Dataset Information

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

ABSTRACT: 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.

ORGANISM(S): Pseudomonas putida

PROVIDER: GSE197899 | GEO | 2022/03/07

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Time-series transcriptional profiles of Shewanella oneidensis type strain MR-1 under iron depletion and repletion conditions. Iron homeostasis of Shewanella oneidensis, a gamma-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. In this work, temporal gene expression profiles were examined for iron depletion and repletion to delineate the iron response of S. oneidensis and a gene co-expression network was reconstructed. Modules of iron acquisition systems, anaerobic energy metabolism and protein degradation were the most noteworthy in the gene network. Bioinformatics analyses suggested that genes in each of the modules might be regulated by DNA-binding proteins Fur, CRP and RpoH, respectively. Closer inspection of these modules revealed a transcriptional regulator (SO2426) involved in iron acquisition and ten transcriptional factors involved in anaerobic energy metabolism. Selected genes in the network were analyzed by genetic studies. Disruption of genes encoding a putative alcaligin biosynthesis protein (SO3032) and a gene previously implicated in protein degradation (SO2017) led to severe growth deficiency under iron depletion conditions. Disruption of a novel transcriptional factor (SO1415) caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways. In conclusion, we identified major biological pathways that were differentially expressed during iron depletion and repletion. Four biological replicates of S. oneidensis MR-1 cells were grown to the midlog phase (OD600 = 0.6). Samples were collected at time 0, and then at 1, 5, 10, 20, 40, and 60 min after adding 2,2'-dipyridyl to attain a final concentration of 160 uM. Thereafter, ferrous sulfate was added to final concentration of 200 uM, and cells were collected at 1, 5, 10, 20, 40, and 60 min.

Project description:Iron is an important trace element that affects the growth and development of animals and regulates oxygen transport, hematopoiesis, and hypoxia adaptations. Wujin pig has unique hypoxic adaptability and iron homeostasis; however, the specific regulatory mechanisms have rarely been reported. This study randomly divided 18 healthy Wujin piglets into three groups: the control group, supplemented with 100 mg/kg iron (as iron glycinate); the low-iron group, no iron supplementation; and the high-iron group, supplemented with 200 mg/kg iron (as iron glycinate). The pre-feeding period was 5 days, and the formal period was 30 days. Serum was collected from empty stomachs before slaughter and at slaughter to detect changes in the serum iron metabolism parameters. Gene expression in the liver was analyzed via transcriptome analysis to determine the effects of low- and high- iron diets on transcriptome levels. Correlation analysis was performed for apparent serum parameters, and transcriptome sequencing was performed using weighted gene co-expression network analysis to reveal the key pathways underlying hypoxia regulation and iron metabolism. The main results are as follows. (1) Except for the hypoxia-inducible factor 1 (HIF-1) content (between the low- and high-iron groups), significant differences were not observed among the serum iron metabolic parameters. The serum HIF-1 content of the low-iron group was significantly higher than that of the high-iron group (P<0.05). (2) Sequencing analysis of the liver transcriptome revealed 155 differentially expressed genes (DEGs) between the low-iron and control groups, 229 DEGs between the high-iron and control groups, and 279 DEGs between the low- and high-iron groups . Bioinformatics analysis showed that the HIF-1 and transforming growth factor-beta (TGF-β) signaling pathways were the key pathways for hypoxia regulation and iron metabolism. Four genes were selected for qPCR validation, and the results were consistent with the transcriptome sequencing data. In summary, the serum iron metabolism parameter results showed that under the influence of low- and high-iron diets, Wujin piglets maintain a steady state of physiological and biochemical indices via complex metabolic regulation of the body, which reflects their stress resistance and adaptability. The transcriptome results revealed the effects of low-iron and high-iron diets on the gene expression level in the liver and showed that the HIF-1 and TGF-β signaling pathways were key for regulating hypoxia adaptability and iron metabolism homeostasis under low-iron and high-iron diets. Moreover, HIF-1α and HEPC were the key genes. The findings provide a theoretical foundation for exploring the regulatory pathways and characteristics of iron metabolism in Wujin pigs.

Dataset Information

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

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets