PXD058135

PXD058135 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of the sponge (Porifera) Aggregation Factor implicates an ancient protein domain toolkit for allorecognition and adhesion in animals
Description	The discovery that sponges (Porifera) can fully regenerate from aggregates of dissociated cells launched them as one of the earliest experimental models to study the evolution of cell adhesion and allorecognition in animals. This process depends on an extracellular glycoprotein complex called the Aggregation Factor (AF), which is composed of proteins thought to be unique to sponges. We used label-free quantitative proteomics to identify additional AF components and interacting proteins in the classical model, Clathria prolifera, and compared them to proteins involved in cell interactions in Bilateria. Our results confirm that the MAFp3/p4 proteins are the primary components of the AF, but implicate related proteins with calx-beta and wreath domains as additional components. Using AlphaFold, we unveiled close structural similarities of AF components to protein domains in other animals, previously masked by the mutational decay of sequence similarity. The wreath domain, believed to be unique to the AF, was predicted to contain a central beta-sandwich of the same organization as the vWFD domain (also found in extracellular, gel-forming glycoproteins in other animals). Additionally, many co-purified proteins share a conserved C-terminus, containing divergent Ig and Fn3 domains predicted to serve as an AF-interaction interface. One of these proteins, MAFAP1, resembles immunoglobulin superfamily cell adhesion molecules (IgCAMs) and we hypothesize that it may function to link the AF to the surface of cells. Our results highlight the existence of an ancient toolkit of conserved protein domains regulating cell-cell and cell-ECM interactions in all animals, and likely reflect a common origin of cell adhesion and allorecognition.
HostingRepository	PRIDE
AnnounceDate	2025-06-23
AnnouncementXML	Submission_2025-06-22_16:07:05.670.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fabian Ruperti
SpeciesList	scientific name: Clathria prolifera; NCBI TaxID: 1190602;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-21 05:03:47	ID requested
⏵ 1	2025-06-22 16:07:06	announced

10.1073/pnas.2409125121;

Ruperti F, Dzieciatkowska M, Pankey MS, Asensio CS, Anselmetti D, Fern, à, ndez-Busquets X, Nichols SA, Proteomic analysis of the sponge Aggregation Factor implicates an ancient toolkit for allorecognition and adhesion in animals. Proc Natl Acad Sci U S A, 121(52):e2409125121(2024) [pubmed]

submitter keyword: sponge, evolution, allorecognition, aggregation factor, cell-cell adhesion

Scott Nichols
contact affiliation	Associate Professor Department of Biological Sciences University of Denver
contact email	sa.nichols321@gmail.com
lab head
Fabian Ruperti
contact affiliation	EMBL Heidelberg
contact email	fabian.ruperti@embl.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/2025/06/PXD058135

PRIDE project URI

• PRIDE
  1. PXD058135
     1. Label: PRIDE project
     2. Name: Proteomic analysis of the sponge (Porifera) Aggregation Factor implicates an ancient protein domain toolkit for allorecognition and adhesion in animals