Z-REX uncovers a bifurcation in function of Keap1 paralogs

  1. Alexandra Van Hall-Beauvais
  2. Jesse R Poganik
  3. Kuan-Ting Huang
  4. Saba Parvez
  5. Yi Zhao
  6. Hong-Yu Lin
  7. Xuyu Liu
  8. Marcus John Curtis Long  Is a corresponding author
  9. Yimon Aye  Is a corresponding author
  1. École Polytechnique Fédérale de Lausanne, Switzerland
  2. Brigham and Women's Hospital, United States
  3. University of Utah, United States
  4. Xiamen University, China
  5. University of Sydney, Australia
  6. University of Lausanne, Switzerland

Abstract

Studying electrophile signaling is marred by difficulties in parsing changes in pathway flux attributable to on-target, vis-à-vis off-target, modifications. By combining bolus dosing, knockdown, and Z-REX-a tool investigating on-target/on-pathway electrophile signaling, we document that electrophile labeling of one zebrafish-Keap1-paralog (zKeap1b) stimulates Nrf2- driven antioxidant response (AR) signaling (like the human-ortholog). Conversely, zKeap1a is a dominant-negative regulator of electrophile-promoted Nrf2-signaling, and itself is nonpermissive for electrophile-induced Nrf2-upregulation. This behavior is recapitulated in human cells, wherein following electrophile treatment: (1) zKeap1b-transfected cells are permissive for augmented AR-signaling through reduced zKeap1b-Nrf2 binding; (2) zKeap1a-transfected cells are non-permissive for AR-upregulation, as zKeap1a-Nrf2 binding capacity remains unaltered; (3) 1:1 ZKeap1a:zKeap1b-transfected cells show no Nrf2-release from the Keap1-complex, rendering these cells unable to upregulate AR. We identified a zKeap1a-specific point-mutation (C273I) responsible for zKeap1a's behavior. Human-Keap1(C273I), of known diminished Nrf2-regulatory capacity, dominantly muted electrophile-induced Nrf2-signaling. These studies highlight divergent and interdependent electrophile signaling behaviors, despite conserved electrophile sensing.

Data availability

The data generated in this study using these materials are provided in Main Figure 1-8, accompanied by 17 associated Figure Supplements, and the Source Data Files associated with Main Figure 1-8 and 17 associated Figure Supplements.

Article and author information

Author details

  1. Alexandra Van Hall-Beauvais

    École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2515-5191
  2. Jesse R Poganik

    Department of Medicine, Brigham and Women's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Kuan-Ting Huang

    École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  4. Saba Parvez

    Department of Pharmacology and Toxicology, University of Utah, Salt lake City, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Yi Zhao

    École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6049-1943
  6. Hong-Yu Lin

    Department of Chemical Biology, Xiamen University, Xiamen, China
    Competing interests
    The authors declare that no competing interests exist.
  7. Xuyu Liu

    School of Chemistry, University of Sydney, New South Wales, Australia
    Competing interests
    The authors declare that no competing interests exist.
  8. Marcus John Curtis Long

    Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
    For correspondence
    marcusjohncurtis.long@unil.ch
    Competing interests
    The authors declare that no competing interests exist.
  9. Yimon Aye

    École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
    For correspondence
    yimon.aye@epfl.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1256-4159

Funding

Novartis FreeNovation

  • Yimon Aye

European Research Council

  • Yimon Aye

Swiss Federal Institute od Technology

  • Yimon Aye

National Institutes of Health (NIH T32GM008500)

  • Jesse R Poganik

AHA predoctoral Fellowship (17PRE33670395)

  • Jesse R Poganik

HHMI International Fellow

  • Saba Parvez

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

Reviewing Editor

  1. Jonathan A Cooper, Fred Hutchinson Cancer Research Center, United States

Ethics

Animal experimentation: All procedures performed at Cornell (2017-2018) and EPFL (2018-present) conform to the animal care, maintenance, and experimentation procedures followed by Cornell University's and EPFL's Institutional Animal Care and Use Committee (IACUC) guidelines and approved by the respective institutional committees. All experiments with zebrafish performed at EPFL (2018-present) have been performed in accordance with the Swiss regulations on Animal Experimentation (Animal Welfare Act SR 455 and Animal Welfare Ordinance SR 455.1), in the EPFL zebrafish unit, cantonal veterinary authorization VD-H23).

