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Identification of interactors of Arabidopsis VIN3 and VRN5 proteins in vernalized seedlings

ABSTRACT: The Arabidopsis VEL proteins VIN3 and VRN5 are accessory proteins of the Polycomb Repressive Complex 2 (PRC2). Their function is most well-understood in the epigenetic PRC2-mediated silencing of the floral repressor gene Flowering Locus C (FLC) during prolonged cold (vernalization). To identify protein interactors of VIN3 and VRN5, also dependent on their C-terminal VEL domains, we used stable Arabidopsis transgenic lines expressing VIN3-GFP WT, VIN3-GFP deltaVEL, VRN5-SYFP2 WT and VRN5-SYFP2 deltaVEL under endogenous promoters to perform native co-immunoprecipitation assays in seedlings vernalized for six weeks at 5 °C. Non-transgenic Col-FRI was used as a negative control.

INSTRUMENT(S):

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

TISSUE(S): Seedling

SUBMITTER: Gerhard Saalbach

LAB HEAD: Caroline Dean

PROVIDER: PXD048844 | Pride | 2025-08-28

REPOSITORIES: Pride

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			Action	DRS
	231212_01.raw	Raw
	231212_01_2.msf	Msf
	231212_01_2.mzML	Mzml
	231212_01_2.mzid.gz	Mzid
	231212_02.raw	Raw

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1 - 5 of 19

Publications

VEL-dependent polymerization maintains the chromatin association of Polycomb proteins for the switch to epigenetic silencing.

Schulten Anna A Jang Geng-Jen GJ Payne-Dwyer Alex A Fiedler Marc M Nielsen Mathias L ML Mateo-Bonmatí Eduardo E Bienz Mariann M Leake Mark C MC Dean Caroline C

Molecular cell 20250825 17

Multivalent protein-chromatin interactions facilitated by higher-order protein assemblies are emerging as a crucial theme in eukaryotic gene regulation. However, understanding the underlying mechanisms in their functional context remains challenging. Arabidopsis VEL proteins assemble biomolecular condensates by head-to-tail polymerization. Here, we dissect the role of VEL polymerization domains in conferring the epigenetic switch to Polycomb repressive complex 2 (PRC2) silencing at Arabidopsis F ...[more]

PMID: 40858112

Similar Datasets

: Identification of interactors of Arabidopsis VIN3 wildtype and VIN3 chimeric mutant protein in vernalized seedlings

Project description:The Arabidopsis VEL proteins VIN3 and VRN5 are accessory proteins of the Polycomb Repressive Complex 2 (PRC2). Their function is most well-understood in the epigenetic PRC2-mediated silencing of the floral repressor gene Flowering Locus C (FLC) during prolonged cold (vernalization). To identify protein interactors of VIN3 and VIN3 chimeric mutant protein carrying VRN5VEL instead of VIN3VEL, we used stable Arabidopsis transgenic lines expressing VIN3-GFP WT and VIN3-GFP VRN5VEL under endogenous promoters to perform native co-immunoprecipitation assays in seedlings vernalized for six weeks at 5 °C. Non-transgenic Col-FRI was used as a negative control.

2025-08-28 | PXD064199 | Pride

VRN1-associated proteins in Arabidopsis thaliana plants during cold exposure

Project description:The epigenetic silencing of the Arabidopsis floral repressor gene FLOWERING LOCUS C (FLC) is induced by a prolonged period of cold and promotes the developmental transition to flowering post-cold. FLC silencing requires the function of VRN1, a non-sequence-specific DNA binding protein. Here, we used Arabidopsis seedlings subjected to cold, carrying a FLAG-tagged VRN1 under its endogenous promoter in the vrn1FRI mutant background. We performed FLAG immunoprecipitation followed by mass spectrometry (IP-MS) on crosslinked tissue. The proteomics analysis revealed several proteins that support the role of VRN1 as a chromatin regulator. The identified proteins associated with VRN1 in vivo also support its contribution to gene silencing.

2025-05-07 | PXD060769 | Pride

VRN1-associated proteins in Arabidopsis thaliana

Project description:The epigenetic silencing of the Arabidopsis floral repressor gene FLOWERING LOCUS C (FLC) is induced by a prolonged period of cold and promotes the developmental transition to flowering post-cold. FLC silencing requires the function of VRN1, a non-sequence-specific DNA binding protein. Here, we used Arabidopsis seedlings growing at ambient temperature carrying a FLAG-tagged VRN1 under its endogenous promoter in the vrn1FRI mutant background. We performed FLAG immunoprecipitation followed by mass spectrometry (IP-MS) on crosslinked tissue. The proteomics analysis revealed several proteins that support the role of VRN1 as a chromatin regulator. The identified proteins associated with VRN1 in vivo also support its contribution to gene silencing.

