Proximity‐dependent biotinylation reveals an interaction between ubiquitin‐specific peptidase 46 and centrosome‐related proteins
Protein ubiquitination extensively modulates protein functions and controls various biological processes, such as protein degradation, signal transduction, transcription, and DNA repair. Ubiquitination is a reversible post‐translational modification, and deubiquitinating enzymes cleave ubiquitin fro...
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2025-01-01
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| Online Access: | https://doi.org/10.1002/2211-5463.13918 |
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| author | Kazuma Yoshioka Reiko Nakagawa Chi Lieu Kim Nguyen Hayate Suzuki Kiyohiro Ishigaki Seiya Mizuno Tsukasa Okiyoneda Shizufumi Ebihara Kazuya Murata |
| author_facet | Kazuma Yoshioka Reiko Nakagawa Chi Lieu Kim Nguyen Hayate Suzuki Kiyohiro Ishigaki Seiya Mizuno Tsukasa Okiyoneda Shizufumi Ebihara Kazuya Murata |
| author_sort | Kazuma Yoshioka |
| collection | DOAJ |
| description | Protein ubiquitination extensively modulates protein functions and controls various biological processes, such as protein degradation, signal transduction, transcription, and DNA repair. Ubiquitination is a reversible post‐translational modification, and deubiquitinating enzymes cleave ubiquitin from proteins. Ubiquitin‐specific peptidase 46 (USP46), a deubiquitinase, is highly expressed in the brain and regulates neural functions. Deleting lysine 92 (ΔK92) in USP46 reduces murine depression‐like behavior in the tail suspension test. However, the molecular basis for USP46's role in regulating neural function has not yet been fully understood. Here we employed a proximity‐dependent biotinylation approach to characterize the USP46 protein interaction partners. Using homology‐independent targeted integration (HITI), a genome editing technique, we established knockin cell lines that stably express USP46 wildtype‐ or ΔK92‐biotin ligase fusion protein. We identified 286 candidate interaction partners, including well‐known binding partners of USP46. Although there were no obvious differences in the interactome of USP46 between wildtype and ΔK92, a gene ontology analysis revealed that centrosome‐related proteins were significantly enriched in the proximal proteins of USP46. Several centrosome‐related proteins were bound to USP46 in Neuro2a cells, but their protein expression levels were not affected in the brains of USP46‐deficient mice. These results uncover a potential relationship between USP46 and centrosome regulation independently of protein stabilization. |
| format | Article |
| id | doaj-art-77d0b377df854c14b5deffac9308439a |
| institution | Kabale University |
| issn | 2211-5463 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Wiley |
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| series | FEBS Open Bio |
| spelling | doaj-art-77d0b377df854c14b5deffac9308439a2025-01-07T02:27:34ZengWileyFEBS Open Bio2211-54632025-01-0115115116410.1002/2211-5463.13918Proximity‐dependent biotinylation reveals an interaction between ubiquitin‐specific peptidase 46 and centrosome‐related proteinsKazuma Yoshioka0Reiko Nakagawa1Chi Lieu Kim Nguyen2Hayate Suzuki3Kiyohiro Ishigaki4Seiya Mizuno5Tsukasa Okiyoneda6Shizufumi Ebihara7Kazuya Murata8Department of Biomedical Chemistry, School of Science and Technology Kwansei Gakuin University Sanda JapanLaboratory for Cell‐Free Protein Synthesis RIKEN Center for Biosystems Dynamics Research (BDR) Kobe JapanDoctoral Program in Human Biology, Degree Programs in Comprehensive Human Sciences, Graduate School of Comprehensive Human Sciences University of Tsukuba JapanLaboratory Animal Resource Center in Transborder Medical Research Center, Institute of Medicine University of Tsukuba JapanDepartment of Biomedical Chemistry, School of Science and Technology Kwansei Gakuin University Sanda JapanLaboratory Animal Resource Center in Transborder Medical Research Center, Institute of Medicine University of Tsukuba JapanDepartment of Biomedical Sciences, School of Biological and Environmental Sciences Kwansei Gakuin University Sanda JapanDepartment of Biomedical Chemistry, School of Science and Technology Kwansei Gakuin University Sanda JapanDepartment of Biomedical Chemistry, School of Science and Technology Kwansei Gakuin University Sanda JapanProtein ubiquitination extensively modulates protein functions and controls various biological processes, such as protein degradation, signal transduction, transcription, and DNA repair. Ubiquitination is a reversible post‐translational modification, and deubiquitinating enzymes cleave ubiquitin from proteins. Ubiquitin‐specific peptidase 46 (USP46), a deubiquitinase, is highly expressed in the brain and regulates neural functions. Deleting lysine 92 (ΔK92) in USP46 reduces murine depression‐like behavior in the tail suspension test. However, the molecular basis for USP46's role in regulating neural function has not yet been fully understood. Here we employed a proximity‐dependent biotinylation approach to characterize the USP46 protein interaction partners. Using homology‐independent targeted integration (HITI), a genome editing technique, we established knockin cell lines that stably express USP46 wildtype‐ or ΔK92‐biotin ligase fusion protein. We identified 286 candidate interaction partners, including well‐known binding partners of USP46. Although there were no obvious differences in the interactome of USP46 between wildtype and ΔK92, a gene ontology analysis revealed that centrosome‐related proteins were significantly enriched in the proximal proteins of USP46. Several centrosome‐related proteins were bound to USP46 in Neuro2a cells, but their protein expression levels were not affected in the brains of USP46‐deficient mice. These results uncover a potential relationship between USP46 and centrosome regulation independently of protein stabilization.https://doi.org/10.1002/2211-5463.13918BioIDcentrosomegenome editinginteractomeUSP46 |
| spellingShingle | Kazuma Yoshioka Reiko Nakagawa Chi Lieu Kim Nguyen Hayate Suzuki Kiyohiro Ishigaki Seiya Mizuno Tsukasa Okiyoneda Shizufumi Ebihara Kazuya Murata Proximity‐dependent biotinylation reveals an interaction between ubiquitin‐specific peptidase 46 and centrosome‐related proteins FEBS Open Bio BioID centrosome genome editing interactome USP46 |
| title | Proximity‐dependent biotinylation reveals an interaction between ubiquitin‐specific peptidase 46 and centrosome‐related proteins |
| title_full | Proximity‐dependent biotinylation reveals an interaction between ubiquitin‐specific peptidase 46 and centrosome‐related proteins |
| title_fullStr | Proximity‐dependent biotinylation reveals an interaction between ubiquitin‐specific peptidase 46 and centrosome‐related proteins |
| title_full_unstemmed | Proximity‐dependent biotinylation reveals an interaction between ubiquitin‐specific peptidase 46 and centrosome‐related proteins |
| title_short | Proximity‐dependent biotinylation reveals an interaction between ubiquitin‐specific peptidase 46 and centrosome‐related proteins |
| title_sort | proximity dependent biotinylation reveals an interaction between ubiquitin specific peptidase 46 and centrosome related proteins |
| topic | BioID centrosome genome editing interactome USP46 |
| url | https://doi.org/10.1002/2211-5463.13918 |
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