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PXD061818

PXD061818 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDecreasing Protein Biotinylation Background in a Diatom Facilitates Proximity Labeling of the Periplastidial Compartment Proteome
DescriptionDiatoms 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.
HostingRepositoryiProX
AnnounceDate2025-03-14
AnnouncementXMLSubmission_2025-06-10_00:11:00.407.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJiahuan 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;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive; timsTOF Pro
Dataset History
RevisionDatetimeStatusChangeLog Entry
02025-03-14 00:18:29ID requested
12025-05-19 19:14:59announced
22025-06-10 00:11:01announced2025-06-10: Add Publication.
Publication List
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]
Keyword List
submitter keyword: TurboID, proximity labeling, algae, Phaeodactylum tricornutum, biotin synthase, protein biotinylation, chloroplast, periplastidial compartment
Contact List
Xiaobo Li
contact affiliationWestlake University
contact emaillixiaobo@westlake.edu.cn
lab head
Jiahuan Zhang
contact affiliationWestlake University
contact emailzhangjiahuan@westlake.edu.cn
dataset submitter
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