PXD015162-2

PXD015162 is an original dataset announced via ProteomeXchange.

Title	Analysis of the global nuclear proteome and of the nuclear proteome of FAMA-expressing cells in seedlings of Arabidopsis thaliana using TurboID
Description	Identifying 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.
HostingRepository	PRIDE
AnnounceDate	2019-11-27
AnnouncementXML	Submission_2019-11-27_05:59:53.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shouling Xu
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-27 05:09:35	ID requested
1	2019-09-26 07:27:25	announced
⏵ 2	2019-11-27 05:59:54	announced	2019-11-27: Updated project metadata.

Mair A, Xu SL, Branon TC, Ting AY, Bergmann DC, enabled by TurboID. Elife, 8():(2019) [pubmed]

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

Shouling Xu
contact affiliation	Carnegie Institution at Stanford
contact email	sxu@ciw.edu
lab head
Shouling Xu
contact affiliation	Carnegie Institution at Stanford
contact email	sxu@ciw.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD015162
     1. Label: PRIDE project
     2. Name: Analysis of the global nuclear proteome and of the nuclear proteome of FAMA-expressing cells in seedlings of Arabidopsis thaliana using TurboID