{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Yoshida Y"],"funding":["Japan Society for the Promotion of Science"],"pagination":["4630-5"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC4403176"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["112(15)"],"pubmed_abstract":["The identification of substrates for ubiquitin ligases has remained challenging, because most substrates are either immediately degraded by the proteasome or processed by deubiquitinating enzymes (DUBs) to remove polyubiquitin. Although a methodology that enables detection of ubiquitinated proteins using ubiquitin Lys-ε-Gly-Gly (diGly) remnant antibodies and MS has been developed, it is still insufficient for identification and characterization of the ubiquitin-modified proteome in cells overexpressing a particular ubiquitin ligase. Here, we show that exogenously expressed trypsin-resistant tandem ubiquitin-binding entity(ies) (TR-TUBE) protect polyubiquitin chains on substrates from DUBs and circumvent proteasome-mediated degradation in cells. TR-TUBE effectively associated with substrate"],"journal":["Proceedings of the National Academy of Sciences of the United States of America"],"pubmed_title":["A comprehensive method for detecting ubiquitinated substrates using TR-TUBE."],"pmcid":["PMC4403176"],"funding_grant_id":["24580152","2611377","13J07852","24112008","21000012"],"pubmed_authors":["Shindo M","Saeki Y","Kawawaki J","Murakami A","Yoshihara H","Yoshida Y","Tanaka K","Tsuchiya H"],"additional_accession":[]},"is_claimable":false,"name":"A comprehensive method for detecting ubiquitinated substrates using TR-TUBE.","description":"The identification of substrates for ubiquitin ligases has remained challenging, because most substrates are either immediately degraded by the proteasome or processed by deubiquitinating enzymes (DUBs) to remove polyubiquitin. Although a methodology that enables detection of ubiquitinated proteins using ubiquitin Lys-ε-Gly-Gly (diGly) remnant antibodies and MS has been developed, it is still insufficient for identification and characterization of the ubiquitin-modified proteome in cells overexpressing a particular ubiquitin ligase. Here, we show that exogenously expressed trypsin-resistant tandem ubiquitin-binding entity(ies) (TR-TUBE) protect polyubiquitin chains on substrates from DUBs and circumvent proteasome-mediated degradation in cells. TR-TUBE effectively associated with substrate","dates":{"release":"2015-01-01T00:00:00Z","publication":"2015 Apr","modification":"2026-04-13T08:26:10.177Z","creation":"2026-04-07T13:29:03.365Z"},"accession":"S-EPMC4403176","cross_references":{"pubmed":["25827227"],"doi":["10.1073/pnas.1422313112"]}}