Therapeutic genetic variation revealed in diverse Hsp104 homologs

  1. Zachary M March
  2. Katelyn Sweeney
  3. Hanna Kim
  4. Xiaohui Yan
  5. Laura M Castellano
  6. Meredith E Jackrel
  7. JiaBei Lin
  8. Edward Chuang
  9. Edward Gomes
  10. Corey W Willicott
  11. Karolina Michalska
  12. Robert P Jedrzejczak
  13. Andrzej Joachimiak
  14. Kim A Caldwell
  15. Guy A Caldwell
  16. Ophir Shalem
  17. James Shorter  Is a corresponding author
  1. University of Pennsylvania, United States
  2. The University of Alabama, United States
  3. Washington University in St Louis, United States
  4. Argonne National Laboratory, United States

Abstract

The AAA+ protein disaggregase, Hsp104, increases fitness under stress by reversing stress-induced protein aggregation. Natural Hsp104 variants might exist with enhanced, selective activity against neurodegenerative disease substrates. However, natural Hsp104 variation remains largely unexplored. Here, we screened a cross-kingdom collection of Hsp104 homologs in yeast proteotoxicity models. Prokaryotic ClpG reduced TDP-43, FUS, and a-synuclein toxicity, whereas prokaryotic ClpB and hyperactive variants were ineffective. We uncovered therapeutic genetic variation among eukaryotic Hsp104 homologs that specifically antagonized TDP-43 condensation and toxicity in yeast and TDP-43 aggregation in human cells. We also uncovered distinct eukaryotic Hsp104 homologs that selectively antagonized a-synuclein condensation and toxicity in yeast and dopaminergic neurodegeneration in C. elegans. Surprisingly, this therapeutic variation did not manifest as enhanced disaggregase activity, but rather as increased passive inhibition of aggregation of specific substrates. By exploring natural tuning of this passive Hsp104 activity, we elucidated enhanced, substrate-specific agents that counter proteotoxicity underlying neurodegeneration.

Data availability

All data generated or analysed during this study are included in the manuscript.

Article and author information

Author details

  1. Zachary M March

    Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2441-899X
  2. Katelyn Sweeney

    Genetics, University of Pennsylvania, Philadelphia, United States
    Competing interests
    No competing interests declared.
  3. Hanna Kim

    Biological Sciences, The University of Alabama, Tuscaloosa, United States
    Competing interests
    No competing interests declared.
  4. Xiaohui Yan

    Biological Sciences, The University of Alabama, Tuscaloosa, United States
    Competing interests
    No competing interests declared.
  5. Laura M Castellano

    Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United States
    Competing interests
    No competing interests declared.
  6. Meredith E Jackrel

    Department of Chemistry, Washington University in St Louis, St Louis, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4406-9504
  7. JiaBei Lin

    Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United States
    Competing interests
    No competing interests declared.
  8. Edward Chuang

    Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United States
    Competing interests
    No competing interests declared.
  9. Edward Gomes

    Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United States
    Competing interests
    No competing interests declared.
  10. Corey W Willicott

    Biological Sciences, The University of Alabama, Tuscaloosa, United States
    Competing interests
    No competing interests declared.
  11. Karolina Michalska

    Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Lemont, United States
    Competing interests
    No competing interests declared.
  12. Robert P Jedrzejczak

    Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, United States
    Competing interests
    No competing interests declared.
  13. Andrzej Joachimiak

    Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, United States
    Competing interests
    No competing interests declared.
  14. Kim A Caldwell

    Biological Sciences, The University of Alabama, Tuscaloosa, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1580-6122
  15. Guy A Caldwell

    Biological Sciences, The University of Alabama, Tuscaloosa, United States
    Competing interests
    No competing interests declared.
  16. Ophir Shalem

    Genetics, University of Pennsylvania, Philadelphia, United States
    Competing interests
    No competing interests declared.
  17. James Shorter

    Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United States
    For correspondence
    jshorter@pennmedicine.upenn.edu
    Competing interests
    James Shorter, J.S. is a consultant for Dewpoint Therapeutics..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5269-8533

Funding

National Institute of General Medical Sciences (R01GM099836)

  • James Shorter

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

Reviewing Editor

  1. Franz-Ulrich Hartl, Max Planck Institute for Biochemistry, Germany

Publication history

  1. Received: April 1, 2020
  2. Accepted: December 14, 2020
  3. Accepted Manuscript published: December 15, 2020 (version 1)
  4. Version of Record published: January 5, 2021 (version 2)

Copyright

© 2020, March 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

  • 1,330
    Page views
  • 198
    Downloads
  • 7
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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. Zachary M March
  2. Katelyn Sweeney
  3. Hanna Kim
  4. Xiaohui Yan
  5. Laura M Castellano
  6. Meredith E Jackrel
  7. JiaBei Lin
  8. Edward Chuang
  9. Edward Gomes
  10. Corey W Willicott
  11. Karolina Michalska
  12. Robert P Jedrzejczak
  13. Andrzej Joachimiak
  14. Kim A Caldwell
  15. Guy A Caldwell
  16. Ophir Shalem
  17. James Shorter
(2020)
Therapeutic genetic variation revealed in diverse Hsp104 homologs
eLife 9:e57457.
https://doi.org/10.7554/eLife.57457

Further reading

    1. Biochemistry and Chemical Biology
    Tiantian Wei et al.
    Research Article Updated

    The dual-specificity tyrosine phosphorylation-regulated kinase DYRK2 has emerged as a critical regulator of cellular processes. We took a chemical biology approach to gain further insights into its function. We developed C17, a potent small-molecule DYRK2 inhibitor, through multiple rounds of structure-based optimization guided by several co-crystallized structures. C17 displayed an effect on DYRK2 at a single-digit nanomolar IC50 and showed outstanding selectivity for the human kinome containing 467 other human kinases. Using C17 as a chemical probe, we further performed quantitative phosphoproteomic assays and identified several novel DYRK2 targets, including eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) and stromal interaction molecule 1 (STIM1). DYRK2 phosphorylated 4E-BP1 at multiple sites, and the combined treatment of C17 with AKT and MEK inhibitors showed synergistic 4E-BP1 phosphorylation suppression. The phosphorylation of STIM1 by DYRK2 substantially increased the interaction of STIM1 with the ORAI1 channel, and C17 impeded the store-operated calcium entry process. These studies collectively further expand our understanding of DYRK2 and provide a valuable tool to pinpoint its biological function.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Lukas P Feilen et al.
    Research Article

    Cleavage of membrane proteins in the lipid bilayer by intramembrane proteases is crucial for health and disease. Although different lipid environments can potently modulate their activity, how this is linked to their structural dynamics is unclear. Here we show that the carboxy-peptidase-like activity of the archaeal intramembrane protease PSH, a homolog of the Alzheimer's disease-associated presenilin/γ-secretase is impaired in micelles and promoted in a lipid bilayer. Comparative molecular dynamics simulations revealed that important elements for substrate binding such as transmembrane domain 6a of PSH are more labile in micelles and stabilized in the lipid bilayer. Moreover, consistent with an enhanced interaction of PSH with a transition-state analog inhibitor, the bilayer promoted the formation of the enzyme´s catalytic active site geometry. Our data indicate that the lipid environment of an intramembrane protease plays a critical role in structural stabilization and active site arrangement of the enzyme-substrate complex thereby promoting intramembrane proteolysis.