Regulatory response of methanogen cells to different forms of iron and sulfur
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PROVIDER: PRJNA714524 | ENA |
REPOSITORIES: ENA
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Project description:We used comparative transcriptomics to explore cellular responses to growth on pyrite (FeS2) or aqueous iron (Fe(II)) and sulfur (cysteine or sulfide). Transcriptomic data from wild type M. barkeri identified subset of genes that was significantly upregulated during grown on FeS2 versus ferrous iron and cysteine or sulfide. Several of these genes, including a membrane-bound hydrolase, alpha-keto reductases, and flavin mononucleotide-dependent flavodoxin reductases were highly conserved among known FeS2-reducing methanogens and were located in a single gene cassette. Putative enzymatically catalyzed mechanisms of FeS2 reduction are proposed for each of these enzyme systems to guide their future biochemical and biophysical study. Transcriptomic data from wild type M. barkeri identified subset of genes that was significantly upregulated during grown on FeS2 versus ferrous iron and cysteine or sulfide. Several of these genes, including a membrane-bound hydrolase, alpha-keto reductases, and flavin mononucleotide-dependent flavodoxin reductases were highly conserved among known FeS2-reducing methanogens and were located in a single gene cassette. Putative enzymatically catalyzed mechanisms of FeS2 reduction are proposed for each of these enzyme systems to guide their future biochemical and biophysical study.
2022-03-13 | GSE168895 | GEO
Project description:Methanogens inhabit euxinic (sulfide-rich) or ferruginous (iron-rich) environments that promote the precipitation of transition metals as metal sulfides, such as pyrite, reducing metal or sulfur availability. Such environments have been common throughout Earth’s history raising the question as to how anaerobes obtain(ed) these elements for the synthesis of enzyme cofactors. Here, we show a methanogen can synthesize molybdenum nitrogenase metallocofactors from pyrite as the source of iron and sulfur, enabling nitrogen fixation. Pyrite-grown, nitrogen-fixing cells grow faster and require 25-fold less molybdenum than cells grown under euxinic conditions. Growth yields are 3 to 8 times higher in cultures grown under ferruginous relative to euxinic conditions. Physiological, transcriptomic, and geochemical data indicate these observations are due to sulfide-promoted metal limitation, in particular molybdenum. These findings suggest that molybdenum nitrogenase may have originated in a ferruginous environment that titrated sulfide to form pyrite, facilitating the availability of sufficient iron, sulfur, and molybdenum for cofactor biosynthesis.
2023-05-01 | GSE216895 | GEO
Project description:Deprivation of mineral nutrients causes significant retardation of plant growth. This slow growth is assumed to be associated with both nutrient specific transcriptional responses and additionally with common transcription patterns. In this study we adjusted the external supply of iron, potassium and sulfur to cause a similar retardation of growth. Global transcriptome analyses were performed to investigate whether the growth limitation by the different nutrient deficiencies triggered specific or similar transcriptional responses. The global transcriptome responded specifically to sulfur, iron or potassium deprivation.
2016-07-21 | GSE77602 | GEO
Project description:Deprivation of mineral nutrients causes significant retardation of plant growth. This slow growth is assumed to be associated with both nutrient specific transcriptional responses and additionally with common transcription patterns. In this study we adjusted the external supply of iron, potassium and sulfur to cause a similar retardation of growth. Global transcriptome analyses were performed to investigate whether the growth limitation by the different nutrient deficiencies triggered specific or similar transcriptional responses. The global transcriptome responded specifically to sulfur, iron or potassium deprivation. Arabidopsis thaliana plants were grown hydroponically under short-day conditions (8h light / 16h dark cycles) under full nutrient supply or under the limitation of sulfur, iron or potassium. Arabidopsis root material was harvested when the plants reached the age of 7 weeks (from sowing) and used for RNA extraction and hybridization on Affymetrix microarrays. Four biological replicates from each condition were analyzed.
