Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic Analysis of the Peroxisomal Retrograde Signaling in C. elegans

ABSTRACT: While retrograde signalling pathways have been identified for several organelles, the existence of such a pathway for peroxisomes remains elusive. We identified a peroxisomal retrograde signalling (PRS) in C. elegans, which is activated in response to peroxisomal import stress. We analyzed the PRS using a proteomic approach.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Caenorhabditis Elegans

SUBMITTER: Ignasi Forne

LAB HEAD: Dr. Stephane Rolland

PROVIDER: PXD014720 | Pride | 2021-01-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Ref1571_ER_prx5_R1_20181012.raw	Raw
	Ref1571_ER_prx5_R2_20181012.raw	Raw
	Ref1571_ER_prx5_R3_20181012.raw	Raw
	Ref1571_ER_prx5_R4_20181012.raw	Raw
	Ref1571_ER_tag208_R1_20181012.raw	Raw

Items per page:

1 - 5 of 9

Similar Datasets

Peroxisomal retrograde signaling in C. elegans

Project description:Distinct retrograde signaling pathways have been identified for several cellular organelles. These pathways are important to maintain the function of these organelles in response to organelle-specific stress. Using Caenorhabditis elegans, we show for the first time that such a retrograde signaling also exists for peroxisomes. Analysis of the C. elegans transcriptome revealed that peroxisomal import stress caused by the knock-down of the peroxisomal matrix protein import receptor prx-5/PEX5 induces the compensatory up-regulation of genes involved in defense response and lipid metabolic processes, especially peroxisomal beta oxidation. We, therefore, propose that the peroxisomal retrograde signaling participates in the maintenance of peroxisomal function in response to peroxisomal import stress.

2020-12-19 | GSE156318 | GEO

Peroxisomal retrograde signaling in C. elegans

Project description:Peroxisomal retrograde signaling in C. elegans

| PRJNA657442 | ENA

Control of protein accumulation by LON2 peroxisomal protease and autophagy

Project description:Peroxisomes are membrane-bound eukaryotic organelles that house essential metabolic pathways. Many of these pathways generate damaging reactive oxygen species (ROS) that also function as signaling molecules. In Arabidopsis thaliana, damaged or obsolete peroxisomal proteins can be degraded by the LON2 peroxisomal protease. In addition, peroxisomes can be entirely degraded through a specialized form of autophagy (pexophagy), a process that is amplified when LON2 is dysfunctional. As a first step towards surveying the transcriptional landscape of dysfunctional LON2 , we used RNA-seq analysis to compare transcript that are induced and reduced when LON2 is dysfunctional in the presence and absence of autophagy.

2024-12-27 | GSE208057 | GEO

Gene network downstream plant stress response modulated by peroxisomal H2O2

Project description:Study of the effect of cadmium on KO and overexpressor mutants of glycolate oxidase-GOX2, which is one of the main sources of H202 from peroxisomes. Reactive oxygen species (ROS) act as secondary messengers that can be sensed by specific redox sensitive proteins responsible for the activation of signal transduction culminating in altered gene expression. ROS, which are involved in different activities, elicit a wide range of protein modifications, which might elicit different gene expressions. The subcellular site, in which modifications in ROS/oxidation state occur, can also act as a specific cellular redox network signal. The chemical identity of ROS and their subcellular origin actually is a specific imprint on the transcriptome response. In recent years, a number of transcriptomic studies related to altered ROS metabolism in plant peroxisomes have been carried out. In this study, we made a meta-analysis of these transcriptomic findings to identify common transcriptional footprints for plant peroxisomal-dependent signaling at early and later time points. These footprints highlight the regulation of various metabolic pathways and gene families, which are also found in plant responses to several abiotic stresses. Major peroxisomal-dependent genes are associated with protein and endoplasmic reticulum (ER) protection at later stages of stress while, at earlier stages, these genes are related to hormone biosynthesis and signaling regulation. Further, in silico analyses allowed us to assign human orthologs to some of the peroxisomal-dependent genes, which are mainly associated with different cancer types pathologies. Peroxisomal footprints provide a valuable resource for assessing and supporting key peroxisomal functions in cellular metabolism under control and stress conditions across species.

2022-09-20 | GSE199325 | GEO

Integrative Omics reveals changes in the cellular landscape of yeast without peroxisomes

Project description:Peroxisomes are organelles that are crucial for cellular metabolism. However, these organelles play also important roles in non-metabolic processes, such as signalling. To uncover the consequences of peroxisome deficiency, we compared two extremes, namely Saccharomyces cerevisiae wild-type and pex3 cells, which lack functional peroxisomes, employing transcriptomics and quantitative proteomics technology. Cells were grown on acetate, a carbon source that involves peroxisomal enzymes of the glyoxylate cycle and does not repress peroxisomal proteins. Transcripts of peroxisomal β-oxidation genes and the corresponding proteins were enhanced in pex3 cells. Peroxisome-deficiency also caused reduced levels of membrane bound peroxins, while the soluble receptors Pex5 and Pex7 were enhanced at the protein level. In addition, we observed alterations in non-peroxisomal transcripts and proteins, especially mitochondrial proteins involved in respiration or import processes. Our results not only reveal the impact of the absence of peroxisomes in yeast, but also represent a rich resource of candidate genes/proteins that are relevant in peroxisome biology.

