Application of STUPPIT to identify novel intermediary proteins between SMAD4 and β-catenin, central hubs of BMP and Wnt pathway.
<p><b>(A)</b> Schematic of the opposing effects of BMP and Wnt signaling on stem cell behavior. <b>(B)</b> STUPPIT strategy for labeling proteins that bridge SMAD4 and β-catenin. <b>(C)</b> STUPPIT workflow for capturing intermediary proteins between SMAD4 a...
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| _version_ | 1849927641700761600 |
|---|---|
| author | Lin Xie (136792) |
| author2 | Lijuan Gao (5093777) Weihong Fu (8430690) Gangyun Wu (22676687) Hua Li (46469) Wenxiu Ning (18239607) |
| author2_role | author author author author author |
| author_facet | Lin Xie (136792) Lijuan Gao (5093777) Weihong Fu (8430690) Gangyun Wu (22676687) Hua Li (46469) Wenxiu Ning (18239607) |
| author_role | author |
| dc.creator.none.fl_str_mv | Lin Xie (136792) Lijuan Gao (5093777) Weihong Fu (8430690) Gangyun Wu (22676687) Hua Li (46469) Wenxiu Ning (18239607) |
| dc.date.none.fl_str_mv | 2025-11-24T18:33:58Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pbio.3003227.g005 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/Application_of_STUPPIT_to_identify_novel_intermediary_proteins_between_SMAD4_and_-catenin_central_hubs_of_BMP_and_Wnt_pathway_/30697640 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biophysics Biochemistry Cell Biology Genetics Molecular Biology Physiology Biotechnology Developmental Biology Cancer Inorganic Chemistry Infectious Diseases Plant Biology Virology Chemical Sciences not elsewhere classified step enzymatic reaction offering new insights capturing intermediary proteins capture intermediary proteins biotinylate intermediary proteins plit -< u div >< p labeling intermediary proteins tu </ u proximity labeling tools proximity labeling tool characterized protein triads bmp signaling pathways p </ u bridge two non </ u signaling pathways interacting proteins tools available powerful tool two non protein interactions key components interacting partners identifying upstream downstream effectors disease pathogenesis directly label |
| dc.title.none.fl_str_mv | Application of STUPPIT to identify novel intermediary proteins between SMAD4 and β-catenin, central hubs of BMP and Wnt pathway. |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p><b>(A)</b> Schematic of the opposing effects of BMP and Wnt signaling on stem cell behavior. <b>(B)</b> STUPPIT strategy for labeling proteins that bridge SMAD4 and β-catenin. <b>(C)</b> STUPPIT workflow for capturing intermediary proteins between SMAD4 and β-catenin. 3 × Flag-TbN-PupE stably expressed cells were co-transfected with SMAD4-PafA-Myc&HA-TbC or SMAD4-PafA-Myc&HA-TbC-β-catenin. STUPPIT labeled intermediary proteins between SMAD4 and β-catenin were enriched by streptavidin pulldown and analyzed by mass spectrometry. Samples 1–6 (SMAD4&TbC) and 7–12 (SMAD4&TbC-β-catenin) were each pooled into three groups (1 + 2, 3 + 4, 5 + 6) and (7 + 8, 9 + 10, 11 + 12) to yield three replicates per condition. <b>(D)</b> Volcano plots of the potential intermediary proteins between SMAD4 and β-catenin enriched by STUPPIT approach I after mass spectrometry analysis. Proteins with unique peptides ≥10 in the SMAD4&TbC-β-catenin over SMAD4&TbC control group were first filtered. Proteins with fold change (SMAD4&TbC-β-catenin over SMAD4&TbC) > 1.5 were labeled as red dots in the volcano plots. <b>(E)</b> Heatmap of the unique peptide counts for the indicated candidates in SMAD4&β-catenin and SMAD4&control groups identified by mass spectrometry analysis. Underlying mass spectrometry data can be found in the ProteomeXchange (PXD069286).</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_00f2918eb1f3f10173325a8face358c6 |
| identifier_str_mv | 10.1371/journal.pbio.3003227.g005 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30697640 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Application of STUPPIT to identify novel intermediary proteins between SMAD4 and β-catenin, central hubs of BMP and Wnt pathway.Lin Xie (136792)Lijuan Gao (5093777)Weihong Fu (8430690)Gangyun Wu (22676687)Hua Li (46469)Wenxiu Ning (18239607)BiophysicsBiochemistryCell BiologyGeneticsMolecular BiologyPhysiologyBiotechnologyDevelopmental BiologyCancerInorganic ChemistryInfectious DiseasesPlant BiologyVirologyChemical Sciences not elsewhere classifiedstep enzymatic reactionoffering new insightscapturing intermediary proteinscapture intermediary proteinsbiotinylate intermediary proteinsplit -< udiv >< plabeling intermediary proteinstu </ uproximity labeling toolsproximity labeling toolcharacterized protein triadsbmp signaling pathwaysp </ ubridge two non</ usignaling pathwaysinteracting proteinstools availablepowerful tooltwo nonprotein interactionskey componentsinteracting partnersidentifying upstreamdownstream effectorsdisease pathogenesisdirectly label<p><b>(A)</b> Schematic of the opposing effects of BMP and Wnt signaling on stem cell behavior. <b>(B)</b> STUPPIT strategy for labeling proteins that bridge SMAD4 and β-catenin. <b>(C)</b> STUPPIT workflow for capturing intermediary proteins between SMAD4 and β-catenin. 