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The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles

ABSTRACT: The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles

PROVIDER: PRJNA566007 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10134600.fastq.gz	Fastqsanger.gz
	SRR10134601.fastq.gz	Fastqsanger.gz
	SRR10134602.fastq.gz	Fastqsanger.gz
	SRR10134603.fastq.gz	Fastqsanger.gz
	SRR10134604.fastq.gz	Fastqsanger.gz

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The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (smRNA-seq dataset)

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The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (lrgRNA-seq dataset)

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The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (lrgRNA-seq dataset)

Project description:The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (lrgRNA-seq dataset)

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The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (smRNA-seq dataset)

Project description:The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (smRNA-seq dataset)

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The LC3-conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles.

Project description:Traditionally viewed as an autodigestive pathway, autophagy also facilitates cellular secretion; however, the mechanisms underlying these processes remain unclear. Here, we demonstrate that components of the autophagy machinery specify secretion within extracellular vesicles (EVs). Using a proximity-dependent biotinylation proteomics strategy, we identify 200 putative targets of LC3-dependent secretion. This secretome consists of a highly interconnected network enriched in RNA-binding proteins (RBPs) and EV cargoes. Proteomic and RNA profiling of EVs identifies diverse RBPs and small non-coding RNAs requiring the LC3-conjugation machinery for packaging and secretion. Focusing on two RBPs, heterogeneous nuclear ribonucleoprotein K (HNRNPK) and scaffold-attachment factor B (SAFB), we demonstrate that these proteins interact with LC3 and are secreted within EVs enriched with lipidated LC3. Furthermore, their secretion requires the LC3-conjugation machinery, neutral sphingomyelinase 2 (nSMase2) and LC3-dependent recruitment of factor associated with nSMase2 activity (FAN). Hence, the LC3-conjugation pathway controls EV cargo loading and secretion.

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The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles

Project description:This SuperSeries is composed of the SubSeries listed below.

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Secretory autophagy mediates mitochondria clearance in the absence of the mATG8-conjugation machinery

Project description:PINK1-Parkin mediated mitophagy, a selective form of autophagy, represents an important mechanism in mitochondrial quality control (MQC) via clearance of damaged mitochondria. Although it is well known that the conjugation of mammalian ATG8s to phosphatidylethanolamine (PE) is a key step in autophagy, its role in mitophagy remains controversial. In this study, we attempted to clarify the role of the mATG8-conjugation system in mitophagy by generating knockouts of the mATG8-conjugation machinery. Unexpectedly, we show that mitochondria could still be cleared in the absence of mATG8 lipidation, in a process that was found to be independent of lysosomal degradation. Instead, mitochondria were found to be cleared via a secretory autophagy pathway, resulting in the extracellular release of mitochondria, in a process we defined as autophagic secretion of mitochondria (ASM). Functionally, increased ASM promoted the activation of the innate immune cGAS-STING pathway in recipient cells. Overall, data from this study reveal ASM as a novel mechanism in MQC, especially when the cellular mATG8-conjugation machinery is dysfunctional.

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Project description:Horizontal gene transfer (HGT) is the major mechanism responsible for spread of antibiotic resistance. Antibiotic treatment has been suggested to promote HGT, either by directly affecting the conjugation process itself or by selecting for conjugations subsequent to DNA transfer. However, recent research suggests that the effect of antibiotic treatment on plasmid conjugation frequencies, and hence the spread of resistance plasmids, may have been overestimated. We addressed the question by quantifying transfer proteins and conjugation frequencies of a blaCTX-M-1 encoding IncI1 resistance plasmid in Escherichia coli MG1655 in the presence and absence of therapeutically relevant concentrations of cefotaxime (CTX). Analysis of the proteome by iTRAQ labeling and liquid chromatography tandem mass spectrometry revealed that Tra proteins were significantly up regulated in the presence of CTX. The up-regulation of the transfer machinery was confirmed at the transcriptional level for five selected genes. The CTX treatment did not cause induction of the SOS39 response as revealed by absence of significantly regulated SOS associated proteins in the proteome and no significant up-regulation of recA and sfiA genes. The frequency of plasmid conjugation, measured in an antibiotic free environment, increased significantly when the donor was pre-grown in broth containing CTX compared to growth without this drug, regardless of whether blaCTX-M-1 was located on the plasmid or in trans on the chromosome. The results shows that antibiotic treatment can affect expression of a plasmid conjugation machinery and subsequent DNA transfer.

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