Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pupylation-based proximity labelling reveals regulatory factors in cellulose biosynthesis in Arabidopsis

ABSTRACT: We introduce pupylation-based proximity labelling (PUP-IT) as a tool for protein interaction detection in plant biology. We show that PUP-IT readily confirmed and extended protein interactions for several known protein complexes, across different types of plant systems.

INSTRUMENT(S):

ORGANISM(S): Nicotiana Tabacum (common Tobacco) Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Cotyledon, Cell Suspension Culture, Root, Leaf

SUBMITTER: Staffan Persson

LAB HEAD: Staffan Persson

PROVIDER: PXD048346 | Pride | 2025-01-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20210929_PRI_TIMS4_PRIEvo1_P091_R0266_44min_S1_S2-A1_1_2755.d.zip	Other
	20210929_PRI_TIMS4_PRIEvo1_P091_R0266_44min_S2_S2-A2_1_2756.d.zip	Other
	20210929_PRI_TIMS4_PRIEvo1_P091_R0266_44min_S4_S2-A4_1_2758.d.zip	Other
	20210929_PRI_TIMS4_PRIEvo1_P091_R0266_44min_S5_S2-A5_1_2759.d.zip	Other
	20210929_PRI_TIMS4_PRIEvo1_P091_R0266_44min_S7_S2-A7_1_2761.d.zip	Other

Items per page:

1 - 5 of 38

Similar Datasets

Identification of potential interactors of NKS1 and QUA1

Project description:Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Pectins are made in the Golgi apparatus by the coordinated action of transporters and enzymes. Here, in this project, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. We did an immunoprecipitation-mass spectrometry (IP-MS) analysis to identify potential interactors of NKS1. And we also performed an IP-MS analysis of QUA1, which is one of the interactors of NKS1.

2024-03-20 | PXD047727 | Pride

The adaptor protein AP-3β disassembles heat-induced stress granules via 19S RP-associated deubiquitylation in Arabidopsis

Project description:To survive under adverse conditions, plants form stress granules (SGs) to temporally store mRNA and halt translation as a primary response. Dysregulation in SG disassembly can have detrimental effects on plant survival after stress release, yet the underlying mechanism remains poorly understood. Using Arabidopsis as a model system, we demonstrated that the AP-3 subunit AP-3β participates in heat response independently of its conventional role in vacuolar transportinteracts with the SG core RNA-binding proteins TSN1/2 in vivo and in vitro. We also showed that AP-3β is rapidly recruited to SGs upon heat induction and plays a key role in SG disassembly after heat release. We also discovered thatGenetic evidences support that AP-3β serves as an adaptor to recruit the 19S regulatory particle (RP) of the proteasome to SGs upon heat induction. Notably, the 19S RP promotes SG disassembly through RP-associated deubiquitylation, independent of its proteolytic catalytic activity. This deubiquitylation process of SG components is crucial for translation reinitiation and growth recovery after heat release. Our findings shed light on the non-proteolytic catalytic function of the RP in regulating SG dynamics disassembly and reveal highlight the importance of endomembrane proteins in supporting RNA granule dynamics in plant cells.a non-degradation mechanism for cellular adaptation to environmental stresses.

2025-01-24 | PXD058194 | Pride

Comprehensive chromatome profiling identifies metabolic enzymes on chromatin in healthy and cancer cells

Project description:we have performed a subcellular fractionation protocol, which enriches the chromatin-bound proteins across a panel of tissue types, both for cancerous and untransformed cells. Indeed we identify both metabolic enzymes which are consistently moonlighting on chromatin, while others are tissue and cancer specific. By comparing the chromatin levels of proteins with their essentiality, we identify enzymes which perform essential functions on chromatin and thus could represent cancer specific metabolic vulnerabilities.

2025-11-13 | PXD047504 | Pride

Proteome of Agave angustifolia Haw.: insights about metabolism of amino acids in albino plantlets

Project description:Amino acids (AA) are essential molecules for life because they are precursors for the synthesis of proteins and other organic compounds. Their metabolism in plants involves more than one cellular compartment, among which the chloroplast plays a key role. From the 20 essential AA, ten (Arg, Lys, Thr, Leu, Ile, Val, Trp, Phe, Tyr and His) are only synthesized in the plastids and seven (Asp, Cys, Gln, Glu, Gly, Ser and Met) can be synthesized in both chloroplast and other parts of the cell. Despite knowing the roles of AA in plant physiology, little has been assessed in plants with albino phenotypes, lacking chloroplasts. To assess the effect of chloroplast biogenesis disturbances on AA metabolism in albino and variegated somaclonal variations of Agave angustifolia Haw., a comparative proteomic based TMT- synchronous precursor selection (SPS)-MS3 strategy was used to determine the status of AA biosynthetic pathways. Besides the 20 essential AA was quantified to underpin proteomics finding. A total of 2,442 different proteins were identified in the proteome of the somaclonal variants, from which 82 correspond to enzymes participating in AA biosynthesis. From these 82, 32 proteins were differentially accumulated. On the other hand, the concentration of 16 and 12 of the AA synthesized by the chloroplast were over-accumulated in the variegated and albino somaclonal variant, respectively. In plantlets devoid of functional chloroplasts, there is a surprising increase of AA and key enzymes of the AA biosyntethic pathways, compared to green plantlets. This could suggest que la activation of AA biosynthesis is key to sustaining albino and variegated plantlets survival that lack chloroplasts.

