PXD033467

PXD033467 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Proteome of choline-grown Eubacterium limosum ATCC 8486
Description	Eubacterium limosum ATCC 8486 makes acetate and butyrate from various substrates and is found in the human intestine. The proteome of choline -grown Eubacterium limosum was obtained in order to identify enzymes required for growth on choline, in particular to identify components that are unique to growth on choline in comparison to other substrates for acetogenesis, such as lactic acid, L-carnitine, or proline betaine. Choline is converted to trimethylamine (TMA) by certain members of the gut microbiome. Subsequent liver metabolism of TMA is now tied to progression of cardiovascular disease. Demethylation of choline is observed during growth of Eubacterium limosum on this substrate, and does not produce TMA. Choline demethylation by organisms like Eubacterium limosum could lessen TMA production in the gut, thereby lessening the propensity towards atherosclerosis caused by metabolism of TMA in the body. This proteome led to discovery of a phosphocholine:tetrahydrofolate methyltransferase system. The key choline demethylating enzyme is a member of the widespread TMA methyltransferase protein superfamily.
HostingRepository	PRIDE
AnnounceDate	2025-06-16
AnnouncementXML	Submission_2025-06-15_16:11:02.279.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD033467
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Joseph Krzycki
SpeciesList	scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: Eubacterium limosum; NCBI TaxID: 1736;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-27 03:46:18	ID requested
⏵ 1	2025-06-15 16:11:03	announced

Publication List

Jiang R, Kountz DJ, Zhang L, Krzycki JA, A cobalamin-dependent pathway of choline demethylation from the human gut acetogen Eubacterium limosum. J Biol Chem, 301(6):108524(2025) [pubmed]
10.6019/PXD033467;
10.1016/j.jbc.2025.108524;

Jiang R, Kountz DJ, Zhang L, Krzycki JA, A cobalamin-dependent pathway of choline demethylation from the human gut acetogen Eubacterium limosum. J Biol Chem, 301(6):108524(2025) [pubmed]

10.6019/PXD033467;

10.1016/j.jbc.2025.108524;

Keyword List

submitter keyword: choline demethylation pathway, human gut isolate,Acetogenic bacteria

submitter keyword: choline demethylation pathway, human gut isolate,Acetogenic bacteria

Contact List

Joseph Adrian Krzycki
contact affiliation	Microbiology, Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
contact email	Krzycki.1@osu.edu
lab head
Joseph Krzycki
contact affiliation	The Ohio State University
contact email	Krzycki.1@osu.edu
dataset submitter

Full Dataset Link List

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PRIDE project URI

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/06/PXD033467

PRIDE project URI

Repository Record List

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