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Proteome dysregulation induced by 5-fluoro-2′-deoxyuridine (FUdR) in C. elegans

ABSTRACT: The effect of 5-fluoro-2′-deoxyuridine (FUdR) on the proteome of C. elegans (wild type and glp-1/skn-1 mutants) was studied. Total protein extracts were obtained from the wild type and mutant worms subjected to the FUdR or control treatment and relative protein levels assessed by shotgun proteomics (TMT).

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Caenorhabditis Elegans

TISSUE(S): Whole Body

SUBMITTER: Remigiusz Serwa

LAB HEAD: Wojciech Pokrzywa

PROVIDER: PXD045805 | Pride | 2024-07-18

REPOSITORIES: Pride

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Cathepsin B Promotes Aβ Proteotoxicity by Modulating Aging Regulating Mechanisms

Project description:While the activities of certain proteases promote proteostasis and prevent neurodegeneration-associated phenotypes, the protease cathepsin B (CTSB) enhances proteotoxicity in Alzheimer’s disease (AD) model mice, and its levels are elevated in brains of AD patients. How CTSB exacerbates the toxicity of the ADcausing Amyloid β (Aβ), is controversial. Using an activity-based probe, aging-altering interventions and the nematode C. elegans we discovered that the CTSB CPR-6 promotes Aβ proteotoxicity but mitigates the toxicity of polyQ stretches. While the knockdown of cpr-6 does not affect lifespan, it alleviates Aβ toxicity by reducing the expression of swsn-3 and elevating the level of the protein SMK-1, both involved in the regulation of aging. These observations unveil a novel mechanism by which CTSB aggravates Aβ– mediated toxicity, indicate that it plays opposing roles in the face of distinct proteotoxic insults and highlight the importance of tailoring specific remedies for distinct neurodegenerative disorders.

2024-09-04 | PXD045561 | Pride

The RDE-10/RDE-11 complex triggers RNAi induced mRNA degradation by association with target mRNA in C. elegans

Project description:The molecular mechanisms for target mRNA degradation in C. elegans undergoing RNA interference (RNAi) are not fully understood. Using a combination of genetic, proteomic and biochemical approaches, we report a divergent RDE-10/RDE-11 complex that is required for RNAi in C. elegans. The RDE-10/RDE-11 complex acts in parallel of nuclear RNAi. Association of the complex with target mRNA is dependent on RDE-1 but not RRF-1, suggesting that target mRNA recognition depends on primary but not secondary siRNA. Furthermore, RDE-11 is required for mRNA degradation subsequent to target engagement. Deep sequencing reveals a 5-fold decrease in secondary siRNA abundance in rde-10 and rde-11 mutant animals, while primary siRNA and micro-RNA biogenesis is normal. Therefore, the RDE-10/RDE-11 complex is critical for amplifying the exogenous RNAi response. Our work uncovers an essential output of the RNAi pathway in C. elegans. 21-24nt small RNA were purifed from different C. elegans strain populations that underwent sel-1 RNAi

2012-04-25 | E-GEOD-36494 | biostudies-arrayexpress

The effect of Y145C mutation in AHCY-1 on the total proteome of young adults C.elegans

Project description:Supplementation with S-adenosylhomocysteine (SAH) extends the lifespan of model organisms. To explore the impact of SAH on aging, we generated a Caenorhabditis elegans model with increased SAH levels through pathogenic mutation in the S-adenosylhomocysteine hydrolase (AHCY-1), which impairs SAH hydrolysis to adenosine and homocysteine. This submission contains results of the quantitative (TMT) measurements of the proteins in whole worm extracts originated from AHCY-1 Y143C mutant (equivalent to the human pathogenic variant) and control worms.

