Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress

Buchwalter, Abigail, University of California, San Francisco

Schulte, Roberta, Salk Institute for Biological Studies

Tsai, Hsiao, Salk Institute for Biological Studies

Capitanio, Juliana, Salk Institute for Biological Studies

Hetzer, Martin, Salk Institute for Biological Studies

abigail.buchwalter@ucsf.edu

Published Oct 28, 2019 on Dryad. https://doi.org/10.5061/dryad.n0r525h

Cite this dataset

Buchwalter, Abigail et al. (2019). Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress [Dataset]. Dryad. https://doi.org/10.5061/dryad.n0r525h

Abstract

The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs.

Usage notes

Day 0 SILAC labeling C2C12 myotubes

Raw peptide data for day 0 timepoint of 3 day SILAC pulse-chase timecourse in C2C12 myotubes

Original-0D.txt

Day 1 SILAC labeling C2C12 myotubes

raw peptide data for 1 day timepoint of SILAC pulse-chase timecourse in C2C12 myotubes

Original-1D.txt

Day 2 SILAC labeling C2C12 myotubes

Raw peptide data for day 2 timepoint from SILAC pulse-chase timecourse in C2C12 myotubes

Original-2D.txt

Day 3 SILAC labeling C2C12 myotubes

raw peptide data for day 3 timepoint of SILAC pulse-chase timecourse in C2C12 myotubes

Original-3D.txt

Table S1 filtered peptide data for half-life reviewed only

Supplementary Table 1: peptide data for all peptides passing quality control filters (see R script and manuscript methods)

Table S2 filtered protein data for half-life reviewed only

Supplementary Table 2. Filtered and averaged protein data. See R script and Methods for details.

Table S3. results of half life fits passing quality filters

Supplementary Table 3. half life fits that surpass quality filters

Table S3. results of half life fits.xlsx

Table S4. All half life fits

Supplementary Table 4. All half life fits

Table S4. proteins successful fits only.xlsx

Table S5. Selected data related to Figure 1

Table S5. half lives and topology data related to Figure 1.xlsx

R script for data filtering and half life fitting

3 day SILAC timecourse LM only.Rmd