Ratiometric sensing of BiP-client versus BiP levels by the unfolded protein response determines its signaling amplitude

  1. Anush Bakunts
  2. Andrea Orsi
  3. Milena Vitale
  4. Angela Cattaneo
  5. Federica Lari
  6. Laura Tadè
  7. Roberto Sitia
  8. Andrea Raimondi
  9. Angela Bachi
  10. Eelco van Anken  Is a corresponding author
  1. San Raffaele Scientific Institute, Italy
  2. FIRC Institute of Molecular Oncology, Italy

Abstract

Insufficient folding capacity of the endoplasmic reticulum (ER) activates the unfolded protein response (UPR) to restore homeostasis. Yet, how the UPR achieves ER homeostatic readjustment is poorly investigated, since in most studies the ER-stress that is elicited cannot be overcome. Here we show that a proteostatic insult, achieved by persistent expression of the secretory heavy chain of immunoglobulin M (µs), is well-tolerated in HeLa cells. Upon µs expression, its levels temporarily eclipse those of the ER-chaperone BiP, leading to acute, full-geared UPR activation. Once BiP is in excess again, the UPR transitions to chronic, submaximal activation, indicating that the UPR senses ER-stress in a ratiometric fashion. In the process the ER expands about threefold and becomes dominated by BiP. Since the UPR is essential for successful ER homeostatic readjustment in the HeLa-µs model, it provides an ideal system for dissecting the intricacies of how the UPR evaluates and alleviates ER-stress.

Article and author information

Author details

  1. Anush Bakunts

    Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
    Competing interests
    The authors declare that no competing interests exist.
  2. Andrea Orsi

    Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2839-1640
  3. Milena Vitale

    Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7007-402X
  4. Angela Cattaneo

    FIRC Institute of Molecular Oncology, Milan, Italy
    Competing interests
    The authors declare that no competing interests exist.
  5. Federica Lari

    Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
    Competing interests
    The authors declare that no competing interests exist.
  6. Laura Tadè

    Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
    Competing interests
    The authors declare that no competing interests exist.
  7. Roberto Sitia

    Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7086-4152
  8. Andrea Raimondi

    Experimental Imaging Center, San Raffaele Scientific Institute, Milan, Italy
    Competing interests
    The authors declare that no competing interests exist.
  9. Angela Bachi

    Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
    Competing interests
    The authors declare that no competing interests exist.
  10. Eelco van Anken

    Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
    For correspondence
    evananken@mac.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9529-2701

Funding

Giovanni Armenise-Harvard Foundation

  • Eelco van Anken

Ministero della Salute (RF - 2011-02352852)

  • Eelco van Anken

Associazione Italiana per la Ricerca sul Cancro (MFAG 13584)

  • Eelco van Anken

Ministero della Salute (PE-2011-02352286)

  • Roberto Sitia
  • Eelco van Anken

Associazione Italiana per la Ricerca sul Cancro (IG 2016-18824)

  • Roberto Sitia

Fondazione Telethon (GGP15059)

  • Roberto Sitia

Fondazione Cariplo (2015-0591)

  • Roberto Sitia

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Davis Ng, Temasek Life Sciences Laboratory and National University of Singapore, Singapore

Version history

  1. Received: April 6, 2017
  2. Accepted: December 15, 2017
  3. Accepted Manuscript published: December 18, 2017 (version 1)
  4. Version of Record published: January 31, 2018 (version 2)

Copyright

© 2017, Bakunts et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 3,532
    views
  • 761
    downloads
  • 67
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Anush Bakunts
  2. Andrea Orsi
  3. Milena Vitale
  4. Angela Cattaneo
  5. Federica Lari
  6. Laura Tadè
  7. Roberto Sitia
  8. Andrea Raimondi
  9. Angela Bachi
  10. Eelco van Anken
(2017)
Ratiometric sensing of BiP-client versus BiP levels by the unfolded protein response determines its signaling amplitude
eLife 6:e27518.
https://doi.org/10.7554/eLife.27518

Share this article

https://doi.org/10.7554/eLife.27518

Further reading

    1. Cancer Biology
    2. Cell Biology
    Francesca Butera, Julia E Sero ... Chris Bakal
    Research Article

    The canonical NF-κB transcription factor RELA is a master regulator of immune and stress responses and is upregulated in PDAC tumours. In this study, we characterised previously unexplored endogenous RELA-GFP dynamics in PDAC cell lines through live single cell imaging. Our observations revealed that TNFα stimulation induces rapid, sustained, and non-oscillatory nuclear translocation of RELA. Through Bayesian analysis of single cell datasets with variation in nuclear RELA, we predicted that RELA heterogeneity in PDAC cell lines is dependent on F-actin dynamics. RNA-seq analysis identified distinct clusters of RELA-regulated gene expression in PDAC cells, including TNFα-induced RELA upregulation of the actin regulators NUAK2 and ARHGAP31. Further, siRNA-mediated depletion of ARHGAP31 and NUAK2 altered TNFα-stimulated nuclear RELA dynamics in PDAC cells, establishing a novel negative feedback loop that regulates RELA activation by TNFα. Additionally, we characterised the NF-κB pathway in PDAC cells, identifying how NF-κB/IκB proteins genetically and physically interact with RELA in the absence or presence of TNFα. Taken together, we provide computational and experimental support for interdependence between the F-actin network and the NF-κB pathway with RELA translocation dynamics in PDAC.

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Birol Cabukusta, Shalom Borst Pauwels ... Jacques Neefjes
    Research Article

    Numerous lipids are heterogeneously distributed among organelles. Most lipid trafficking between organelles is achieved by a group of lipid transfer proteins (LTPs) that carry lipids using their hydrophobic cavities. The human genome encodes many intracellular LTPs responsible for lipid trafficking and the function of many LTPs in defining cellular lipid levels and distributions is unclear. Here, we created a gene knockout library targeting 90 intracellular LTPs and performed whole-cell lipidomics analysis. This analysis confirmed known lipid disturbances and identified new ones caused by the loss of LTPs. Among these, we found major sphingolipid imbalances in ORP9 and ORP11 knockout cells, two proteins of previously unknown function in sphingolipid metabolism. ORP9 and ORP11 form a heterodimer to localize at the ER-trans-Golgi membrane contact sites, where the dimer exchanges phosphatidylserine (PS) for phosphatidylinositol-4-phosphate (PI(4)P) between the two organelles. Consequently, loss of either protein causes phospholipid imbalances in the Golgi apparatus that result in lowered sphingomyelin synthesis at this organelle. Overall, our LTP knockout library toolbox identifies various proteins in control of cellular lipid levels, including the ORP9-ORP11 heterodimer, which exchanges PS and PI(4)P at the ER-Golgi membrane contact site as a critical step in sphingomyelin synthesis in the Golgi apparatus.