Dataset Information

Proximity labeling – LC/MS-MS with TurboID-ATG8e/atg2-1 Arabidopsis seedlings

ABSTRACT: By employing a proximity labeling approach using Arabidopsis ATG8e tagged with TurboID as bait in atg2-1 background, we discovered a protein family of unknown function, consisting of two homologs (AT4G02880 and AT1G03290). Both proteins contain coil-coiled domains that are predicted to be closely related to the mammalian ELKS/Rab6-interacting/CAST (ERC) protein family, which acts as a central scaffold for forming a multidomain protein complex involved in synaptic vesicle secretion. As there is no available information about this protein family in plants, we have named these two proteins as ERC1 and ERC2, respectively.

INSTRUMENT(S):

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Seedling

SUBMITTER: Shouling Xu

LAB HEAD: Shouling Xu

PROVIDER: PXD067352 | Pride | 2025-10-07

REPOSITORIES: Pride

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Publications

Biomolecular condensation of ERC1 recruits ATG8 and NBR1 to drive autophagosome formation for plant heat tolerance.

Chung Ka Kit KK Zhao Ziwei Z Law Kai Ching KC Ma Juncai J Chiang Cheuk Him CH Leung Kwan Ho KH Shrestha Ruben R Wu Yixin Y Li Chaorui C Lee Ka Ming KM Feng Lei L Li Xibao X Wong Kam Bo KB Xu Shou-Ling SL Gao Caiji C Zhuang Xiaohong X

bioRxiv : the preprint server for biology 20240910

Macroautophagy (hereafter autophagy) is essential for cells to respond to nutrient stress by delivering cytosolic contents to vacuoles for degradation via the formation of a multi-layer vesicle named autophagosome. A set of autophagy-related (ATG) regulators are recruited to the phagophore assembly site for the initiation of phagophore, as well as its expansion and closure and subsequent delivery into the vacuole. However, it remains elusive that how the phagophore assembly is regulated under di ...[more]

PMID: 39314317

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Project 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.

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