Dataset Information

SILAC-based quantitative proteomics using mass spectrometry identifies BAG-6 mediated changes in the subproteome degraded by endosomal microautophagy (eMI).

ABSTRACT: To identify the subproteome degraded by endosomal microautophagy (eMI) in a Bag6-dependent manner, we compared the proteome of late endosomal compartments LE/MVBs isolated from control(wild type) and Bag6(-) cells using SILAC labeling and quantitative proteomics.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Dendritic Cell, Cell Culture

SUBMITTER: Cristina Clement

LAB HEAD: Anna-Maria Cuervo

PROVIDER: PXD046760 | Pride | 2024-01-26

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	20160523_LSantambrogio_S1.mgf	Mgf
	20160523_LSantambrogio_S1.mzid.gz	Mzid
	20160523_LSantambrogio_S1.raw	Raw
	20160523_LSantambrogio_S2.mgf	Mgf
	20160523_LSantambrogio_S2.mzid.gz	Mzid

Items per page:

1 - 5 of 10

Publications

Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy.

Krause Gregory J GJ Kirchner Philipp P Stiller Barbara B Morozova Kateryna K Diaz Antonio A Chen Kuei-Ho KH Krogan Nevan J NJ Agullo-Pascual Esperanza E Clement Cristina C CC Lindenau Kristen K Swaney Danielle L DL Dilipkumar Shilpa S Bravo-Cordero Jose Javier JJ Santambrogio Laura L Cuervo Ana Maria AM

Cell reports 20231206 12

Chaperone-mediated autophagy (CMA) and endosomal microautophagy (eMI) are pathways for selective degradation of cytosolic proteins in lysosomes and late endosomes, respectively. These autophagic processes share as a first step the recognition of the same five-amino-acid motif in substrate proteins by the Hsc70 chaperone, raising the possibility of coordinated activity of both pathways. In this work, we show the existence of a compensatory relationship between CMA and eMI and identify a role for ...[more]

PMID: 38060380

Similar Datasets

Project description:Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA–seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially expressed DNA TEs (78%) were up-regulated in the mop1 mutant. In contrast, most differentially expressed retrotransposons (68%) were down-regulated. This striking difference suggests that distinct silencing mechanisms are applied to different silencing templates. In addition, 6,000 genes (24% of analyzed genes), including nearly 80% (286/361) of genes in chromatin modification pathways, were differentially expressed. Overall, two-thirds of differentially regulated genes were down-regulated in the mop1 mutant. This finding suggests that RDR2 plays a significant role in regulating the expression of not only transposons, but also of genes. A re-analysis of existing small RNA data identified both RDR2–sensitive and RDR2–resistant species of 24 nt siRNAs that we hypothesize may at least partially explain the complex changes in the expression of genes and transposons observed in the mop1 mutant. Single sequencing library was constructed for mop1 mutant and non-mutant. Each library was sequenced using 2 lanes on a Solexa flow cell. Processed data file 'ZmB73_4a.53_filtered_genes.fasta' and its README file are linked below as supplementary files. The fasta file contains the gene model ID and corresponding sequence generated from maize genome project. This fasta file was used for the following samples: GSM418173, GSM418174, GSM420173, GSM420174, GSM422828, GSM422829.