PXD038515-2

PXD038515 is an original dataset announced via ProteomeXchange.

Title	TurboID reveals the interaction network of VESICLE-INDUCING PROTEIN IN PLASTIDS (VIPPs) in Chlamydomonas reinhardtii
Description	In Chlamydomonas reinhardtii, VIPP1 and VIPP2 play a role in the sensing and coping with membrane stress and in thylakoid membrane biogenesis. To gain more insight into these processes, we aimed to identify proteins interacting with VIPP1/2 in the chloroplast under ambient and H2O2 stress conditions and chose proximity labeling (PL) for this purpose. While PL with APEX2 and BioID proved to be inefficient, TurboID resulted in significant biotinylation in vivo, which could be enhanced by exogenously added biotin. Using TurboID-mediated PL with VIPP1/2 as baits we could confirm known interactions of VIPP1 with VIPP2, HSP70B and CDJ2. Novel proteins in the VIPP1/2 interaction network can be grouped into proteins involved in the biogenesis of thylakoid membrane complexes and the regulation of photosynthetic electron transport. A third group comprises 11 proteins of unknown function whose genes are upregulated under chloroplast stress conditions. We named these proteins VIPP PROXIMITY LABELING (VPL1-11) and confirmed the proximity of VIPP1 and VPL2 in a reciprocal experiment. Our results demonstrate the robustness of TurboID-mediated PL for studying protein interaction networks in the chloroplast of Chlamydomonas and pave the way for targeted analyses of the functions of VIPPs in thylakoid biogenesis and chloroplast stress responses.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:27:21.050.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Frederik Sommer
SpeciesList	scientific name: Chlamydomonas reinhardtii; NCBI TaxID: 3055;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-02 06:02:06	ID requested
1	2024-01-26 11:03:13	announced
⏵ 2	2024-10-22 06:27:24	announced	2024-10-22: Updated project metadata.

Kreis E, K, ö, nig K, Misir M, Niemeyer J, Sommer F, Schroda M, TurboID reveals the proxiomes of Chlamydomonas proteins involved in thylakoid biogenesis and stress response. Plant Physiol, 193(3):1772-1796(2023) [pubmed]

10.1093/plphys/kiad335;

submitter keyword: APEX2, VIPP2, VIPP1, Chlamydomonas reinhardtii,TurboID, LC-MS/MS

Michael Schroda
contact affiliation	TU Kaiserslautern Dep. Biology Molecular Biotechnology & Systems Biology Paul-Ehrlich-Straße 23, Room 103 67663 Kaiserslautern Germany
contact email	schroda@bio.uni-kl.de
lab head
Frederik Sommer
contact affiliation	Technische Universität Kaiserslautern
contact email	frsommer@bio.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/2024/01/PXD038515

PRIDE project URI

• PRIDE
  1. PXD038515
     1. Label: PRIDE project
     2. Name: TurboID reveals the interaction network of VESICLE-INDUCING PROTEIN IN PLASTIDS (VIPPs) in Chlamydomonas reinhardtii