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Shared and distinctive neighborhoods of emerin and LBR revealed by proximity labeling and quantitative proteomics

Li-Chun Cheng, Xi Zhang, Kanishk Abhinav, Julie A Nguyen, Sabyasachi Baboo, Salvador Martinez-Bartolomé, Tess C Branon, Alice Y Ting, Esther Loose, View ORCID ProfileJohn R Yates III, View ORCID ProfileLarry Gerace
doi: https://doi.org/10.1101/2022.05.11.491529
Li-Chun Cheng
*Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla CA, USA
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Xi Zhang
*Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla CA, USA
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Kanishk Abhinav
*Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla CA, USA
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Julie A Nguyen
*Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla CA, USA
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Sabyasachi Baboo
*Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla CA, USA
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Salvador Martinez-Bartolomé
*Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla CA, USA
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Tess C Branon
†Department of Genetics, Stanford University, Stanford, CA, USA
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Alice Y Ting
†Department of Genetics, Stanford University, Stanford, CA, USA
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Esther Loose
*Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla CA, USA
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John R Yates III
*Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla CA, USA
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  • ORCID record for John R Yates III
  • For correspondence: lgerace@scripps.edu
Larry Gerace
*Department of Molecular Medicine, Scripps Research, 10550 N Torrey Pines Rd, La Jolla CA, USA
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  • ORCID record for Larry Gerace
  • For correspondence: lgerace@scripps.edu
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Abstract

Emerin and LBR are abundant transmembrane proteins of the nuclear envelope (NE) that are concentrated at the inner nuclear membrane (INM). Although both proteins interact with chromatin and nuclear lamins, they have distinctive biochemical and functional properties. Here we have deployed proximity labeling using the engineered biotin ligase TurboID (TbID) and quantitative proteomics to compare the neighborhoods of emerin and LBR in cultured mouse embryonic fibroblasts (MEFs). Our analysis revealed 232 high confidence proximity partners (HCPP) that interact selectively with emerin and/or LBR, 49 of which are shared by both. These included previously characterized NE-concentrated proteins, as well as a host of additional proteins not previously linked to emerin or LBR functions. Many of these are TM proteins of the ER and include two E3 ubiquitin ligases. Using the proximity ligation assay as an orthogonal approach, we validated the interactions described by proximity labeling for 11/12 proteins analyzed, supporting the robustness of our analysis. Overall, this work presents methodology that may be used for large-scale mapping of the landscape of the INM and reveals a group of new proteins with potential functional connections to emerin and LBR.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 11, 2022.
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Shared and distinctive neighborhoods of emerin and LBR revealed by proximity labeling and quantitative proteomics
Li-Chun Cheng, Xi Zhang, Kanishk Abhinav, Julie A Nguyen, Sabyasachi Baboo, Salvador Martinez-Bartolomé, Tess C Branon, Alice Y Ting, Esther Loose, John R Yates III, Larry Gerace
bioRxiv 2022.05.11.491529; doi: https://doi.org/10.1101/2022.05.11.491529
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Shared and distinctive neighborhoods of emerin and LBR revealed by proximity labeling and quantitative proteomics
Li-Chun Cheng, Xi Zhang, Kanishk Abhinav, Julie A Nguyen, Sabyasachi Baboo, Salvador Martinez-Bartolomé, Tess C Branon, Alice Y Ting, Esther Loose, John R Yates III, Larry Gerace
bioRxiv 2022.05.11.491529; doi: https://doi.org/10.1101/2022.05.11.491529

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