PXD008394

PXD008394 is an original dataset announced via ProteomeXchange.

Title	AMpylation is a hallmark of human neuronal differentiation
Description	The AMPylation is novel protein post-translation modification. In consist of attachment of the adenosine monophosphate onto the serine, threonine or tyrosine amino acid residues of the protein. This process is catalysed by bacterial effectors or in human by protein FICD (also called HYPE) which contain conserved fic domain. In our study we have focused on identification of the unknown AMPylated proteins and their function in human cells (HeLa, A549, SH-SY5Y, iPSCs, NPCs and neurons) and cerebral organoids (COs). For this purpose we designed and synthesized the small molecule N6-propargyl phosphoramidate adenosine (PAK-76) which was used for in situ labelling of the AMPylation in cells and COs. Subsequnetly the the propargyl tag was employed for preparation of chemical-proteomic samples which were measured by LC-MS/MS. This approach confirmed the known AMPylation of heat shock protein HSPA5 and found diverse group of novel AMPylation targets. Several cathepsins found as AMPylation targets were further characterized by identification of AMP binding site. Based on our chemical proteomic data we found out that neurons and neuronal like cells contain distinct AMPylatino pattern from other studied cell types. This also suggested the importance of the AMPylation in these cell types which were then studied in cerebral organoids by overexpressing the FICD wt and E234G highly active mutant. This led to the accelerated differentiation of progenitors into the neurons. Overall our approach is suitable for identification of the AMPylated proteins in living cells and led to characterization of FICD function.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:40:18.668.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pavel Kielkowski
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion ETD; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-07 23:44:51	ID requested
1	2024-05-21 11:10:39	announced
⏵ 2	2024-10-22 06:40:21	announced	2024-10-22: Updated project metadata.

Russell-Hallinan A, Cappa O, Kerrigan L, Tonry C, Edgar K, Glezeva N, Ledwidge M, McDonald K, Collier P, Simpson DA, Watson CJ, Single-Cell RNA Sequencing Reveals Cardiac Fibroblast-Specific Transcriptomic Changes in Dilated Cardiomyopathy. Cells, 13(9):(2024) [pubmed]

10.3390/cells13090752;

submitter keyword: chemical-proteomics, cerebral organoids., phosphoramidate prodrugs, FICD,AMPylation, neuronal development

Stephan Axel Sieber
contact affiliation	Technical University of Munich Chair of Organic Chemistry II Lichtenbergstraße 4 D-85748 Garching Germany
contact email	stephan.sieber@tum.de
lab head
Pavel Kielkowski
contact affiliation	LMU Munich
contact email	pavel.kielkowski@tum.de
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/2024/05/PXD008394

PRIDE project URI

• PRIDE
  1. PXD008394
     1. Label: PRIDE project
     2. Name: AMpylation is a hallmark of human neuronal differentiation