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Transcriptomic analysis of Pseudomonas putida exposed to nZVI and dissolved iron

ABSTRACT: Transcriptomic analysis of Pseudomonas putida exposed to nZVI and dissolved iron

PROVIDER: PRJNA812775 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18218800.fastq.gz	Fastqsanger.gz
	SRR18218801.fastq.gz	Fastqsanger.gz
	SRR18218802.fastq.gz	Fastqsanger.gz
	SRR18218803.fastq.gz	Fastqsanger.gz
	SRR18218804.fastq.gz	Fastqsanger.gz

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Dissolved iron released from nanoscale zero-valent iron (nZVI) activates the defense system in bacterium Pseudomonas putida, leading to high tolerance to oxidative stress

Project description:Objective: We aimed to decipher how the transcriptome of P.putida would regulate in the presence of 100 mg/L nZVI and its surplus iron released from nZVI, (44.5 μg/L of dissolved iron obtained from nZVI suspension over 24 h in environmental-sourced reservoir) using Next-Seq RAN-sequencing on an Illumina Next-Seq platform Results: Transcriptomic analysis revealed more pronounced differentially expressed genes (DEGs) caused by dissolved iron (3,839 DEGs) against nZVI (945 DEGs). Dissolved iron (but not nZVI) triggered mostly hypothetical genes, and genes which dual-regulating the oxidative stress-antioxidant response, carbohydrate metabolism, and energy metabolism, a cascade effect which demands high ATP and NADPH energy fuels, but downregulated genes associated with flagellar assembly and two-component systems. The results compare and deepen our understanding of iron particle and ionic stressors effect which triggered different transcriptomic trajectories on soil bacterium, and uncovers the underlying energy-fueled mechanism to resolve oxidative insults due to the iron-exchanging activity within cells.

2022-03-07 | GSE197899 | GEO

Transcription profiling of P. putida KT2440 cultivated at 7 bar and at 7 bar with elevated dissolved oxygen tension

Project description:We investigated the changes of gene expression in PHA-producing Pseudomonas putida KT2440 cultivated under elevated pressure (7 bar) and under combined elevated pressure (7 bar) and elevated dissolved oxygen tension by means of DNA microarrays. RNA samples were isolated from cells cultivated in chemostat under very well defined growth conditions (growth rate, medium, temperature, pH,...)

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Green alga (Raphidocelis subcapitata) response to nanoscale zero valent iron (nZVI): The DNA damage repair pathways as sentinel response

Project description:Nanoscale zero valent iron (nZVI) is used to remediate aquifers polluted by organochlorines or heavy metals has been also considered for elimination of harmful algal blooms. Highly reactive nZVI then affects microorganisms in the application area. To date, various nZVI toxicity endpoints have been studied on different organisms. However, the underlying mechanistic related to iron defense pathways have not been explained sufficiently. Here we aim to describe the physiological and transcriptomic response of the microalga, Raphidocelis subcapitata ATCC 22662, to 100 mg/L of non-reactive nFe3O4, and reactive nZVI. The combined effect of shading by nanoparticles and release of Fe2+ from nZVI posed a stronger inhibition leading to deformed cells and cytosol leakage in 15% of cells. Transcriptomic analysis confirmed the stronger physiological effect of nZVI (7,380 differentially expressed genes [DEGs]) than nFe3O4 (4,601 DEGs) after 1 h. nZVI (but not nFe3O4) caused increased DNA repair and replication, while deactivated carbohydrate-energy metabolisms, mitochondria signaling, and transmembrane ion transport. The defense response of algal cells was immediate to successfully face oxidative stress.

2023-06-06 | GSE234088 | GEO

Microarray analysis on human neuroblastoma cells exposed to iron, B-amyloid or the B-amyloid iron complex

Project description:Microarray analysis on human neuroblastoma cells exposed to iron, B-amyloid or the B-amyloid iron complex. Alzheimer's disease is associated with an abnormal accumulation of certain metal ions.

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Influence of the Hfq and Crc global regulators on the control of iron homeostasis in Pseudomonas putida

Project description:Metabolically versatile bacteria use catabolite repression control to select their preferred carbon sources, thus optimizing carbon metabolism. In pseudomonads, this occurs through the combined action of the proteins Hfq and Crc, which form stable tripartite complexes at target mRNAs, inhibiting their translation. The activity of Hfq/Crc is antagonised by small RNAs of the CrcZ family, the amounts of which vary according to carbon availability. The present work examines the role of Pseudomonas putida Hfq protein under conditions of low-level catabolite repression, in which Crc protein would have a minor role since it is sequestered by CrcZ/CrcY. The results suggest that, under these conditions, Hfq remains operative and plays an important role in iron homeostasis. In this scenario, Crc appears to participate indirectly by helping CrcZ/CrcY to control the amount of free Hfq in the cell. Iron homeostasis in pseudomonads relies on regulatory elements such as the Fur protein, the PrrF1-2 sRNAs, and several extracytoplasmic sigma factors. Our results show that the absence of Hfq is paralleled by a reduction in PrrF1-2 small RNAs. Hfq thus provides a regulatory link between iron and carbon metabolism, coordinating the iron supply to meet the needs of the enzymes operational under particular nutritional regimes.

2019-02-05 | GSE110803 | GEO

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2012-07-09 | GSE36489 | GEO

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Project description:transcriptomic study of the impact of iron toxicity on rice plant (Oryza sativa L.; cv ‘I Kong Pao’ ) after short term (3 days) or long term (3 weeks) exposure to ferrous iron (125 ppm). Twenty five days old rice seedlings were exposed to 0 or 125 mg/L ferrous iron for 3 days and 3 weeks in hydroponic culture. Comparison between control and iron stressed plants were done at the shoot and the root levels. The assays were replicated twice on two independent plant cultures.

2012-05-15 | GSE36299 | GEO

Genome wide expression responses of Fusarium oxysporum wt and ΔhapX mutant to iron depleted and iron replete conditions.

Project description:Soilborne fungal pathogens cause devastating yield losses, are highly persistent and difficult to control. To culminate infection, these organisms must cope with limited availability of iron. Here we show that the bZIP protein HapX functions as a key regulator of iron homeostasis and virulence in the vascular wilt fungus Fusarium oxysporum. Deletion of hapX does not affect iron uptake, but causes derepression of genes involved in iron-consuming pathways, leading to impaired growth under iron-depleted conditions. F. oxysporum strains lacking HapX are reduced in their capacity to invade and kill tomato plants and immunodepressed mice. The virulence defect of ΔhapX on tomato plants is exacerbated by coinoculation of roots with a biocontrol strain of Pseudomonas putida, but not with a siderophore-deficient mutant, indicating that HapX contributes to iron competition of F. oxysporum in the tomato rhizosphere. These results establish a conserved role for HapX-mediated iron homeostasis in fungal infection of plants and mammals.

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Transcriptomic study of the impact of iron toxicity on rice plant

Project description:transcriptomic study of the impact of iron toxicity on rice plant (Oryza sativa L.; cv M-bM-^@M-^XI Kong PaoM-bM-^@M-^Y ) after short term (3 days) or long term (3 weeks) exposure to ferrous iron (125 ppm). Twenty five days old rice seedlings were exposed to 0 or 125 mg/L ferrous iron for 3 days and 3 weeks in hydroponic culture. Comparison between control and iron stressed plants were done at the shoot and the root levels. The assays were replicated twice on two independent plant cultures. 8 samples, Two-condition experiment, control (0 ppm ferrous iron) vs. iron treated (125 ppm ferrous iron). Biological replicates: 2 replicates for comparison shoot 3 days of stress, root 3 days of stress, shoot 3 weeks of stress and root 3 weeks of stress.

2012-05-14 | E-GEOD-36299 | biostudies-arrayexpress

iron response-Transcriptomic response to iron signaling

Project description:no27_iron_signaling - iron response - Effect of exceed of Iron - Time course experiment, star design and 3 biological repeats. Keywords: time course

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