Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function

  1. Adedeji M Aderounmu
  2. P Joseph Aruscavage
  3. Bryan Kolaczkowski
  4. Brenda L Bass  Is a corresponding author
  1. University of Utah, United States
  2. University of Florida, United States

Abstract

Antiviral defense in ecdysozoan invertebrates requires Dicer with a helicase domain capable of ATP hydrolysis. But despite well-conserved ATPase motifs, human Dicer is incapable of ATP hydrolysis, consistent with a muted role in antiviral defense. To investigate this enigma, we used ancestral protein reconstruction to resurrect Dicer’s helicase in animals and trace the evolutionary trajectory of ATP hydrolysis. Biochemical assays indicated ancient Dicer possessed ATPase function, that like extant invertebrate Dicers, is stimulated by dsRNA. Analyses revealed that dsRNA stimulates ATPase activity by increasing ATP affinity, reflected in Michaelis constants. Deuterostome Dicer-1 ancestor, while exhibiting lower dsRNA affinity, retained some ATPase activity; importantly, ATPase activity was undetectable in the vertebrate Dicer-1 ancestor, which had even lower dsRNA affinity. Reverting residues in the ATP hydrolysis pocket was insufficient to rescue hydrolysis, but additional substitutions distant from the pocket rescued vertebrate Dicer-1's ATPase function. Our work suggests Dicer lost ATPase function in the vertebrate ancestor due to loss of ATP affinity, involving motifs distant from the active site, important for coupling dsRNA binding to the active conformation. By competing with Dicer for viral dsRNA, RIG-I-like receptors important for interferon signaling may have allowed, or actively caused, loss of ATPase function.

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files. Source Data files have been provided for all gels displayed in Figures 2, 3 and 4. Phylogenetic and ancestral protein reconstruction data are provided as Supplementary Files.

Article and author information

Author details

  1. Adedeji M Aderounmu

    Department of Biochemistry, University of Utah, Salt Lake City, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. P Joseph Aruscavage

    Department of Biochemistry, University of Utah, Salt Lake City, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Bryan Kolaczkowski

    Department of Microbiology and Cell Science, University of Florida, Gainesville, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Brenda L Bass

    Department of Biochemistry, University of Utah, Salt Lake City, United States
    For correspondence
    bbass@biochem.utah.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1728-2254

Funding

School of Medicine (Graduate Student Fellowship)

  • Adedeji M Aderounmu

National Institute of General Medical Sciences (R35GM141262)

  • Brenda L Bass

National Cancer Institute (R01CA260414)

  • Brenda L Bass

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

Reviewing Editor

  1. Volker Dötsch, Goethe University, Germany

Publication history

  1. Received: November 23, 2022
  2. Preprint posted: December 30, 2022 (view preprint)
  3. Accepted: April 14, 2023
  4. Accepted Manuscript published: April 17, 2023 (version 1)
  5. Version of Record published: May 4, 2023 (version 2)

Copyright

© 2023, Aderounmu 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.

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  1. Adedeji M Aderounmu
  2. P Joseph Aruscavage
  3. Bryan Kolaczkowski
  4. Brenda L Bass
(2023)
Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function
eLife 12:e85120.
https://doi.org/10.7554/eLife.85120

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