2023-09-29 | PXD041645 | Pride

Shotgun measurements of proteome fractionations: mitochondria, aggregates, and soluble fraction of NDUFA11 KO and WT HEK293T cells

Project description:Perturbed proteostasis and mitochondrial dysfunction are often associated with age-related diseases such as Alzheimer’s and Parkinson’s diseases. However, the link between them remains incompletely understood. Mitochondrial dysfunction causes proteostasis imbalance, and cells respond to restore proteostasis by increasing proteasome activity and molecular chaperons in yeast and C. elegans. Here, we demonstrate the presence of similar responses in humans. Mitochondrial dysfunction upregulates a small heat shock protein HSPB1 and an immunoproteasome subunit PSMB9 leading to an increase in proteasome activity. HSPB1 and PSMB9 are required to prevent protein aggregation upon mitochondrial dysfunction. Moreover, PSMB9 expression is dependent on a translation elongation factor EEF1A2, and PSMB9-containing proteasomes are located near mitochondria, enabling fast local degradation of aberrant proteins. Our findings put a step forward in understanding the stress response triggered by mitochondrial dysfunction, and may be useful for therapeutic strategies to prevent or delay the onset of age-related diseases and attenuate their progression.

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Defining changes in the total levels of proteins upon RPN-6 RNAi

Project description:Here we defined changes in the total levels of individual proteins upon RPN-6 RNAi in young C. elegans adults (day 5)

2021-05-26 | PXD024095 | Pride

Defining changes in the levels of Ub-modified peptides upon rpn-6 knockdown

Project description:Here we defined changes in the levels of Ub-modified peptides upon rpn-6 knockdownthat in young C. elegans adults (day 5)

2021-05-26 | PXD024094 | Pride

Mass spectrometry analysis of synaptic proteome of adult Fmr1 KO and wild-type mice.

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Shotgun analysis of proteins in NDUFA11 KO and WT HEK 293T cells.

Project description:The effect of the depletion of an ETC complex I protein component - NDUFA11 on the proteome in HEK 293T cells was studied. TMT-based relative quantification of protein levels were performed in NDUFA11 KO vs WT cells and in NDUFA11 KO vs WT cells that expressed an EGFP-MAPT (Tau protein) construct. In this dataset relative levels of proteins in total cell extracts and in the soluble fraction (post centrifugation at 125,000 g, at which speed protein aggregates were isolated as pellets) were measured. This dataset is directly related to the dataset PXD031374 (protein aggregates isolated as pellets post centrifugation at 125,000 g).

2023-07-03 | PXD038397 | Pride

Transcriptomic analysis of germline tumor in fasted C. elegans

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2016-01-15 | E-GEOD-65406 | biostudies-arrayexpress

Ribosomal and tRNA Biogenesis Interact to Control Hypoxic Injury and Translation

Project description:Protein translation is an essential cellular process, but paradoxically, it can also promote aging and other stresses. In a screen for mutations that protect C. elegans from hypoxic stress, we isolated multiple genes that impact translation, including a ribosomal RNA helicase gene, ddx-52, tRNA biosynthesis genes, and a gene controlling amino acid availability. To better define the mechanisms whereby these genes control hypoxic injury, we performed a second screen for genetic suppressors of the ddx-52(lf) phenotypes. This screen identified multiple genes involved in ribosome biogenesis. Surprisingly, the suppressor mutations were able to restore normal hypoxic sensitivity and protein synthesis to the tRNA biosynthesis mutants, but not to the mutant reducing amino acid uptake. Proteomic characterization of the mutants demonstrated that reduced tRNA biosynthetic activity produces a corresponding reduction in ribosomal structural subunits. Our study uncovers an uncharacterized regulatory interaction between ribosomal biogenesis and tRNA abundance controlling translation and hypoxic survival. A proteomic analysis of a threonyl-tRNA synthetase mutant with and without the ribosomal biogenesis suppressors revealed an uncharacterized feedback mechanism whereby disruption of tRNA aminoacylation results in a corresponding reduction in ribosomal subunits, thereby explaining the ability of enhanced ribosomal biogenesis to suppress reduced tRNA aminoacylation.

2022-02-15 | PXD017267 | Pride

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