1. Biochemistry and Chemical Biology
  2. Cell Biology
Download icon

Light-Regulated allosteric switch enables temporal and subcellular control of enzyme activity

  1. Mark Shaaya
  2. Jordan Fauser
  3. Anastasia Zhurikhina
  4. Jason E Conage-Pough
  5. Vincent Huyot
  6. Martin Brennan
  7. Cameron T Flower
  8. Jacob Matsche
  9. Shazeb Khan
  10. Viswanathan Natarajan
  11. Jalees Rehman
  12. Pradeep Kota
  13. Forest M White
  14. Denis Tsygankov
  15. Andrei V Karginov  Is a corresponding author
  1. University of Illinois at Chicago, United States
  2. Georgia Institute of Technology and Emory University School of Medicine, United States
  3. Massachusetts Institute of Technology, United States
  4. University of North Carolina, United States
  5. Koch Institute for Integrative Cancer Research at MIT, United States
Tools and Resources
  • Cited 5
  • Views 2,481
  • Annotations
Cite this article as: eLife 2020;9:e60647 doi: 10.7554/eLife.60647

Abstract

Engineered allosteric regulation of protein activity provides significant advantages for the development of robust and broadly applicable tools. However, the application of allosteric switches in optogenetics has been scarce and suffers from critical limitations. Here, we report an optogenetic approach that utilizes an engineered Light-Regulated (LightR) allosteric switch module to achieve tight spatiotemporal control of enzymatic activity. Using the tyrosine kinase Src as a model, we demonstrate efficient regulation of the kinase and identify temporally distinct signaling responses ranging from seconds to minutes. LightR-Src off-kinetics can be tuned by modulating the LightR photoconversion cycle. A fast cycling variant enables the stimulation of transient pulses and local regulation of activity in a selected region of a cell. The design of the LightR module ensures broad applicability of the tool, as we demonstrate by achieving light-mediated regulation of Abl and bRaf kinases as well as Cre recombinase.

Data availability

The raw mass spectrometry data and associated tables have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier: PXD018162. All data generated or analyzed during this study are included in the manuscript and supporting files.

The following data sets were generated

Article and author information

Author details

  1. Mark Shaaya

    Department of Pharmacology, University of Illinois at Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Jordan Fauser

    Department of Pharmacology, University of Illinois at Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Anastasia Zhurikhina

    Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Jason E Conage-Pough

    The David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1614-9374
  5. Vincent Huyot

    Department of Pharmacology, University of Illinois at Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Martin Brennan

    Department of Pharmacology, University of Illinois at Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Cameron T Flower

    The David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9632-9913
  8. Jacob Matsche

    Department of Pharmacology, University of Illinois at Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Shazeb Khan

    Department of Pharmacology, University of Illinois at Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Viswanathan Natarajan

    Department of Pharmacology, University of Illinois at Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Jalees Rehman

    Department of Pharmacology, University of Illinois at Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2787-9292
  12. Pradeep Kota

    Department of Medicine, University of North Carolina, Chapel Hill, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Forest M White

    Biological Engineering, Koch Institute for Integrative Cancer Research at MIT, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1545-1651
  14. Denis Tsygankov

    Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1180-3584
  15. Andrei V Karginov

    Department of Pharmacology, University of Illinois at Chicago, Chicago, United States
    For correspondence
    karginov@uic.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2370-6383

Funding

National Institutes of Health (R21CA212907)

  • Jordan Fauser

National Institutes of Health (CA238720)

  • Forest M White

Chicago Biomedical Consortium

  • Andrei V Karginov

Army Research Office (W911NF-17-1-0395)

  • Denis Tsygankov

National Institutes of Health (R21CA159179)

  • Andrei V Karginov

National Institutes of Health (R01GM118582)

  • Andrei V Karginov

National Institutes of Health (R21CA223915)

  • Jalees Rehman
  • Andrei V Karginov

National Institutes of Health (HL007829-22)

  • Mark Shaaya
  • Jordan Fauser
  • Martin Brennan

National Institutes of Health (P01 HL060678)

  • Viswanathan Natarajan
  • Jalees Rehman
  • Andrei V Karginov

National Institutes of Health (CA210180)

  • Forest M White

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

Reviewing Editor

  1. Luis F Larrondo, Pontificia Universidad Católica de Chile, Chile

Publication history

  1. Received: July 2, 2020
  2. Accepted: September 22, 2020
  3. Accepted Manuscript published: September 23, 2020 (version 1)
  4. Accepted Manuscript updated: September 24, 2020 (version 2)
  5. Version of Record published: October 21, 2020 (version 3)
  6. Version of Record updated: November 11, 2020 (version 4)

Copyright

© 2020, Shaaya 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

  • 2,481
    Page views
  • 457
    Downloads
  • 5
    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)

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

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

Further reading

    1. Biochemistry and Chemical Biology
    2. Developmental Biology
    Lucas C Pantaleão et al.
    Research Article Updated

    Maternal obesity during pregnancy has immediate and long-term detrimental effects on the offspring heart. In this study, we characterized the cardiac and circulatory lipid profiles in late gestation E18.5 fetuses of diet-induced obese pregnant mice and established the changes in lipid abundance and fetal cardiac transcriptomics. We used untargeted and targeted lipidomics and transcriptomics to define changes in the serum and cardiac lipid composition and fatty acid metabolism in male and female fetuses. From these analyses we observed: (1) maternal obesity affects the maternal and fetal serum lipidome distinctly; (2) female fetal heart lipidomes are more sensitive to maternal obesity than males; (3) changes in lipid supply might contribute to early expression of lipolytic genes in mouse hearts exposed to maternal obesity. These results highlight the existence of sexually dimorphic responses of the fetal heart to the same in utero obesogenic environment and identify lipids species that might mediate programming of cardiovascular health.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Marella D Canny, Michael Latham
    Research Article

    The Mre11-Rad50-Nbs1 protein complex is one of the first responders to DNA double strand breaks. Studies have shown that the catalytic activities of the evolutionarily conserved Mre11-Rad50 (MR) core complex depend on an ATP-dependent global conformational change that takes the macromolecule from an open, extended structure in the absence of ATP to a closed, globular structure when ATP is bound. We have previously identified an additional ‘partially open’ conformation using Luminescence Resonance Energy Transfer (LRET) experiments. Here, a combination of LRET and the molecular docking program HADDOCK was used to further investigate this partially open state and identify three conformations of MR in solution: closed, partially open, and open, which are in addition to the extended, apo conformation. Mutants disrupting specific Mre11-Rad50 interactions within each conformation were used in nuclease activity assays on a variety of DNA substrates to help put the three states into a functional perspective. LRET data collected on MR bound to DNA demonstrate that the three conformations also exist when nuclease substrates are bound. These models were further supported with SAXS data which corroborate the presence of multiple states in solution. Together, the data suggest a mechanism for the nuclease activity of the MR complex along the DNA.