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.

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.

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

Share this article

https://doi.org/10.7554/eLife.57457

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Angel D'Oliviera, Xuhang Dai ... Jeffrey S Mugridge
    Research Article

    The SARS-CoV-2 main protease (Mpro or Nsp5) is critical for production of viral proteins during infection and, like many viral proteases, also targets host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 is recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes cellular protein synthesis and redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain. Evolutionary analysis shows the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 is likely resistant to cleavage. TRMT1 proteolysis results in reduced tRNA binding and elimination of tRNA methyltransferase activity. We also determined the structure of an Mpro-TRMT1 peptide complex that shows how TRMT1 engages the Mpro active site in an uncommon substrate binding conformation. Finally, enzymology and molecular dynamics simulations indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis following substrate binding. Together, these data provide new insights into substrate recognition by SARS-CoV-2 Mpro that could help guide future antiviral therapeutic development and show how proteolysis of TRMT1 during SARS-CoV-2 infection impairs both TRMT1 tRNA binding and tRNA modification activity to disrupt host translation and potentially impact COVID-19 pathogenesis or phenotypes.

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Qian Wang, Jinxin Liu ... Qian Liu
    Research Article

    Paramyxovirus membrane fusion requires an attachment protein for receptor binding and a fusion protein for membrane fusion triggering. Nipah virus (NiV) attachment protein (G) binds to ephrinB2 or -B3 receptors, and fusion protein (F) mediates membrane fusion. NiV-F is a class I fusion protein and is activated by endosomal cleavage. The crystal structure of a soluble GCN4-decorated NiV-F shows a hexamer-of-trimer assembly. Here, we used single-molecule localization microscopy to quantify the NiV-F distribution and organization on cell and virus-like particle membranes at a nanometer precision. We found that NiV-F on biological membranes forms distinctive clusters that are independent of endosomal cleavage or expression levels. The sequestration of NiV-F into dense clusters favors membrane fusion triggering. The nano-distribution and organization of NiV-F are susceptible to mutations at the hexamer-of-trimer interface, and the putative oligomerization motif on the transmembrane domain. We also show that NiV-F nanoclusters are maintained by NiV-F–AP-2 interactions and the clathrin coat assembly. We propose that the organization of NiV-F into nanoclusters facilitates membrane fusion triggering by a mixed population of NiV-F molecules with varied degrees of cleavage and opportunities for interacting with the NiV-G/receptor complex. These observations provide insights into the in situ organization and activation mechanisms of the NiV fusion machinery.