Spatial proteomics of ER tubules reveals CLMN, an ER-actin tether at focal adhesions that promotes cell migration

  1. Holly Merta
  2. Tadamoto Isogai
  3. Blessy Paul
  4. Gaudenz Danuser
  5. W Mike Henne

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Abstract

The endoplasmic reticulum (ER) is structurally and functionally diverse, yet how its functions are organized within morphological subdomains is incompletely understood. Utilizing TurboID-based proximity labeling and CRISPR knock-in technologies, here we map the proteomic landscape of the human ER and nuclear envelope. Spatial proteomics reveals enrichments of proteins into ER tubules, sheets, and nuclear envelope. We uncover an ER-enriched actin-binding protein, Calmin (CLMN), and define it as an ER-actin tether that localizes to focal adhesions adjacent to ER tubules. CLMN depletion perturbs focal adhesion disassembly, actin dynamics, and cell movement. Mechanistically, CLMN-depleted cells also exhibit defects in calcium signaling near ER-actin interfaces, suggesting CLMN promotes calcium signaling near adhesions to facilitate their disassembly. Collectively, we map the sub-organelle proteome landscape of the ER, identify CLMN as an ER-actin tether, and describe a non-canonical mechanism by which ER tubules engage actin to regulate cell migration.

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  1. PREreview

    This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/12801245.

    Pre-review of "Spatial proteomics of ER tubules reveals CLMN, an ER-actin tether at focal adhesions  that promotes cell migration"

    by Victoria Maltret, Tony Avril, Eric Chevet and Elodie Lafont of the Proteostasis and Cancer team INSERM U1242

    Summary of the article

    In this article by Merta et al, the authors use TurboID-based proximity biotinylation to identify proteins of the ER and nuclear envelope. They then focus on Calmin (CLMN) and demonstrate that it is an ER-actin tether at focal adhesions in proximity to ER tubules They further identify the CLMN domains required for its sub-cellular localisation and ER-actin tethering function. Functionally, the authors demonstrate that CLMN promotes the dissassembly of focal adhesions and cell migration. The authors also provide evidence that CLMN promotes calcium signalling at focal adhesion sites. Overall, this study therefore highlights CLMN as a key protein tethering ER tubules and surface adhesion actin structures and coordinating their dissasembly to promote cell migration.

    General comments

    This study is easy-to-read and the key conclusions are nicely supported by the data. The findings are novel, functionally important and particularly relevant to the cell biology community since they provide a previously unidentified link between the actin adhesion structures and ER tubules through CLMN in human cells. We think that additional quantifications for some of the microscopy experiments and discussion (see specific comments) would further strengthen his study.

    Specific comments

    Figure 1. On the evolutionary considerations in the full text for Figure 1E, the authors may want to include more discussion points. For example, the authors may want to depict other vertebrates for which the Nesprin 3 gene is adjacent to CLMN gene in the supplemental. Is the proximity between Nesprin 3 and CLMN genes actually observed in all vertebrates? Which gene may functionally replace CLMN in non-vertebrates? Figure 1F: The authors may want to include nesprin 1/2 CH domains rather than (or in addition to) alpha-actinin, as this is the comparison mentioned in panel 1E. What is the level of expression of CLMN in healthy human cells?

    Figure 2. A, B, C: how frequent are the colocalization depicted? Some quantification (throughout the section chosen and for several cells) would be really informative here. Does endogenously expressed CLMN also colocalize with paxillin?

    Figure 3. It would be informative, for the mutants depicted in 3C, to also display colocalization plots (throughout the cell section chosen).

    Figure 4. It would be great to also display the scratch assay on the CLMN-overexpressing WT and various mutant cells.

    Figure 5. Would overexpression of the different CLMN mutants affect cell adhesion, as compared to WT CLMN?

    Figure 6. 6C: Stim1 staining (or maybe a colocalization Stim1/Orai1) would be informative here. Is the ER calcium storage mobilized here (maybe this could be assessed experimentally)? It may be interesting to reassess the proteomic results obtained in figure 1 in light of the findings obtained throughout the study: are there any adhesion and/or calcium-related proteins/processes particularly enriched in some of the sub-proteomes?

    In the discussion, the authors may want to further highlight the complementarity of their findings with earlier as well as recent findings, such as (Gong et al, 2024), on ER-PM contact sites regulation through microtubule cytoskeleton and cell migration.

    Competing interests

    The authors declare that they have no competing interests.

    References

    Gong B, Johnston JD, Thiemicke A, de Marco A & Meyer T (2024) Endoplasmic reticulum–plasma membrane contact gradients direct cell migration. Nature: 1–9

    Competing interests

    The authors declare that they have no competing interests.

  2. Version published to 10.1101/2024.01.24.577043v1 on bioRxiv