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A enzymatic program that assembles amyloids

ABSTRACT: A enzymatic program that assembles amyloids

PROVIDER: PRJNA976690 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR24748805_subreads.fastq.gz	Fastqsanger.gz
	SRR24748806_subreads.fastq.gz	Fastqsanger.gz
	SRR24748807_subreads.fastq.gz	Fastqsanger.gz
	SRR24748808_subreads.fastq.gz	Fastqsanger.gz
	SRR24748809_subreads.fastq.gz	Fastqsanger.gz

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Amyloids as protein traps in bladder cancer

Project description:Despite the current diagnostic and therapeutic approaches to bladder cancer being widely accepted, there have been few significant advancements in this field over the past decades. This underscores the necessity for a paradigm shift in the approach to bladder cancer. The role of amyloids in cancer remains unclear despite their identification in several other pathologies. In this study, we present evidence of amyloids in bladder cancer, both in vitro and in vivo. In a murine model of bladder cancer, a positive correlation was observed between amyloids and tumor stage, indicating an association between amyloids and bladder cancer progression. Subsequently, the amyloid proteome of the RT4 non-invasive and HT1197 invasive bladder cancer cell lines was identified and included oncogenes, tumor suppressors, and highly expressed cancer-related proteins. It is proposed that amyloids function as structures that sequester key proteins. Therefore, amyloids should be considered in the study and diagnosis of bladder cancer.

2024-12-19 | PXD053864 | Pride

Cell membrane proteome analysis in HEK293T cells challenged with α-Synuclein amyloids

Project description:Amyloids interact with plasma membranes. Extracellular amyloids cross the plasma membrane barrier. Internalized extracellular amyloids are reported to trigger amyloidogenesis of endogenous proteins in recipient cells. To what extent these extracellular and intracellular amyloids perturb the plasma membrane proteome is not investigated. Using α-Synuclein as a model amyloid protein, we performed membrane shaving followed by mass spectrometry experiment to identify the conformational changes in the cell surface proteins after extracellular amyloid challenge. We also performed membrane proteomics after the biogenesis of intracellular α-Synuclein amyloids. Our results suggest that promiscuous interaction with extracellular amyloids stochastically alter the conformation of plasma membrane proteins. This affects the biological process through the plasma membrane and result in loss in cell viability. Cells that survive the extracellular amyloid shock can grow normally and gradually develop intracellular amyloids which do not directly impact the plasma membrane proteome and associated biological processes. Thus, α-Synuclein amyloids can damage the plasma membrane and related processes only during cell to cell transfer and not during their intracellular biogenesis.

2024-07-09 | PXD046280 | Pride

Amyloids from WT and mstr C. elegans

Project description:200,000 worms were grown to the young adult stage, collected, and washed. Worms were homogenized in lysis buffer (10mM Tris, pH 7.5, 138mM NaCl, 2mM CaCl2, and 0.1% NP-40). After homogenization, 125U/mL Benzonase nuclease was added to homogenates and samples were incubated for 30 mins at room temperature with gentle rocking. Samples were spun at 21,000g for 5 mins, followed by resuspension of the pellet in lysis buffer. Soluble proteins were removed from the pellet with repeated washes in lysis buffer until A280 of the supernatant was equal to A280 of lysis buffer. Resulting pellet was resuspended in ddH2O, spun at 21,000g for 5 mins, and supernatant was transferred to a collection tube. Water resuspensions and recoveries were continued until A280 of H2O supernatants was 0. Recovered water washes were pooled and amyloids salted out by adding NaCl to 200mM final concentration, followed by 1-3 days incubation at 4oC. Precipitated amyloids were recovered by centrifuging at 21,000g for 30 mins, followed by resuspension in 50-100uL ddH2O. Amyloids were digested (trypsin and chymotrypsin) and prepared for mass spectrometry as described in the methods files.

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Project description:Cells respond to stress by blocking translation, rewiring metabolism, and forming transient mRNP assemblies called stress granules (SGs). After stress release, re-establishing homeostasis requires energy-consuming processes. However, the molecular mechanisms whereby cells restore energy production to disassemble SGs and reinitiate growth after stress remain poorly understood. Here we show that, upon stress, the ATP-producing enzyme Cdc19 forms inactive amyloids, and that their rapid re-solubilization is essential to restore energy production and SG disassembly. Cdc19 re-solubilization is initiated by the glycolytic metabolite fructose-1,6-bisphosphate (FBP), which directly binds Cdc19 amyloids and facilitates conformational changes that allow Hsp104 and Ssa2 chaperone recruitment. FBP then promotes Cdc19 tetramerization and activity, which together with trehalose breakdown boosts glycolysis to further enhance SG disassembly. Together, these results provide a molecular mechanism protecting cells during stress by directly coupling metabolism and ATP production with SG dynamics via regulation of Cdc19 amyloids.

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