3 × Flag-TbN-PupE stably expressed cells were co-transfected with SMAD4-PafA-Myc&HA-TbC or SMAD4-PafA-Myc&HA-TbC-β-catenin. STUPPIT labeled intermediary proteins between SMAD4 and β-catenin were enriched by streptavidin pulldown and analyzed by mass spectrometry. Samples 1–6 (SMAD4&TbC) and 7–12 (SMAD4&TbC-β-catenin) were each pooled into three groups (1 + 2, 3 + 4, 5 + 6) and (7 + 8, 9 + 10, 11 + 12) to yield three replicates per condition. <b>(D)</b> Volcano plots of the potential intermediary proteins between SMAD4 and β-catenin enriched by STUPPIT approach I after mass spectrometry analysis. Proteins with unique peptides ≥10 in the SMAD4&TbC-β-catenin over SMAD4&TbC control group were first filtered. Proteins with fold change (SMAD4&TbC-β-catenin over SMAD4&TbC) > 1.5 were labeled as red dots in the volcano plots. <b>(E)</b> Heatmap of the unique peptide counts for the indicated candidates in SMAD4&β-catenin and SMAD4&control groups identified by mass spectrometry analysis. Underlying mass spectrometry data can be found in the ProteomeXchange (PXD069286).</p>2025-11-24T18:33:58ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.pbio.3003227.g005https://figshare.com/articles/figure/Application_of_STUPPIT_to_identify_novel_intermediary_proteins_between_SMAD4_and_-catenin_central_hubs_of_BMP_and_Wnt_pathway_/30697640CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/306976402025-11-24T18:33:58Z |
| spellingShingle | Application of STUPPIT to identify novel intermediary proteins between SMAD4 and β-catenin, central hubs of BMP and Wnt pathway. Lin Xie (136792) Biophysics Biochemistry Cell Biology Genetics Molecular Biology Physiology Biotechnology Developmental Biology Cancer Inorganic Chemistry Infectious Diseases Plant Biology Virology Chemical Sciences not elsewhere classified step enzymatic reaction offering new insights capturing intermediary proteins capture intermediary proteins biotinylate intermediary proteins plit -< u div >< p labeling intermediary proteins tu </ u proximity labeling tools proximity labeling tool characterized protein triads bmp signaling pathways p </ u bridge two non </ u signaling pathways interacting proteins tools available powerful tool two non protein interactions key components interacting partners identifying upstream downstream effectors disease pathogenesis directly label |
| status_str | publishedVersion |
| title | Application of STUPPIT to identify novel intermediary proteins between SMAD4 and β-catenin, central hubs of BMP and Wnt pathway. |
| title_full | Application of STUPPIT to identify novel intermediary proteins between SMAD4 and β-catenin, central hubs of BMP and Wnt pathway. |
| title_fullStr | Application of STUPPIT to identify novel intermediary proteins between SMAD4 and β-catenin, central hubs of BMP and Wnt pathway. |
| title_full_unstemmed | Application of STUPPIT to identify novel intermediary proteins between SMAD4 and β-catenin, central hubs of BMP and Wnt pathway. |
| title_short | Application of STUPPIT to identify novel intermediary proteins between SMAD4 and β-catenin, central hubs of BMP and Wnt pathway. |
| title_sort | Application of STUPPIT to identify novel intermediary proteins between SMAD4 and β-catenin, central hubs of BMP and Wnt pathway. |
| topic | Biophysics Biochemistry Cell Biology Genetics Molecular Biology Physiology Biotechnology Developmental Biology Cancer Inorganic Chemistry Infectious Diseases Plant Biology Virology Chemical Sciences not elsewhere classified step enzymatic reaction offering new insights capturing intermediary proteins capture intermediary proteins biotinylate intermediary proteins plit -< u div >< p labeling intermediary proteins tu </ u proximity labeling tools proximity labeling tool characterized protein triads bmp signaling pathways p </ u bridge two non </ u signaling pathways interacting proteins tools available powerful tool two non protein interactions key components interacting partners identifying upstream downstream effectors disease pathogenesis directly label |