Dataset Information

A Suspension Trapping-based Sample Preparation Workflow for Sensitive Plant Phosphoproteomics

ABSTRACT: Plant phosphoproteomics reveals a global view of phosphorylation-mediated signaling in plants, but it remains demanding a high-throughput method with detection sensitivity and quantification accuracy. In general, the indispensable protein precipitation step requiring for interferences removal limited the sensitivity and throughput in plant phosphoproteomics analysis. Though protein precipitation improves the sample purity, the multiple handling steps cause sample loss and process variability. Here we developed a suspension trapping (S-Trap)-based approach, termed tandem S-Trap-IMAC, by integrating a S-Trap micro column with a Fe-IMAC tip for plant phosphoproteomics. In comparing to precipitation-based approach, tandem S-Trap-IMAC method deepened the coverage of Arabidopsis phosphoproteome more than 30% with improved quantification accuracy and short sample processing time compared to the precipitation-based workflow. The tandem S-Trap-IMAC method was further applied to study the abscisic acid (ABA) signaling in Arabidopsis seedlings. Among a total of 24,055 identified phosphopeptides, several key phosphorylation sites on core ABA signaling components were quantified across four time points. The optimized workflow aids in high-throughput phosphoproteome profiling of low-input plant samples.

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

SUBMITTER: Chuan-Chih Hsu

PROVIDER: PXD039933 | JPOST Repository | Mon Aug 28 00:00:00 BST 2023

REPOSITORIES: jPOST

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			Action	DRS
	111478_R3_S1_A227_220527.raw	Raw
	111480_R3_S3_A227_220527.raw	Raw
	111482_R3_S5_A227_220527.raw	Raw
	111483_R3_US1_A227_220527.raw	Raw
	111485_R3_US3_A227_220527.raw	Raw

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Publications

Suspension Trapping-Based Sample Preparation Workflow for In-Depth Plant Phosphoproteomics.

Chen Chin-Wen CW Tsai Chia-Feng CF Lin Miao-Hsia MH Lin Shu-Yu SY Hsu Chuan-Chih CC

Analytical chemistry 20230808 33

Plant phosphoproteomics provides a global view of phosphorylation-mediated signaling in plants; however, it demands high-throughput methods with sensitive detection and accurate quantification. Despite the widespread use of protein precipitation for removing contaminants and improving sample purity, it limits the sensitivity and throughput of plant phosphoproteomic analysis. The multiple handling steps involved in protein precipitation lead to sample loss and process variability. Herein, we deve ...[more]

PMID: 37552764

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Project description:This model is from the article: A thermodynamic switch modulates abscisic acid receptor sensitivity. Dupeux F, Santiago J, Betz K, Twycross J, Park SY, Rodriguez L, Gonzalez-Guzman M, Jensen MR, Krasnogor N, Blackledge M, Holdsworth M, Cutler SR, Rodriguez PL, Márquez JA EMBO J. [2011 Oct; Volume: 30 (Issue: 20 )] Page info: 4171-84 21847091 , Abstract: Abscisic acid (ABA) is a key hormone regulating plant growth, development and the response to biotic and abiotic stress. ABA binding to pyrabactin resistance (PYR)/PYR1-like (PYL)/Regulatory Component of Abscisic acid Receptor (RCAR) intracellular receptors promotes the formation of stable complexes with certain protein phosphatases type 2C (PP2Cs), leading to the activation of ABA signalling. The PYR/PYL/RCAR family contains 14 genes in Arabidopsis and is currently the largest plant hormone receptor family known; however, it is unclear what functional differentiation exists among receptors. Here, we identify two distinct classes of receptors, dimeric and monomeric, with different intrinsic affinities for ABA and whose differential properties are determined by the oligomeric state of their apo forms. Moreover, we find a residue in PYR1, H60, that is variable between family members and plays a key role in determining oligomeric state. In silico modelling of the ABA activation pathway reveals that monomeric receptors have a competitive advantage for binding to ABA and PP2Cs. This work illustrates how receptor oligomerization can modulate hormonal responses and more generally, the sensitivity of a ligand-dependent signalling system. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.