Version history

  1. Received: September 9, 2022
  2. Preprint posted: October 12, 2022 (view preprint)
  3. Accepted: October 12, 2022
  4. Accepted Manuscript published: October 27, 2022 (version 1)
  5. Accepted Manuscript updated: October 31, 2022 (version 2)
  6. Version of Record published: December 15, 2022 (version 3)
  7. Version of Record updated: June 1, 2023 (version 4)

Copyright

© 2022, Van Hall-Beauvais 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

  • 762
    views
  • 131
    downloads
  • 4
    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. Alexandra Van Hall-Beauvais
  2. Jesse R Poganik
  3. Kuan-Ting Huang
  4. Saba Parvez
  5. Yi Zhao
  6. Hong-Yu Lin
  7. Xuyu Liu
  8. Marcus John Curtis Long
  9. Yimon Aye
(2022)
Z-REX uncovers a bifurcation in function of Keap1 paralogs
eLife 11:e83373.
https://doi.org/10.7554/eLife.83373

Share this article

https://doi.org/10.7554/eLife.83373

Further reading

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Natalia Dolgova, Eva-Maria E Uhlemann ... Oleg Y Dmitriev
    Research Article

    Mediator of ERBB2-driven Cell Motility 1 (MEMO1) is an evolutionary conserved protein implicated in many biological processes; however, its primary molecular function remains unknown. Importantly, MEMO1 is overexpressed in many types of cancer and was shown to modulate breast cancer metastasis through altered cell motility. To better understand the function of MEMO1 in cancer cells, we analyzed genetic interactions of MEMO1 using gene essentiality data from 1028 cancer cell lines and found multiple iron-related genes exhibiting genetic relationships with MEMO1. We experimentally confirmed several interactions between MEMO1 and iron-related proteins in living cells, most notably, transferrin receptor 2 (TFR2), mitoferrin-2 (SLC25A28), and the global iron response regulator IRP1 (ACO1). These interactions indicate that cells with high MEMO1 expression levels are hypersensitive to the disruptions in iron distribution. Our data also indicate that MEMO1 is involved in ferroptosis and is linked to iron supply to mitochondria. We have found that purified MEMO1 binds iron with high affinity under redox conditions mimicking intracellular environment and solved MEMO1 structures in complex with iron and copper. Our work reveals that the iron coordination mode in MEMO1 is very similar to that of iron-containing extradiol dioxygenases, which also display a similar structural fold. We conclude that MEMO1 is an iron-binding protein that modulates iron homeostasis in cancer cells.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Isabelle Petit-Hartlein, Annelise Vermot ... Franck Fieschi
    Research Article

    NADPH oxidases (NOX) are transmembrane proteins, widely spread in eukaryotes and prokaryotes, that produce reactive oxygen species (ROS). Eukaryotes use the ROS products for innate immune defense and signaling in critical (patho)physiological processes. Despite the recent structures of human NOX isoforms, the activation of electron transfer remains incompletely understood. SpNOX, a homolog from Streptococcus pneumoniae, can serves as a robust model for exploring electron transfers in the NOX family thanks to its constitutive activity. Crystal structures of SpNOX full-length and dehydrogenase (DH) domain constructs are revealed here. The isolated DH domain acts as a flavin reductase, and both constructs use either NADPH or NADH as substrate. Our findings suggest that hydride transfer from NAD(P)H to FAD is the rate-limiting step in electron transfer. We identify significance of F397 in nicotinamide access to flavin isoalloxazine and confirm flavin binding contributions from both DH and Transmembrane (TM) domains. Comparison with related enzymes suggests that distal access to heme may influence the final electron acceptor, while the relative position of DH and TM does not necessarily correlate with activity, contrary to previous suggestions. It rather suggests requirement of an internal rearrangement, within the DH domain, to switch from a resting to an active state. Thus, SpNOX appears to be a good model of active NOX2, which allows us to propose an explanation for NOX2’s requirement for activation.