2024-05-01 | GSE261289 | GEO

Divergent evolutionary strategies for selective sex chromosome regulation in Drosophila

Project description:The dosage compensation complex (DCC) of Drosophila identifies its X chromosomal binding sites with exquisite selectivity. The principles that assure this vital targeting are known from the D. melanogaster model: DCC-intrinsic specificity of DNA binding, cooperativity with the CLAMP protein, and non-coding roX2 RNA transcribed from the X chromosome. We found that in D. virilis, a species separated from melanogaster by 40 million years of evolution, all principles are active, but contribute differently to X-specificity. In melanogaster, the DCC subunit MSL2 evolved intrinsic DNA-binding selectivity for rare PionX sites, which mark the X chromosome. In virilis, PionX sites are abundant and not X-enriched. Accordingly, MSL2 lacks specific recognition. Here, roX2 RNA plays a more instructive role, counteracting a non-productive interaction of CLAMP and modulating DCC binding selectivity. Remarkably, roX2 triggers a low-diffusion chromatin binding mode characteristic of DCC. Evidently, X-specific regulation is achieved by divergent evolution of similar components.

2021-06-23 | PXD023747 | Pride

Proteome analysis of Corynebacterium glutamicum ATCC13032 Δefp

Project description:Bacterial translational elongation factor P (EF-P) is required during translation of proteins containing consecutive proline motifs. Several transcription and translational regulators contain polyproline motifs and therefore, EF-P might also affect levels of proteins that do not contain polyproline motifs.

2020-04-06 | PXD014742 | Pride

Mitochondrial dynamics in ovarian granulosa cells during follicular growth and in human KGN cells

Project description:In the ovary, proliferation and differentiation of granulosa cells (GCs) drive the growth of follicles. This is, in part, dependent on gonadotropins. Our immunohistochemical studies provided hints of mitochondrial biogenesis and intracellular redistribution in GCs of growing follicles. A cellular model, human KGN cells (granulosa cell tumor cells, derived from growing follicles) was used to study aspects of mitochondrial dynamics. To elevate cAMP and thereby mimic gonadotropin actions, forskolin (FSK) was used, which increased KGN cell size and mitochondrial DNA within 24 h. MitoTracker experiments and ultrastructural 3D reconstruction revealed that FSK treatment induced the formation of elaborate mitochondrial networks. H89, a protein kinase A (PKA) inhibitor, reduced network formation. A proteomic analysis indicated that FSK among others elevated levels of regulators of the cytoskeleton and the steroidogenic enzyme CYP11A1, located in mitochondria, was more than 3-fold increased, implying that cAMP/PKA-associated structural changes go in parallel with the acquisition of steroidogenic competence of mitochondria in KGN cells. In summary, in situ observations showed increases in mitochondria and suggested intracellular trafficking in GCs during follicular growth and indicated that they may partially be under the control of gonadotropins/cAMP. In line with this, elevation of cAMP in KGN profoundly affected mitochondria dynamics in a PKA-dependent manner and implicated cytoskeletal changes.

2022-10-14 | PXD032160 | Pride

Peroxisome function relies on organelle-associated mRNA translation

Project description:Crucial metabolic functions of peroxisomes rely on a variety of peroxisomal membrane proteins (PMPs). While mRNA transcripts of PMPs were shown to be colocalized with peroxisomes, the process by which PMPs efficiently couple translation with targeting to the peroxisomal membrane remained elusive. Here, we combine quantitative electron microscopy with proximity-specific ribosome profiling and reveal that translation of specific PMPs occurs on the surface of peroxisomes in the yeast Saccharomyces cerevisiae. This places peroxisomes alongside chloroplasts, mitochondria, and the endoplasmic reticulum as organelles that use localized translation for ensuring correct insertion of hydrophobic proteins into their membranes. Moreover, the correct targeting of these transcripts to peroxisomes is crucial for peroxisomal and cellular function, emphasizing the importance of localized translation for cellular physiology.

2022-01-12 | GSE113567 | GEO

ANP32B is a macroh2A histone chaperone

Project description:Interaction proteomics in cell extracts on tagged macroH2A, either expressed in cells or using recombinant dimers with H2B.

2023-10-24 | PXD045696 | Pride