Proteomic analysis of engineered E. coli BL-all under acetophenone stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia Coli
SUBMITTER: 
Bo Wang
PROVIDER: PXD079428 | iProX | Tue Jun 09 00:00:00 BST 2026
REPOSITORIES: iProX
Similar Datasets
Project description:Pentachlorophenol (PCP) is a highly toxic pesticide that was first introduced in the 1930s. The a-proteobacterium Sphingobium chlorophenolicum, which was isolated from PCP-contaminated sediment, has assembled a metabolic pathway capable of mineralizing PCP. Interestingly, this pathway produces four toxic intermediates, which include a chlorinated benzoquinone that is a potent alkylating agent and three chlorinated hydroquinones that produce reactive oxygen species and benzoquinones upon reaction with O2. We sought to identify how the cell tolerates the onslaught of toxic effects associated with these intermediates. RNA-Seq and Tn-Seq were used to probe the response of S. chlorophenolicum to PCP as well as the stresses associated with its exposure and degradation. The results demonstrate that PCP exposure causes dissipation of the proton-motive force and perturbation of the cell envelope, and the downstream intermediates cause oxidative stress. However, the transcriptional response to PCP degradation far exceeds what is actually needed and, for many genes, is actually counter-productive. Prevention of PCP degradation by deletion of the transcriptional regulator, pcpR, increases growth rate in rich medium. These data suggest that, although PCP degradation allows access to a novel nutrient, the benefit of degrading it depends upon the availability of other resources. When resources are abundant, the detrimental effects of the toxic intermediates may outweigh the benefit of the carbon and energy that can be obtained by degrading PCP. However, when resources are scarce, degradation of PCP may provide access to a novel source of carbon and energy as well as detoxification of this anthropogenic pollutant.
2018-11-01 | GSE114123 | GEO
Project description:Pentachlorophenol (PCP) is a highly toxic pesticide that was first introduced in the 1930s. The a-proteobacterium Sphingobium chlorophenolicum, which was isolated from PCP-contaminated sediment, has assembled a metabolic pathway capable of mineralizing PCP. Interestingly, this pathway produces four toxic intermediates, which include a chlorinated benzoquinone that is a potent alkylating agent and three chlorinated hydroquinones that produce reactive oxygen species and benzoquinones upon reaction with O2. We sought to identify how the cell tolerates the onslaught of toxic effects associated with these intermediates. RNA-Seq and Tn-Seq were used to probe the response of S. chlorophenolicum to PCP as well as the stresses associated with its exposure and degradation. The results demonstrate that PCP exposure causes dissipation of the proton-motive force and perturbation of the cell envelope, and the downstream intermediates cause oxidative stress. However, the transcriptional response to PCP degradation far exceeds what is actually needed and, for many genes, is actually counter-productive. Prevention of PCP degradation by deletion of the transcriptional regulator, pcpR, increases growth rate in rich medium. These data suggest that, although PCP degradation allows access to a novel nutrient, the benefit of degrading it depends upon the availability of other resources. When resources are abundant, the detrimental effects of the toxic intermediates may outweigh the benefit of the carbon and energy that can be obtained by degrading PCP. However, when resources are scarce, degradation of PCP may provide access to a novel source of carbon and energy as well as detoxification of this anthropogenic pollutant.
2018-11-01 | GSE114148 | GEO
Project description:Paenarthrobacter strains effectively degrade the fungicide iprodione, exhibiting a specialization rarely seen amongst bacteria. The transformation of iprodione is controlled by an amidase, a deacetylase and a hydrolase encoded by ipaH, ddaH and duaH respectively. We aimed to elucidate the mechanisms of this catabolic specialization and its evolution in Paenarthrobacters. The genomes of two new iprodione-degrading Paenarthrobacter strains TA1.8 and C1 were sequenced and analyzed comparatively with the genomes of two other iprodione-degrading Paenarthrobacter strains YJN-5 and YJN-D. Comparative genomics revealed different gene organization motifs amongst strains which suggest that the strains are at different stages of pathway evolution, in accord with their prior exposure to iprodione. Strains TA1.8, YJN-5 and YJN-D, all isolated from soils heavily exposed to iprodione, carried multiple copies of ipaH, ddaH and duaH in their chromosomes and plasmids that were assigned to two distinct phylogenetic clusters based on genome topology. Conversely, strain C1, isolated from a pristine soil, carried ipaH, ddaH and duaH in the chromosome. Pangenome analysis of the genus Paenarthrobacter placed ipaH and duaH in the core genome reinforcing their specialization in the degradation of iprodione as they need to acquire only ddaH, the sole gene of the pathway associated with transposable elements in strains C1 and TA1.8, to complete the pathway. We propose an evolution route of the iprodione transformation pathway which involves acquisition of ddaH through horizontal gene transfer, gene duplication of the chromosomally encoded ipaH and ddaH, and further genetic rearrangements for pathway optimization, complementing duaH, a core gene in Paenarthrobacters. Transcriptomic analysis of strain TA1.8 verified the involvement of all copies of ipaH, ddaH and duaH in the transformation of iprodione, and identified hydantoinases, upregulated during iprodione degradation, as potential facilitators of the transformation of the hydantoin-containing intermediate N-(3,-5-dichlorophenyl)- 2,4-dioxoimida-zolidine, a step mediated by DdaH.
2025-04-06 | GSE293458 | GEO
Project description:Deoxynivalenol (DON) is a fungal toxin mainly produced by Fusarium graminearum and Fusarium graminearum, and is present in cereal crops such as wheat, barley, oats, rye, and corn. It is widely polluted worldwide. DON and its related derivatives have a wide range of toxic effects on humans and animals. This study used zebrafish models and different cell models to verify the toxic effects of DON, and explored the mechanism of DON mediated Jurkat apoptosis and inhibition of M2 macrophage differentiation. The results indicate that the toxic effects of these fungal toxins differ significantly among various cell types. For Jurkat T cells, the IC50 values of DON, NIV, 15 Ac DON, and 3-Ac DON were 488.6 nM, 318.2 nM, 544 nM, and 6516 nM, respectively. There are significant differences in the effects on M2 polarization of macrophages, and DON, NIV, and 15 Ac DON can inhibit M2 differentiation and function of macrophages at lower dose levels. Indicating that immune toxicity is an important toxic effect of DON and its related substances. Research on its mechanism has shown that DON can target protein processing processes, interfere with the normal synthesis and folding of proteins in cells, and trigger cellular stress responses. These findings reveal the toxic effects and potential mechanisms of DON on human immune cells, providing a scientific basis for preventing and controlling DON pollution and its harm to human health.
2025-12-20 | GSE284987 | GEO
Project description:Deoxynivalenol (DON) is a fungal toxin mainly produced by Fusarium graminearum and Fusarium graminearum, and is present in cereal crops such as wheat, barley, oats, rye, and corn. It is widely polluted worldwide. DON and its related derivatives have a wide range of toxic effects on humans and animals. This study used zebrafish models and different cell models to verify the toxic effects of DON, and explored the mechanism of DON mediated Jurkat apoptosis and inhibition of M2 macrophage differentiation. The results indicate that the toxic effects of these fungal toxins differ significantly among various cell types. For Jurkat T cells, the IC50 values of DON, NIV, 15 Ac DON, and 3-Ac DON were 488.6 nM, 318.2 nM, 544 nM, and 6516 nM, respectively. There are significant differences in the effects on M2 polarization of macrophages, and DON, NIV, and 15 Ac DON can inhibit M2 differentiation and function of macrophages at lower dose levels. Indicating that immune toxicity is an important toxic effect of DON and its related substances. Research on its mechanism has shown that DON can target protein processing processes, interfere with the normal synthesis and folding of proteins in cells, and trigger cellular stress responses. These findings reveal the toxic effects and potential mechanisms of DON on human immune cells, providing a scientific basis for preventing and controlling DON pollution and its harm to human health.