2025-05-07 | PXD054597 | Pride

Co-immuno precipitation of the aphid saliva protein Mp10 and the plant de-ubiquitinating enzyme AMSH2

Project description:This dataset corresponds to experiments described in the manuscript “The conserved aphid saliva chemosensory protein effector Mp10 targets plant AMSH deubiquitinases at cellular membranes to suppress pattern-triggered immunity”, and includes mass spectrometry analysis of Co-immuno-precipitation experiments of membrane-enriched fractions of Nicotiana benthamiana leaves transiently co-expression the aphid saliva effector protein Mp10 and it’s interacting plant target AMSH2.

2024-11-06 | PXD057543 | Pride

Co-immuno precipitation of the aphid saliva protein Mp10 and the plant de-ubiquitinating enzyme AMSH2

2024-11-06 | PXD055941 | Pride

The proximity interactome of the peach-potato aphid (Myzus persicae) cathepsin B in Arabidopsis thaliana

Project description:The peach-potato aphid, Myzus persicae, is a globally pervasive crop pest, primarily reproducing clonally, allowing single females to rapidly generate exact copies of themselves. Moreover, its extreme polyphagy enables it to colonize over 400 plant species. Studies on the genetic underpinnings of M. persicae colonization have highlighted the differential expression and transcriptional regulation of a family of cysteine proteases, Cathepsin B (CathB), in response to various plant species. Among all M. persicae CathB proteins, CathB6 is most highly expressed in aphids on A. thaliana and most abundantly detected in M. persicae oral secretions. To investigate the potential plant target of CathB6 in A. thaliana, we conducted TurboID-based proximity labelling and MS (PL-MS).

2024-11-18 | PXD057789 | Pride

A CPSF-like phosphatase module links transcription termination to chromatin silencing

Project description:Aiming to find the connection between RNA processing and chromatin remodelling, we found that a complex removing activating histone marks at FLC named FLD complex interacts with ARPF1, one of the homologs in Arabidopsis of the yeast Swd2. In this experiment, we used a FLAG-tagged version of the ARPF1 protein to find its protein partners.

2024-05-13 | PXD049114 | Pride

The salivary proteome of the green peach aphid/peach-potato aphid (Myzus persicae) (Sulzer, 1776) (Hemiptera, Aphididae).

Project description:The green peach aphid/peach-potato aphid Myzus persicae can colonize hundreds of plant species, an ability that is in part due to the delivery of saliva proteins – often referred to as effectors – into the host plant that suppress plant defence. As a generalist herbivore with a remarkable ability to colonize new host plants M. persicae represents an outstanding model system for studying the molecular mechanisms underlying plant-insect interactions. Recent advancements in mass spectrometry instrumentation and database search software along with a new high-quality reference genome assembly for M. persicae and a simplified method for improved aphid saliva recovery, collectively enhance the detection of saliva proteins with unprecedented sensitivity and specificity.

2024-08-28 | PXD055051 | Pride

o The CutRS two-component system controls the Streptomyces secretion stress response by monitoring extracellular disulphide bond formation

Project description:o Translocating unfolded proteins across cell membranes is essential in all domains of life and requires the conserved Sec machinery. In bacteria, Sec substrates fold on the extracellular face of the cytoplasmic membrane and misfolding triggers a stress response that involves production of HtrA-family proteins that act as dual function chaperone-proteases. In monoderm bacteria such as Streptomyces species, Sec substrates are translocated directly into the oxidising environment and typically contain even numbers of cysteine residues that form disulphide bonds to help the proteins fold. The Streptomyces secretion stress response is mediated by conserved two-component systems CssRS and CutRS and here we provide evidence that CutS senses disulphide bond formation via two conserved cysteine residues in its extracellular sensor domain. Breaking this disulphide bond activates CutRS and modulates the production of the quality control chaperones HtrA3 and HtrB. To our knowledge this represents a unique extracellular a sensing mechanism in bacteria.

2025-08-09 | PXD051851 | Pride

o Differential temporal release and lipoprotein loading in B. thetaiotaomicron bacterial extracellular vesicles

Project description:o Bacterial extracellular vesicles (BEVs) contribute to stress responses, quorum sensing, biofilm formation, and interspecies and interkingdom communication. However, the factors that regulate their release and heterogeneity are not well understood. We set out to investigate these factors in the common gut commensal Bacteroides thetaiotaomicron by studying BEV release throughout their growth cycle. Utilising a range of methods, we demonstrate that vesicles released at different stages of growth have significantly different composition, with early vesicles enriched in specifically released outer membrane vesicles (OMVs) containing a larger proportion of lipoproteins, while late phase BEVs primarily contain lytic vesicles with enrichment of cytoplasmic proteins. Furthermore, we demonstrate that lipoproteins containing a negatively charged signal peptide are preferentially incorporated in OMVs. We use this observation to predict all Bacteroides thetaiotaomicron OMV enriched lipoproteins and analyse their function. Overall, our findings highlight the need to understand media composition and BEV release dynamics prior to functional characterisation and define the theoretical functional capacity of Bacteroides thetaiotaomicron OMVs.

2024-01-22 | PXD043651 | Pride

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