{"database":"iProX","file_versions":[],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Hongwei Xue"],"species":["Arabidopsis Thaliana"],"full_dataset_link":["http://www.iprox.org/page/project.html?id=IPX0004672000"],"submitter_email":["hwxue@sjtu.edu.cn"],"submitter_affiliation":["Shanghai Jiaotong University"],"sample_protocol":[""],"repository":["iProX"],"data_protocol":[""],"pubmed_abstract":["Casein kinase 1 (CK1) is serine/threonine protein kinase highly conserved among eukaryotes, and regulates multiple developmental and signaling events through phosphorylation of target proteins. Arabidopsis early flowering 1 (EL1)-like (AELs) are plant-specific CK1s with varied functions, but identification and validation of their substrates is a major bottleneck in elucidating their physiological roles. Here, we conducted a quantitative phosphoproteomic analysis in data-independent acquisition mode to systematically identify CK1 substrates. We extracted proteins from seedlings overexpressing individual AEL genes (AEL1/2/3/4-OE) or lacking AEL function (all ael single mutants and two triple mutants) to identify the high-confidence phosphopeptides with significantly altered abundance compared to wild-type Col-0. Among these, we selected 3985 phosphopeptides with higher abundance in AEL-OE lines or lower abundance in ael mutants compared with Col-0 as AEL-upregulated phosphopeptides, and defined 1032 phosphoproteins. Eight CK1s substrate motifs were enriched among AEL-upregulated phosphopeptides and verified, which allowed us to predict additional candidate substrates and functions of CK1s. We functionally characterized a newly identified substrate C3H17, a CCCH-type zinc finger transcription factor, through biochemical and genetic analyses, revealing a role for AEL-promoted C3H17 protein stability and transactivation activity in regulating embryogenesis. As CK1s are highly conserved across eukaryotes, we searched the rice, mouse, and human protein databases using newly identified CK1 substrate motifs, yielding many more candidate substrates than currently known, largely expanding our understanding of the common and distinct functions exerted by CK1s in Arabidopsis and humans, facilitating future mechanistic studies of CK1-mediated phosphorylation in different species."],"pubmed_title":["Data-independent acquisition-based global phosphoproteomics reveal the diverse roles of casein kinase 1 in plant development."],"pubmed_authors":["Qu Li L, Liu Moyang M, Zheng Lingli L, Wang Xu X, Xue Hongwei H"],"additional_accession":[]},"is_claimable":false,"name":"Data-Independent Acquisition-Based global phosphoproteomics reveals diverse roles of AELs (Arabidopsis EL1-like) Casein kinase 1 in plant development","description":"Casein kinase 1 (CK1) is a highly conserved and ubiquitous serine/threonine protein kinase in eukaryotic cells. AELs (Arabidopsis EL1-like) are plant-specific CK1s and function in a wide range of physiological and signaling processes. To comprehensively understand the cellular functions and regulatory mechanism of AELs-mediated phosphorylation, we conducted a quantitative data-independent acquisition (DIA) based phosphoproteomic assay. A total of 3107 phosphopeptides and 1032 putative substrates were detected and enriched novel phosphorylation motifs were identified, which greatly expanded the candidate substrates and functions of CK1, as well as those from human and rice.","dates":{"publication":"Tue Jul 05 00:00:00 GMT+01:00 2022"},"accession":"PXD035098","cross_references":{"TAXONOMY":["3702"],"pubmed":["37599176"]}}