Dataset Information

Dimethyl labeling-based quantitative PTM proteomic analysis of drought-regulated phosphoproteomes in soybean drought-tolerant cultivar

ABSTRACT: The isotopic dimethyl labeling-based quantitative post-translational modification proteomics was applied to study the phosphoproteomic changes associated with the drought responses of two contrasting soybean cultivars. A total of 9,457 non-redundant, unambiguous, label-independent and repeatable phosphopeptides were subsequently identified from six experimental replicates, corresponding to 9,234 of deduced unique phosphoproteins. These soybean proteins contain a total of 20,880 phosphosites, 84.9% of which were found to be novel phosphosites of the soybean phosphoproteome. The overly post-translationally modified proteins is 2.05% of the phosphoproteins identified. Most of these extensively phosphorylated proteins are photoreceptors, mRNA-, histone- and phospholipid-binding as well as serine/threonine/tyrosine protein kinase/phosphatases. The subgroup population distribution of phosphoproteins over the number of the phosphosite of phosphoprotein follows the exponential decay law, Y=4.13e^(-0.098X)-0.04. From 218 significantly regulated unique phosphopeptide groups, 188 significantly regulated phosphoproteins were found, and they are enriched in biological functions of water transport and deprivation, methionine metabolic process, photosynthesis/light reaction, and response to cadmium ion, osmotic stress and ABA under drought treatment. A total of 15 and 20 drought-tolerant cultivar significantly regulated phosphoproteins are transcription factors and protein kinases/phosphatases, respectively. More than 50% of these phosphoproteins are considered to be novel regulatory components, presumably mediating the development of the soybean drought tolerance under water deprivation process. The association of five randomly selected phosphoproteins with the drought response was corroborated with the qRT-PCR method.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Glycine Max

TISSUE(S): Plant Cell

SUBMITTER: Shuaijian DAI

LAB HEAD: Ning, Li

PROVIDER: PXD022794 | Pride | 2021-09-09

REPOSITORIES: Pride

ACCESS DATA

Publications

Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars.

Moradi Atieh A Dai Shuaijian S Wong Emily Oi Ying EOY Zhu Guang G Yu Fengchao F Lam Hon-Ming HM Wang Zhiyong Z Burlingame Al A Lin Chengtao C Afsharifar Alireza A Yu Weichuan W Wang Tingliang T Li Ning N

Biomolecules 20210816 8

Isotopically dimethyl labeling was applied in a quantitative post-translational modification (PTM) proteomic study of phosphoproteomic changes in the drought responses of two contrasting soybean cultivars. A total of 9457 phosphopeptides were identified subsequently, corresponding to 4571 phosphoprotein groups and 3889 leading phosphoproteins, which contained nine kinase families consisting of 279 kinases. These phosphoproteins contained a total of 8087 phosphosites, 6106 of which were newly ide ...[more]

PMID: 34439883

Similar Datasets

Project description:Proteomics, the temporal study of proteins expressed by an organism, is a powerful technique that can reveal how organisms respond to biological perturbations, such as disease and environmental stress. Yet, the use of proteomics for addressing ecological questions has been limited, partly due to inadequate protocols for the sampling and preparation of animal tissues from the field. Although RNAlater is an ideal alternative to freezing for tissue preservation in transcriptomics studies, its suitability for the field could be more broadly examined. Moreover, existing protocols require samples to be preserved immediately to maintain protein integrity, yet the effects of delays in preservation on proteomic analyses have not been thoroughly tested. Hence, we optimised a proteomic workflow for wild-caught samples. First, we conducted a preliminary in-lab test using SDS-PAGE analysis on aquaria-reared Octopus berrima confirming that RNAlater can effectively preserve proteins up to 6 h after incubation, supporting its use in the field. Subsequently, we collected arm tips from wild-caught Octopus berrima and preserved them in homemade RNAlater immediately, 3 h, and 6 h after euthanasia. Processed tissue samples were analysed by liquid chromatography tandem mass spectrometry to ascertain protein differences between time delay in tissue preservation, as well as the influence of sex, tissue type, and tissue homogenisation methods. Over 3500 proteins were identified from all tissues, with bioinformatic analysis revealing protein abundances were largely consistent regardless of sample treatment. However, nearly 10 % additional proteins were detected from tissues homogenised with metal beads compared to liquid nitrogen methods, indicating the beads were more efficient at extracting proteins. Our optimised workflow demonstrates that sampling non-model organisms from remote field sites is achievable and can facilitate extensive proteomic coverage without compromising protein integrity.

Project description:Ubash3b, also known as suppressor of T-cell receptor signaling or Sts-1, is an ill-studied atypical tyrosine phosphatase with ubiquitin binding ability. In our previous study, we hypothesized that Ubash3b plays an inhibitory role in BCR-ABL signaling through binding and dephosphorylating BCR-ABL and its interactors. The Hantschel lab recently solved the crystal structures of the p210 PH and DH domains, which are absent in the p190 variant, and demonstrated that loss-of-function mutations in the PH domain altered BCR-ABL localization, thereby reducing the interaction between Ubash3b and p2104. Taken together, this suggests differential subcellular localization of Ubash3b as a mechanism by which it interacts more strongly with p201 as compared to p190. To better understand the global impact Ubash3b has on p210, its direct kinase substrates and proteins in its phosphotyrosine signaling network, we have taken an integrative approach by combining global phosphotyrosine profiling, proximity-dependent biotinylation (BioID) and total protein analysis to investigate p210 signaling upon Ubash3b knockdown (KD). The BioID system was used to characterize Ubash3b function in p210 signaling by examining its interactome. Importantly, in all of our BioID experiments, we employed a newly technique that we have recently developed, Biotinylation Site Identification Technology (BioSITe), which directly identifies biotinylated peptides thereby increasing the reliability of the identified interactors. Here, we additionally used short hairpin RNA (shRNA) interference and generated Ubash3b knock-down (KD) and non-targeting control shRNA lines in Ba/F3 BirA*-p210 cells. Ubash3b expression was reduced >90 % in the KD cells and had a substantial effect on global tyrosine phosphorylation and on the interactome of p210. Of the 1,421 unique tyrosine phosphorylation sites identified from 830 proteins, 379 sites (from 286 proteins) exhibited a substantial increase (ÃƒÂ¢Ã¢â‚¬Â°Ã‚Â¥2-fold) in tyrosine phosphorylation upon Ubash3b KD cells compared to control cells. To date, the interactome of Ubash3b has not been extensively investigated, however, some examination of Ubash3b in the context p210 signaling has been undertaken. We designed constructs of C-terminal BirA* tagged full length Ubash3b and a deletion mutant lacking the UBA and SH3 domains leaving only the phosphatase domain tethered to BirA*. A comparative analysis of the core interactors of p210 from previous studies and Ubash3b interactome from the current study revealed 36 proteins that interact with both p210 and Ubash3b.

Dataset Information

Dimethyl labeling-based quantitative PTM proteomic analysis of drought-regulated phosphoproteomes in soybean drought-tolerant cultivar

Publications

Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure