<<< Full experiment listing

PXD015162

PXD015162 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAnalysis of the global nuclear proteome and of the nuclear proteome of FAMA-expressing cells in seedlings of Arabidopsis thaliana using TurboID
DescriptionIdentifying specific protein interactors and spatially or temporally restricted local proteomes contributes significantly to our understanding of cellular processes in virtually all aspects of life. Obtaining such data is challenging, especially when the protein, cell type or event of interest is rare. In recent years, different proximity labeling techniques have been developed that have greatly improved our ability to tackle these questions. However, while effective in mammalian systems, use in plants has been extremely limited due to technical challenges. Recent technological improvements in the form of two highly active versions of the biotin ligase BirA* (TurboID and miniTurboID), prompted us to test this new system on two challenging but widely asked questions in plants: what are interaction partners of low-abundant proteins and what are organellar proteomes in rare and transient cell types. To address the second question, we used nuclei of developing stomatal guard cells, which express the transcription factor FAMA, as our test case. FAMA is a master regulator of guard cell development and promotes terminal differentiation of the guard cell precursor by both activating and repressing hundreds of genes. FAMA-expressing young guard cells are rare and restricted to the epidermis of developing aerial tissues, which makes them a good model system to test TurboID applicability under material-limiting conditions. For this experiment, young Arabidopsis seedlings expressing nuclear TurboID under the FAMA or UBIQUITIN10 (UBQ10) promoter were treated with biotin to label nuclear proteomes. Col-0 wild type was used as controls for unspecific binding of proteins to the beads. Biotinylated proteins were isolated by affinity purification with streptavidin-coupled beads and identified by LC-MS/MS. By targeting TurboID to the nucleus we were able to purify nuclear proteins with relatively high specificity. Enrichment of FAMA-stage specific proteins, when nuclear TurboID was driven by the FAMA compared to the UBQ10 promoter, supports general applicability of TurboID for identification of subcellular proteomes.
HostingRepositoryPRIDE
AnnounceDate2019-11-27
AnnouncementXMLSubmission_2019-11-27_05:59:53.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterShouling Xu
SpeciesList scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-08-27 05:09:35ID requested
12019-09-26 07:27:25announced
22019-11-27 05:59:54announced2019-11-27: Updated project metadata.
Publication List
Mair A, Xu SL, Branon TC, Ting AY, Bergmann DC, enabled by TurboID. Elife, 8():(2019) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: Plant, seedling, Arabidopsis thaliana, bHLH transcription factor, FAMA, stomatal guard cell, nuclear proteome, proximity labeling, TurboID, streptavidin affinity purification, LC-MS/MS
Contact List
Shouling Xu
contact affiliationCarnegie Institution at Stanford
contact emailsxu@ciw.edu
lab head
Shouling Xu
contact affiliationCarnegie Institution at Stanford
contact emailsxu@ciw.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
PRIDE project URI
Repository Record List
[ + ]