PXD061818

PXD061818 is an original dataset announced via ProteomeXchange.

Title	Decreasing Protein Biotinylation Background in a Diatom Facilitates Proximity Labeling of the Periplastidial Compartment Proteome
Description	Diatoms are ecologically and industrially significant microalgae, crucial for global carbon fixation and biotechnological applications. Their complex plastid membrane structures, resulting from secondary endosymbiosis, remain poorly characterized, particularly the periplastidial compartment (PPC). Proximity labeling techniques like TurboID and APEX2 are powerful tools for identifying protein-protein interactions and spatial proteomes, but their application in diatoms is hindered by unknown factors. In this study, we identified and characterized the high biotinylation background in diatoms, including Phaeodactylum tricornutum and other microalgae, which significantly impairs the effectiveness of proximity labeling. We also characterized the biotin synthase (BIOB) in P. tricornutum, a key enzyme in biotin biosynthesis. By using a biob mutant to deplete biotin, we successfully decreased the biotinylation background, enhancing the sensitivity and quality of proximity labeling. Applying this approach to the PPC, we identified several proteins previously undetectable through bioinformatics and confocal microscopy. Our results demonstrate that inhibiting biotin synthesis improves proximity labeling, providing a robust method for studying protein interactions and spatial proteomics in diatoms. The case study of the improved proximity labeling system in PPC also increased our understanding of the complex plastids derived from higher-order endosymbiosis.
HostingRepository	iProX
AnnounceDate	2025-03-14
AnnouncementXML	Submission_2025-06-10_00:11:00.407.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jiahuan Zhang
SpeciesList	scientific name: Phaeodactylum tricornutum; NCBI TaxID: 2850; scientific name: Thalassiosira pseudonana; NCBI TaxID: 35128; scientific name: Nannochloropsis oceanica; NCBI TaxID: 145522; scientific name: Arabidopsis thaliana; NCBI TaxID: 3702; scientific name: Nicotiana benthamiana; NCBI TaxID: 4100; scientific name: Oryza sativa; NCBI TaxID: 4530; scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive; timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-14 00:18:29	ID requested
1	2025-05-19 19:14:59	announced
⏵ 2	2025-06-10 00:11:01	announced	2025-06-10: Add Publication.

Zhang J, Cao T, Jiang Y, Feng Y, Guo K, Yang J, Zhang H, Li X, Decreasing protein biotinylation background in a diatom facilitates proximity labeling of the periplastidial compartment proteome. Plant J, 122(5):e70259(2025) [pubmed]

submitter keyword: TurboID, proximity labeling, algae, Phaeodactylum tricornutum, biotin synthase, protein biotinylation, chloroplast, periplastidial compartment

Xiaobo Li
contact affiliation	Westlake University
contact email	lixiaobo@westlake.edu.cn
lab head
Jiahuan Zhang
contact affiliation	Westlake University
contact email	zhangjiahuan@westlake.edu.cn
dataset submitter

iProX dataset URI