PXD011457-3

PXD011457 is an original dataset announced via ProteomeXchange.

Title	Protein turnover rate along the gastrointestinal tract is coordinated by the spatial location and the microbiota
Description	The gastrointestinal tract is covered by a single layer of epithelial cells that, together with the mucus layers, protect the underlying tissue from bacterial invasion. The epithelium has one of the highest turnover rates in the body, renewing every 4-5 days. Using stable isotope labelling, high-resolution mass spectrometry and computational analysis, we report here a comprehensive dataset of the turnover rate of 3041 and the expression of 5012 intestinal epithelial cell proteins, analyzed under conventional and germ-free conditions across five different segments in mouse intestine. The median protein half-life was shorter in small intestine compared to colon, ranging from 3.5 to 4.2 days. Differences in protein turnover rates along the intestinal tract can be explained by distinct physiological functions and site-specific immune responses between the small and large intestine. Absence of microflora resulted in increased protein half-life by approximately one day.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:50:08.386.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Liisa Arike
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	6x(13)C labeled residue; iodoacetamide derivatized residue
Instrument	Q Exactive; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2018-10-23 05:45:59	ID requested
1	2020-01-24 02:06:04	announced
2	2020-02-04 02:28:33	announced	2020-02-04: Updated publication reference for PubMed record(s): 31995731.
⏵ 3	2024-10-22 04:50:16	announced	2024-10-22: Updated project metadata.

10.1016/j.celrep.2019.12.068;

Arike L, Seiman A, van der Post S, Rodriguez Pi, ñ, eiro AM, Ermund A, Sch, ü, tte A, B, ä, ckhed F, Johansson MEV, Hansson GC, Protein Turnover in Epithelial Cells and Mucus along the Gastrointestinal Tract Is Coordinated by the Spatial Location and Microbiota. Cell Rep, 30(4):1077-1087.e3(2020) [pubmed]

curator keyword: Metaproteomics, Biological

submitter keyword: Germ-free, Colon, Mass Spectrometry, Protein turnover, Commensals, Lipid Metabolism,Proteomics, Colonization, Small Intestine, Bacteria

Liisa Arike
contact affiliation	Mucin Biology Group, Proteomics Laboratory, Department of Medical Biochemistry and Cell Biology, University of Gothenburg
contact email	liisaarike@gmail.com
lab head
Liisa Arike
contact affiliation	PhD
contact email	liisaarike@gmail.com
dataset submitter

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/2020/01/PXD011457

PRIDE project URI

• PRIDE
  1. PXD011457
     1. Label: PRIDE project
     2. Name: Protein turnover rate along the gastrointestinal tract is coordinated by the spatial location and the microbiota