2016-07-21 | E-GEOD-77602 | biostudies-arrayexpress
Project description:Purpose: To understand the effects of two different chemical forms of iron fertilizer on cadmium accumulation Methods:Cultivation and treatment for three weeks of dwarf Polish wheat seedlings by hydroponics, in triplicate, qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Iron fertilizer can effectively reduce cadmium concentration in plants Conclusions: Our study represents the different chemical forms of iron fertilizer have different mitigation effects on cadmium. The transcriptome gata showed that iron fertilizer have changed the cadimium metabolism
2019-04-24 | GSE130170 | 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:Oncogenic KRAS rewires pancreatic ductal adenocarcinoma (PDAC) metabolism to promote dependence on autophagy and iron metabolism. NCOA4-mediated ferritinophagy links autophagy and iron metabolism as NCOA4 selectively targets ferritin, the cellular iron storage complex, via autophagy to the lysosome for ferritin degradation and release of iron for utilization. Using patient-derived and genetically engineered murine models of PDAC we now demonstrate that ferritinophagy is upregulated in PDAC to sustain iron availability thereby promoting PDAC progression. PDAC global quantitative proteomics reveals that ferritinophagy fuels iron-sulfur cluster synthesis to support mitochondrial homeostasis. Targeting NCOA4 leads to tumor growth delay and prolonged survival but with development of compensatory iron acquisition pathways. Finally, a ferritinophagy gain-of-function PDAC murine model demonstrates worse survival, and an elevated ferritinophagy expression signature predicts for worse overall survival in human PDAC patients. Together, our data define NCOA4-mediated ferritinophagy as a therapeutic target in PDAC and reveal that maintenance of cellular iron homeostasis is a critical cell autonomous function of PDAC autophagy.
2022-08-17 | PXD033356 | Pride
Project description:Toxoplasma gondii is a parasitic protist that is the agent of toxoplasmosis. It is capable of infecting all mammals, 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. T. gondii contains two organelles of endosymbiotic origin: the mitochondrion and the apicoplast, which is a non-photosynthetic plastid. These organelles contain important biochemical pathways which might be interesting targets for future therapeutic strategies. Iron-sulfur clusters are one of the most ancient and ubiquitous prosthetic groups, and they are required by a variety of proteins involved in important metabolic processes. As for plants, T. gondii has several pathways for biosynthesis of iron-sulfur proteins, located in three different cellular compartments: the cytoplasm, the mitochondrion and the apicoplast. We have investigated the relative contributions of the mitochondrion and the apicoplast to the iron-sulfur proteome of the parasite by generating specific mutants for key proteins of the mitochondrial (TgIscU) and plastidic (TgSufS) pathways, on which we performed a quantitative proteomic analysis.
2021-11-09 | PXD023854 | Pride
Project description:Abstract: The crenarchaeal order Sulfolobales collectively contains at least five major terminal oxidase complexes. Based on genome sequence information, all five complexes are found only in Metallosphaera sedula and Sulfolobus tokodaii, the two sequenced Sulfolobales capable of iron oxidization. While specific respiratory complexes in certain Sulfolobales have been characterized previously as proton pumps for maintaining intracellular pH and generating proton motive force (pmf), their contribution to sulfur and iron biooxidation has not been considered. For M. sedula growing in the presence of ferrous iron and reduced inorganic sulfur compounds (RISCs), global transcriptional analysis was used to track the response of specific genes associated with these complexes, as well as other known and putative respiratory electron transport chain elements. ORFs from all five terminal oxidase or bc1-like complexes were stimulated on one or more conditions tested. Components of the fox (Msed0467-0489) and soxNL-cbsABA (Msed0500-0505) terminal/quinol oxidase clusters were triggered by ferrous iron, while the soxABCDD' terminal oxidase cluster (Msed0285-0291) were induced by tetrathionate and S°. Chemolithotrophic electron transport elements, including a putative tetrathionate hydrolase (Msed0804), a novel polysulfide/sulfur/DMSO reductase-like complex (Msed0812-0818), and a novel heterodisulfide reductase-like complex (Msed1542-1550), were also stimulated by RISCs. Furthermore, several hypothetical proteins were found to have strong responses to ferrous iron or RISCs, suggesting additional candidates in iron or sulfur oxidation-related pathways. From this analysis, a comprehensive model for electron transport in M. sedula could be proposed as the basis for examining specific details of iron and sulfur oxidation in this bioleaching archaeon.
2008-10-22 | GSE12044 | GEO