Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells
Abstract Liquid-liquid phase separations (LLPS) are membraneless organelles driven by biomolecule assembly and are implicated in cellular physiological activities. However, spatiotemporal deciphering of the dynamic proteome in living cells during LLPS formation remains challenging. Here, we introduc...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-05-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-59457-z |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850190577593745408 |
|---|---|
| author | Sunfengda Song Haiyang Xie Qingwen Wang Xinyi Sun Jiasu Xu Rui Chen Yuankang Zhu Lai Jiang Xianting Ding |
| author_facet | Sunfengda Song Haiyang Xie Qingwen Wang Xinyi Sun Jiasu Xu Rui Chen Yuankang Zhu Lai Jiang Xianting Ding |
| author_sort | Sunfengda Song |
| collection | DOAJ |
| description | Abstract Liquid-liquid phase separations (LLPS) are membraneless organelles driven by biomolecule assembly and are implicated in cellular physiological activities. However, spatiotemporal deciphering of the dynamic proteome in living cells during LLPS formation remains challenging. Here, we introduce the Composition of LLPS proteome Assembly by Proximity labeling-assisted Mass spectrometry (CLAPM). We demonstrate that CLAPM can instantaneously label and monitor the FUS interactome shifts within intracellular droplets undergoing spatiotemporal LLPS. We report 129, 182 and 822 proteins specifically present in the LLPS droplets of HeLa, HEK 293 T and neuronal cells respectively. CLAPM further categorizes spatiotemporal dynamic proteome in droplets for living neuronal cells and identifies 596 LLPS-aboriginal proteins, 226 LLPS-dependent proteins and 58 LLPS-sensitive proteins. For validation, we uncover 11 previously unknown LLPS proteins in vivo. CLAPM provides a versatile tool to decipher proteins involved in LLPS and enables the accurate characterization of dynamic proteome in living cells. |
| format | Article |
| id | doaj-art-6a55b1bc5a514b3b95265eac44cfe465 |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-6a55b1bc5a514b3b95265eac44cfe4652025-08-20T02:15:15ZengNature PortfolioNature Communications2041-17232025-05-0116111610.1038/s41467-025-59457-zSpatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cellsSunfengda Song0Haiyang Xie1Qingwen Wang2Xinyi Sun3Jiasu Xu4Rui Chen5Yuankang Zhu6Lai Jiang7Xianting Ding8Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong UniversityDepartment of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong UniversityDepartment of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong UniversityDepartment of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong UniversityDepartment of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong UniversityDepartment of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong UniversityDepartment of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong UniversityDepartment of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong UniversityDepartment of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong UniversityAbstract Liquid-liquid phase separations (LLPS) are membraneless organelles driven by biomolecule assembly and are implicated in cellular physiological activities. However, spatiotemporal deciphering of the dynamic proteome in living cells during LLPS formation remains challenging. Here, we introduce the Composition of LLPS proteome Assembly by Proximity labeling-assisted Mass spectrometry (CLAPM). We demonstrate that CLAPM can instantaneously label and monitor the FUS interactome shifts within intracellular droplets undergoing spatiotemporal LLPS. We report 129, 182 and 822 proteins specifically present in the LLPS droplets of HeLa, HEK 293 T and neuronal cells respectively. CLAPM further categorizes spatiotemporal dynamic proteome in droplets for living neuronal cells and identifies 596 LLPS-aboriginal proteins, 226 LLPS-dependent proteins and 58 LLPS-sensitive proteins. For validation, we uncover 11 previously unknown LLPS proteins in vivo. CLAPM provides a versatile tool to decipher proteins involved in LLPS and enables the accurate characterization of dynamic proteome in living cells.https://doi.org/10.1038/s41467-025-59457-z |
| spellingShingle | Sunfengda Song Haiyang Xie Qingwen Wang Xinyi Sun Jiasu Xu Rui Chen Yuankang Zhu Lai Jiang Xianting Ding Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells Nature Communications |
| title | Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells |
| title_full | Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells |
| title_fullStr | Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells |
| title_full_unstemmed | Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells |
| title_short | Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells |
| title_sort | spatiotemporal deciphering of dynamic the fus interactome during liquid liquid phase separation in living cells |
| url | https://doi.org/10.1038/s41467-025-59457-z |
| work_keys_str_mv | AT sunfengdasong spatiotemporaldecipheringofdynamicthefusinteractomeduringliquidliquidphaseseparationinlivingcells AT haiyangxie spatiotemporaldecipheringofdynamicthefusinteractomeduringliquidliquidphaseseparationinlivingcells AT qingwenwang spatiotemporaldecipheringofdynamicthefusinteractomeduringliquidliquidphaseseparationinlivingcells AT xinyisun spatiotemporaldecipheringofdynamicthefusinteractomeduringliquidliquidphaseseparationinlivingcells AT jiasuxu spatiotemporaldecipheringofdynamicthefusinteractomeduringliquidliquidphaseseparationinlivingcells AT ruichen spatiotemporaldecipheringofdynamicthefusinteractomeduringliquidliquidphaseseparationinlivingcells AT yuankangzhu spatiotemporaldecipheringofdynamicthefusinteractomeduringliquidliquidphaseseparationinlivingcells AT laijiang spatiotemporaldecipheringofdynamicthefusinteractomeduringliquidliquidphaseseparationinlivingcells AT xiantingding spatiotemporaldecipheringofdynamicthefusinteractomeduringliquidliquidphaseseparationinlivingcells |