PXD053033

PXD053033 is an original dataset announced via ProteomeXchange.

Title	Biogenesis of DNA-carrying extracellular vesicles by the dominant human gut methanogenic archaeon
Description	Extrachromosomal vesicles (EVs) are membrane-bound particles secreted by cells from all domains of life and implicated in a variety of important processes, from intercellular communication to pathogenesis. Here, we characterize EVs produced by the dominant human gut methanogen, Methanobrevibacter smithii, which, unlike most archaea, contains a peptidoglycan-like cell wall. Using quantitative proteomics, we show that M. smithii EVs are enriched in various proteins responsible for chromatin structure, including histones, and DNA repair. Consistently, the M. smithii EVs carry DNA, with fragments covering the entire cellular chromosome. Notably, the EVs are strongly enriched in extrachromosomal circular DNA (eccDNA) molecules which originate from excision of a 2.9-kb chromosomal fragment and a proviral genome. The eccDNA and the provirus are respectively ~600× and ~30× more abundant in the EVs compared to other chromosomal regions. The eccDNA encodes two of the key methanogenesis enzymes and could boost their expression inside the cells through the gene dosage effect. Furthermore, four of the top ten most abundant EV proteins are implicated in methanogenesis. Cryo-electron tomography (Cryo-ET) suggests that EVs are formed by budding from the cell membrane and are trapped under the cell wall prior to liberation through local disruptions in the cell wall. Collectively, our results reveal parallels with EV biogenesis in bacteria and suggest that M. smithii EVs facilitate the export of both cellular and viral DNA as well as key metabolic proteins in the gut environment, with potential impact on methane production.
HostingRepository	PRIDE
AnnounceDate	2025-02-18
AnnouncementXML	Submission_2025-02-18_06:26:17.943.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Thibaut Douché
SpeciesList	scientific name: Methanobrevibacter smithii ATCC 35061; NCBI TaxID: 420247;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-12 02:32:19	ID requested
⏵ 1	2025-02-18 06:26:18	announced

Dataset with its publication pending

submitter keyword: Archea, extracellular vesicle, shotgun proteomics, Orbitrap Lumos tribrid

Mart Krupovic
contact affiliation	Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 75015 Paris, France
contact email	mart.krupovic@pasteur.fr
lab head
Thibaut Douché
contact affiliation	Institut Pasteur
contact email	thibaut.douche@pasteur.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD053033
     1. Label: PRIDE project
     2. Name: Biogenesis of DNA-carrying extracellular vesicles by the dominant human gut methanogenic archaeon