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: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: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.
2022-06-06 | PXD033557 | panorama
Project description:The iron sensing protein FBXL5 is the substrate adaptor for a SKP1-CUL1-RBX1 E3 ubiquitin ligase complex that regulates the degradation of iron regulatory proteins (IRPs). Here we describe a mechanism of FBXL5 regulation involving its interaction with the cytosolic Fe-S cluster assembly (CIA) targeting complex comprised of MMS19, FAM96B, and CIAO1. We demonstrate that the CIA targeting complex promotes the ability of FBXL5 to degrade IRPs. In addition, the FBXL5-CIA targeting complex interaction is regulated by oxygen tension displaying a robust association in 21% O2 that is severely diminished in 1% O2 and contributes to O2-dependent regulation of IRP degradation. Together, these data identify a novel oxygen-dependent signaling axis that links IRP-dependent iron homeostasis with the Fe-S cluster assembly machinery.
2019-05-02 | MSV000083739 | MassIVE
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
Project description: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. This delivery process is regulated by availability of iron and oxygen, but it remains unclear how CIA components orchestrate the cluster transfer under varying cellular environments. Here, we investigated the organization of CIA machinery under various conditions. We developed a targeted proteomics assay monitoring known CIA factors. Using this assay, we were able to detect NUBP1, CIAO3 and CIA substrates in immunoprecipitates of NUBP2, a component of the CIA scaffold complex. We also revealed that NUBP2 transiently associates with the CIA targeting complex (MMS19, CIAO1, CIAO2B), indicating the possible existence of CIA metabolons. We observed stronger interactions between CIAO3 and the CIA scaffold complex upon iron supplementation or low oxygen tension, while iron chelation and reactive oxygen species weaken CIAO3 interactions with CIA components. We further demonstrated that CIAO3 mutant with defective Fe-S cluster binding failed to integrate into the metabolons. However, these mutants unexpectedly exhibit stronger association with CIA substrates regardless of their reduced association with the CIA targeting complex, implicating that CIAO3 and CIA substrates may present in complexes independent of the CIA targeting complex. Together, our data suggested that CIA components potentially form metabolons whose assembly are regulated by environmental cues and require Fe-S cluster incorporation in CIAO3. These findings provided additional evidence that the CIA pathway adapts to changes in cellular environment through complex reorganization.
2021-11-16 | MSV000088394 | MassIVE
Project description:Disruption of iron metabolism is closely related to metabolic diseases. Iron deficiency is frequently associated with obesity and hepatic steatosis. However, the effects of iron supplementation on obesity and energy metabolism remain unclear. Here we show that a high-fat diet supplemented with iron reduces body weight gain and hepatic lipid accumulation in mice. Iron supplementation was found to reduce mitochondrial morphological abnormalities and upregulate gene transcription involved in mitochondrial function and beta oxidation in the liver and skeletal muscle. In both these tissues, iron supplementation increased the expression of genes involved in heme or iron–sulfur (Fe–S) cluster synthesis. Heme and Fe–S cluster, which are iron prosthetic groups contained in electron transport chain complex subunits, are essential for mitochondrial respiration. The findings of this study demonstrated that iron regulates mitochondrial signaling pathways—gene transcription of mitochondrial component molecules synthesis and their energy metabolism. Overall, the study elucidates the molecular basis underlying the relationship between iron supplementation and obesity and hepatic steatosis progression, and the role of iron as a signaling molecule.
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