2025-12-20 | GSE284984 | GEO
Project description:Deoxynivalenol (DON) is a fungal toxin mainly produced by Fusarium graminearum and Fusarium graminearum, and is present in cereal crops such as wheat, barley, oats, rye, and corn. It is widely polluted worldwide. DON and its related derivatives have a wide range of toxic effects on humans and animals. This study used zebrafish models and different cell models to verify the toxic effects of DON, and explored the mechanism of DON mediated Jurkat apoptosis and inhibition of M2 macrophage differentiation. The results indicate that the toxic effects of these fungal toxins differ significantly among various cell types. For Jurkat T cells, the IC50 values of DON, NIV, 15 Ac DON, and 3-Ac DON were 488.6 nM, 318.2 nM, 544 nM, and 6516 nM, respectively. There are significant differences in the effects on M2 polarization of macrophages, and DON, NIV, and 15 Ac DON can inhibit M2 differentiation and function of macrophages at lower dose levels. Indicating that immune toxicity is an important toxic effect of DON and its related substances. Research on its mechanism has shown that DON can target protein processing processes, interfere with the normal synthesis and folding of proteins in cells, and trigger cellular stress responses. These findings reveal the toxic effects and potential mechanisms of DON on human immune cells, providing a scientific basis for preventing and controlling DON pollution and its harm to human health.
2025-12-20 | GSE284982 | GEO
Project description:Chemical signaling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via a novel auxin degradation locus was essential for maintaining stereotypic root development in an ecologically-relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. We identify auxin-degradation operons across the bacterial tree of life and define two distinct types based on gene content and metabolic products: iac-like and iad-like. We solve the structures of MarRs from representatives of each auxin degradation operon type, establishing that each have distinct IAA binding pockets. Comparison of representative IAA degrading strains from diverse bacterial genera show that while all degrade IAA, only strains containing iad-like auxin degrading operons interfere with auxin signaling in a complex synthetic community context. This suggests that iad-like operon containing strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
2022-08-11 | GSE210968 | GEO
Project description:To assess the impact of surface water across the Hun River, several sampling sites located in the mainstream and the tributary were selected representative of pollution gradient and different pollution source. Male adult zebrafish were exposed to surface water from seven sites for 4 days. The obiectives of the study was to evaluate the ability of transcriptomic profiles exposed to surface water to determine the potential biological effects, to differentiate different pollution source, and to identify the toxic components.
2017-12-19 | GSE108227 | GEO
Project description:To assess the impact of surface water across the Hun River, several sampling sites located in the mainstream and the tributary were selected representative of pollution gradient and different pollution source. Male adult zebrafish were exposed to surface water from seven sites for 4 days. The obiectives of the study was to evaluate the ability of transcriptomic profiles exposed to surface water to determine the potential biological effects, to differentiate different pollution source, and to identify the toxic components.
2017-04-01 | GSE92330 | GEO
Project description:<p>Background: The use of sulfonamides (SAs) caused residual pollution in the environment. Bacteria play an important role in the degradation of sulfonamide antibiotics, and microbial consortium offers advantages over single bacterium. However, the complex degradation process and interaction mechanisms within such consortiums still poorly understood. </p><p>Results: Here, a consortium named ACJ, consisting of Leucobacter sp. HA-1, Bacillus sp. HC-1 and Gordonia sp. HAEJ-1, obtained from activated sludge of pharmaceutical plants, was identified as capable of degrading various SAs. Several papers failed to get the pure culture of Leucobacter sp. in the degradation of SAs, here we successfully obtained the Leucobacter sp. HA-1 pure culture involved in the degradation of SAs with the growth factors provided by strain HC-1 or HAEJ-1. Strain HA-1 was responsible for the initial attack of sulfonamide molecules resulting in the release of 2-aminoquinoxaline (2-AQ) and trihydroxybenzene (HHQ), which were further degraded and used for growth by strain HAEJ-1. Genomic, metabolomic and transcriptomic analyses revealed genes associated with nucleotide repair, ABC transporters, quorum sensing, TCA cycle and cell cycle in strain HA-1 were up-regulated during co-culture compared without the other two strains, which indicated that HA-1 utilized certain factors from strain HC-1 or HAEJ-1 for growth. </p><p>Conclusion: These results revealed that there was a bidirectional ecological relationship of cross-feeding and co-degradation among consortium ACJ. In summary, this study provides new insights into the mechanisms of microbial consortium interaction and co-degradation in antibiotic-contaminated environments.</p>
2024-11-08 | MTBLS11473 | MetaboLights