Ontology highlight
ABSTRACT:
PROVIDER: PRJNA565634 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10130034_1.fastq.gz | Fastqsanger.gz | |||
| SRR10130034_2.fastq.gz | Fastqsanger.gz | |||
| SRR10130035_1.fastq.gz | Fastqsanger.gz | |||
| SRR10130035_2.fastq.gz | Fastqsanger.gz | |||
| SRR10130036_1.fastq.gz | Fastqsanger.gz |
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Project description:Four Fe(II) concentrations (0.03, 0.09, 0.12 & 0.75 mM) were tested to investigate the stimulation and inhibition effects of ferrous iron on anammox bacterial activity. RNAs were extracted from the cultures, and the synthesized cDNAs by reverse transcription were used to carry out GeoChip analysis, by which the functional communities and expression level differences in functional genes under different Fe(II) concentrations conditions were obtained, and the response of anammox bacteria to Fe(II) stimulation and inhibition are speculated.
2020-08-28 | GSE120704 | GEO
Project description:Several phytohormones and other small molecules have been demonstrated to be involved in iron (Fe) homeostasis. However, how salicylic acid (SA), an essential hormone in plant immunity and defense responses, participates in Fe-deficiency responses in plants is largely unknown. Here, we took advantage of a SA biosynthesis defect mutant phytoalexin deficient 4 (pad4: T-DNA Salk_089936) to explore the possible effects of endogenous SA on the morphological and physiological responses to Fe deprivation. Under a Fe-deficiency treatment, Col-0 showed more severe leaf chlorosis and root growth inhibition compared with the pad4 mutant. The soluble Fe concentrations were significant higher in pad4 than Col-0 under the Fe-deficiency treatment, suggesting that a mutation in the PAD4 gene may alleviate the Fe-deficiency-induced symptoms by regulating the soluble Fe concentrations. Furthermore, a SA signaling maker line (PR1promoter: GUS) was used to investigate how Fe deficiency affects endogenous SA biosynthesis and metabolism. The data showed that Fe deficiency significantly induced SA accumulation in Col-0, and the loss function of PAD4 blocked this process. The requirement of endogenous SA accumulation for Fe-deficiency responses was confirmed using a series of SA biosynthetic mutants and transgenic lines.
2016-10-01 | GSE74515 | GEO
Project description:Iron (Fe) is an essential element to plants, but can be harmful if accumulated to toxic concentrations. Fe toxicity can be a major nutritional disorder in rice (Oryza sativa) when cultivated under waterlogged conditions, as a result of excessive Fe solubilization of in the soil. However, little is known about the basis of Fe toxicity and tolerance at both physiological and molecular level. Here we aim at understand the genotypic differences in two rice cultivars with contrasting phenotypes under Fe toxicity.
2019-05-16 | GSE131287 | GEO
Project description:IRT1 is the root high-affinity Fe uptake system. Despite severe Fe deficiency symptoms and reduced Fe levels in the shoots of irt1 mutants, we find that root Fe concentrations are higher in the irt1-2 mutant than in the wild type, unexpectedly. The goal of this experiment was to identify candidate transcripts contributing to the observed alteration in root-to-shoot Fe partitioning of irt1. We analysed gene expression in shoots and roots of the wild type grown under control conditions, the wild type exposed to severe Fe deficiency for 5 d, as well as of the irt1-2 (pam42) mutant grown under control conditions.
2021-03-31 | GSE166269 | GEO
Project description:Iron-oxidizing bacteria are widely found in natural and man-made environments where they influence varied biogeochemical cycles. Despite their prevalence, the mechanisms and Fe(II) substrates used by these organisms remain understudied. To date, there has been limited exploration of the ability of iron-oxidizing bacteria to utilize solid minerals as electron donors. Sideroxydans lithotrophicus ES-1 is a robust, facultative iron oxidizer with multiple enzymatic pathways for iron oxidation, making it a prime candidate for evaluating extracellular electron uptake mechanisms. In this study, S. lithotrophicus ES-1 was grown on dissolved Fe(II)-citrate and three preparations of magnetite that provided different ratios of soluble and solid Fe(II). S. lithotrophicus ES-1 grew equally well on the different batches of magnetite, suggesting it can adapt to the type of iron present during growth. S. lithotrophicus ES-1 oxidized all available dissolved Fe2+ released from magnetite, and continued to build biomass when only solid Fe(II) remained. Quantitative proteomic analyses of S. lithotrophicus ES-1 grown on these substrates revealed proteome remodeling in response to electron donor and growth state, and uncovered potential proteins and metabolic pathways involved in the oxidation of solid magnetite. While the Cyc2 iron oxidases were highly expressed on both dissolved and solid substrates, the MtoAB complex was only expressed during growth on the solid magnetite, suggesting these proteins play a role in oxidation of solid minerals in S. lithotrophicus ES-1. A set of cupredoxin domain-containing proteins were also identified that were specifically expressed during solid iron oxidation. This work confirmed the iron oxidizer, S. lithotrophicus ES-1, utilized distinct extracellular electron transfer pathways when growing on solid mineral electron donors compared to dissolved Fe(II)-citrate. The presence of multiple pathways, and the ability to regulate their expression and use, could benefit iron-oxidizing bacteria that encounter various electron donors in their environments.
2024-01-04 | MSV000093770 | MassIVE
Project description:Fur is a transcriptional regulator whose activity is dependent on Fe(II) concentrations. Chromatin immunoprecipitation (ChIP) coupled to microarray analysis allowed for the identification of Fur binding sites within the G. sulfurreducens genome.
2014-03-10 | GSE54305 | GEO
Project description:Iron and manganese are part of a small group of transition metals required for photosynthetic electron transport. Here, we present evidence for a functional link between iron and manganese homeostasis. In the unicellular cyanobacterium, Synechocystis sp. PCC 6803 Fe and Mn deprivation resulted in distinct modifications of the function of the photosynthetic apparatus. For example, iron limitation modifies the rate of QA re-oxidation in photosystem II, a complex that contains more Mn than Fe. The intracellular elemental quotas of Fe and Mn are also linked. Fe limitation reduces the intracellular Mn quota. Mn limitation did not exert a reciprocal effect on Fe quotas. Microarray analysis comparing Mn and Fe limitation revealed a stark difference in the extent of the transcriptional response to the two limiting conditions, reflective of the physiological data. The effects of Fe limitation on the transcriptional network are widespread while the effects on Mn limitation are highly specific. Our analysis also revealed an overlap in the transcriptional response of specific Fe and Mn transporters. This overlap provides a framework for explaining Fe limitation induced changes in Mn quotas. Fe transporters can serve as a low affinity Mn transport system. Under iron limitation the specificity of the Fe transport system changes, making it a less efficient Mn transport system.
2013-06-29 | GSE48416 | GEO
Project description:We used RNA-Seq to compare the transcriptomes of Fe-replete vs. Fe-deficient vs. Fe-limited Chlamydomonas wild-type cells. Our RNA-Seq data revealed 90 and 49 genes to be specifically expressed under hetero-phototrophic and phototrophic conditions, respectively. Around 30 genes represent putative Fe-deficiency targets, independent of the carbon source used. Many of these Fe-specific responses are conserved between Chlamydomonas and land plants. We identified several transporters (NRAMP4, a CCC1-like proteins and a ferroportin homologue) all of them most likely being involved in intracellular Fe redistribution. RNA-seq of Chlamydomonas Fe-deficient and limited cells indicated that about 40% of differentially expressed genes represent proteins of unknown functions. Whereas Fe-deficiency gave us insides into putative Fe-specific responses, Fe-limitation revealed responses related to increased oxidative stress. Quantitative proteomics on the soluble Chlamydomonas extracts indicated a fair correlation between changes we detected at mRNA levels compared to changes in protein levels in Fe-deficient and Fe-limited Chlamydomonas. We found that Fe-deficient and Fe-limited cells have increased ascorbate levels, a major antioxidant molecule in plants. Ascorbate levels appear to be elevated by de novo synthesis via the L-Galactose pathway and recycling by monodehydroascorbate reductase. Fe-limited cells showed increased transcript and protein levels of enzymatic antioxidant components of the ascorbate-glutathione scavenging system (MSD3, MDAR1 or GSH1). Fe-limited cells showed the increase of several proteases indicative of elevated proteolitic activity under these severe nutrient limitation conditions.
2012-06-18 | GSE35305 | GEO