2024-01-29 | PXD039512 | Pride

Stable Isotope Labeling using Amino acids in Cell culture (SILAC) (local data base)

Project description:Stable Isotope Labeling using Amino acids in Cell culture (SILAC) of CT26 control and IF1-ablated cells

2023-10-24 | PXD038109 | Pride

Stable Isotope Labeling using Amino acids in Cell culture (SILAC) (mus.musculus)

Project description:Targeted SILAC determination of the rate of synthesis of proteins involved in mitochondrial structure and ETC activity in CT26 control and IF1-ablated cell lines

2023-10-24 | PXD038108 | Pride

Global analysis of lysine 2-hydroxyisobutyrylation in wheat leaf

Project description:Lysine 2-hydroxyisobutyrylation (Khib) is a novel naturally occurring PTM, which is firstly discovered in histone. The system Khib detection at proteomics level has been performed in various species and tissues for the function and role characterization of Khib in biological activities. However, the Khib study in plant species is relatively less and the plant root, one of the critical plant organ, haven’t been studied. In the present study, the first root tissues lysine 2-hydroxyisobutyrylome analysis was performed in wheat specie with antibody immunoprecipitation affinity and high resolution mass spectrometry-based proteomics. Bioinformatics analyses including function classification, subcellular location predication, gene ontology enrichment and pathway enrichment were conducted to demonstrate the roles of these Khib sites and proteins in wheat root. In total, 6328 Khib sites corresponding to 2186 proteins were repeatedly identified in three replicates. These Khib proteins showed a wide subcellular location distribution while cytoplasm was the primary subcellular compartment where Khib protein located. Function and pathways characterization of these Khib proteins indicated that many cellular functions and metabolism pathways potentially were affected by this modification. Protein and amino acid metabolism related process may be regulated by Khib, especially ribosome activities and proteins biosynthesis process. Carbohydrate metabolism and energy production related processes including glycolysis/gluconeogenesis, TCA cycle and oxidative phosphorylation pathways were also the hotspots where protein Khib occurred. Our work illustrated the potential regulation role of Khib in wheat leaf physiology and biology, which could be used as a useful reference for Khib studies in plant leaf.

2021-06-08 | PXD020788 | Pride

Data-independent immunopeptidomics discovery of low-abundant bacterial epitopes

Project description:Mass spectrometry-based immunopeptidomics is a powerful approach to uncover peptides presented by human leukocyte antigen (HLA) molecules and serves as an important discovery tool guiding vaccine design and immunotherapies. While data-dependent acquisition (DDA) has been the standard for navigating through the complexity associated with non-enzymatic immunopeptide database searches, data-independent acquisition (DIA) is increasingly adopted in immunopeptidomics research. In this work, we compare diaPASEF to conventional ddaPASEF in terms of global immunopeptidome profiling and bacterial epitope discovery of the model intracellular pathogen Listeria monocytogenes. We show that DIA spectrum-centric searches of pseudo-MS/MS spectra complements DDA analysis by uncovering additional human and bacterial immunopeptides. Furthermore, we leveraged the latest DIA-NN release for proteome-wide predicted spectral library searches of all HLA class I peptides, scoring approximately 150 million immunopeptide peptide precursors. This approached outperformed other methods in identification of MHC class I peptides and recovered low-abundant peptide precursors missed by other methods. Taken together, our results demonstrate how both DIA spectrum- and peptide-centric immunopeptidomics analysis are promising strategies to recover low-abundant immunopeptides.

2025-08-21 | PXD063560 | Pride

Synthetic peptides - Data-independent immunopeptidomics discovery of low-abundant bacterial epitopes

Project description:Synthetic peptide standards for validation of diaPASEF-only immunopeptides of Listeria monocytogenes. More info see PXD063560.

2025-09-16 | PXD068414 | Pride

A strategy to disentangle direct and indirect effects on (de)phosphorylation by chemical modulators of the phosphatase PP1 in complex cellular contexts

Project description:Chemical activators and inhibitors are useful probes to identify substrates and downstream effects ofenzymes; however, due to the complex signaling environment within cells, it is challenging to distinguishbetween direct and indirect effects. This is particularly the case for phosphorylation, where a single(de)phosphorylation event can trigger rapid changes in many other phosphorylation sites. An additionalcomplication arises when a single catalytic entity, which acts in form of many different holoenzymes withdifferent substrates, is activated or inhibited, as it is unclear which holoenzymes are affected, and in turnwhich of their substrates are (de)phosphorylated. Direct target engaging MS-based technologies to studytargets of drugs do not address these challenges. Here, we tackle this by studying the modulation of proteinphosphatase-1 (PP1) activity by PP1-disrupting peptides (PDPs), as well as their selectivity toward PP1, byusing a combination of mass spectrometry-based experiments. By combining cellular treatment with the PDPwith in vitro dephosphorylation by the enzyme, we identify high confidence substrate candidates and beginto separate direct and indirect effects. Together with experiments analyzing which holoenzymes areparticularly susceptible to this treatment, we obtain insights into the effect of the modulator on the complexnetwork of protein (de)phosphorylation. This strategy holds promise for enhancing our understanding of PP1in particular and, due to the broad applicability of the workflow and the MS-based read-out, of chemicalmodulators with complex mode of action in general.

2024-01-12 | PXD044415 | Pride