PXD039700

PXD039700 is an original dataset announced via ProteomeXchange.

Title	Interactome of NbdA containing nanodiscs
Description	Studies of membrane protein-protein interactions are very important to fully understand the biological function of a cell. The solubilization of proteins from the native membrane environment is a critical step in the preparation of membrane proteins that might affect the stability of protein complexes. In this work, we used the amphiphilic diisobutylene / maleic acid copolymer (DIBMA) to create a soluble library of the membrane proteome of the opportunistic pathogen Pseudomonas aeruginosa. Size fractionation of polymer nanodisc-embedded proteins and subsequent mass spectrometry led to the identification of 3358 proteins. The library showed a very good overall coverage compared to previous proteome data. The pattern of size fractionation indicated the preservation of protein complexes in the library. More than 20 previously described complexes, e.g., the SecYEG and Pili complexes, were identified and analyzed for coelution. Although most protein complexes seem to be preserved in the library, the data set does not permit the de novo prediction of protein complexes. However, the experimental approach to identify protein interactions in the soluble library using pulldown assays in combination with mass spectrometry was successful. Employing the membrane phosphodiesterase NbdA, a member of the c-di-GMP network as a bait, 35 novel candidate proteins for interaction were identified. With the ATPase PilB, a novel interaction partner of NbdA was confirmed using the bacterial adenylate cyclase two hybrid assay. Taken together, this work describes the versatility of the soluble membrane proteome library of P. aeruginosa for the investigation of protein interactions and membrane protein complexes.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:03:15.971.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Markus Räschle
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-27 10:49:06	ID requested
1	2023-07-20 11:22:04	announced
⏵ 2	2023-11-14 09:03:16	announced	2023-11-14: Updated project metadata.

Scherhag A, R, ä, schle M, Unbehend N, Venn B, Glueck D, M, ü, hlhaus T, Keller S, P, é, rez Patallo E, Zehner S, Frankenberg-Dinkel N, PAO1 membrane proteome with emphasis on c-di-GMP turnover enzymes. Microlife, 4():uqad028(2023) [pubmed]

submitter keyword: DIBMA polymer, nanodiscs

Markus Räschle
contact affiliation	Molecular genetics, RPTU Kaiserslautern
contact email	raeschle@rhrk.uni-kl.de
lab head
Markus Räschle
contact affiliation	Technical University Kaiserslautern
contact email	raeschle@rhrk.uni-kl.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/2023/07/PXD039700

PRIDE project URI

• PRIDE
  1. PXD039700
     1. Label: PRIDE project
     2. Name: Interactome of NbdA containing nanodiscs