintenance of HSPCs by modulating RNA splicing.
2023-09-26 | PXD045562 | Pride
Project description:Diverse organisms adjust metabolic gene expression during crowding as they encounter nutrient scarcity, oxidative stress, and waste accumulation. Apicomplexan parasites experience these stresses during intracellular growth in host cells, yet lack known regulators of metabolic adaptation. We screened the apicomplexan Toxoplasma gondii to identify genes that support parasite fitness during crowding. NAD(P)+ biosynthesis was required at high parasite density along with several parasite-specific factors, including an RNA-binding protein named T. gondii Parasite Response to Oxidation (TgPRO). TgPRO loss elevated reactive oxygen species under ambient conditions, which was rescued by growth at low oxygen. TgPRO regulates expression of specific transcripts involved in carbon metabolism and iron-sulfur cluster assembly. Regulation of the iron-sulfur cluster assembly protein ISCU relies on TgPRO binding to the transcript’s 3′ UTR. Through convergent evolution, TgPRO performs a role analogous to known metabolic regulators from other species, representing the first dedicated regulator of metabolic gene expression in apicomplexans.
2026-06-16 | GSE329845 | GEO
Project description:The cytosolic iron-sulfur (Fe-S) cluster assembly (CIA) pathway delivers Fe-S clusters to nuclear and cytosolic Fe-S proteins involved in essential cellular functions. Although the delivery process is regulated by the availability of iron and oxygen, it remains unclear how CIA components orchestrate the cluster transfer under varying cellular environments. Here, we utilized a targeted proteomics assay for monitoring CIA factors and substrates to characterize the CIA machinery. We find that NUBP1 (NBP35), CIAO3 (NARFL) and CIA substrates associate with NUBP2 (CFD1), a component of the CIA scaffold complex. We also show that NUBP2 weakly associates with the CIA targeting complex (MMS19, CIAO1, CIAO2B) indicating the possible existence of a higher order complex. Interactions between CIAO3 and the CIA scaffold complex are strengthened upon iron supplementation or low oxygen tension, while iron chelation and reactive oxygen species weaken CIAO3 interactions with CIA components. We further demonstrate that CIAO3 mutants defective in Fe-S cluster binding fail to integrate into the higher order complexes. However, these mutants exhibit stronger associations with CIA substrates under conditions in which the association with the CIA targeting complex is reduced suggesting that CIAO3 and CIA substrates may associate in complexes independently of the CIA targeting complex. Together, our data suggest that CIA components potentially form a metabolon whose assembly is regulated by environmental cues and requires Fe-S cluster incorporation in CIAO3. These findings provide additional evidence that the CIA pathway adapts to changes in cellular environment through complex reorganization.
| PXD033557 | panorama
Project description:E. coli frequently encounters oxidative stress both in its natural environment or in industrial biotechnology. Elucidating the mechanisms behind tolerance to oxidative stress would be beneficial for understanding pathogenesis as well as improving production strain fitness. We make use of adaptive laboratory evolution to develop two strains of E. coli which exhibit 500% increased tolerance to paraquat stress compared to wild type. Evolved strains tolerate oxidative stress by reduction of flux through TCA, dyregulation of iron-uptake genes, and up-regulation of cell motility or iron-sulfur cluster repair genes.
2022-07-07 | GSE134256 | GEO