OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development

  1. Joel Hrit
  2. Leeanne Goodrich
  3. Cheng Li
  4. Bang-An Wang
  5. Ji Nie
  6. Xiaolong Cui
  7. Elizabeth Allene Martin
  8. Eric Simental
  9. Jenna Fernandez
  10. Monica Y Liu
  11. Joseph R Nery
  12. Rosa Castanon
  13. Rahul M Kohli
  14. Natalia Tretyakova
  15. Chuan He
  16. Joseph R Ecker
  17. Mary Goll
  18. Barbara Panning  Is a corresponding author
  1. University of California, San Francisco, United States
  2. Memorial Sloan Kettering Cancer Center, United States
  3. Salk Institute for Biological Studies, United States
  4. University of Chicago, United States
  5. University of Minnesota, United States
  6. University of Pennsylvania, United States

Abstract

TET enzymes convert 5-methylcytosine to 5-hydroxymethylcytosine and higher oxidized derivatives. TETs stably associate with and are post-translationally modified by the nutrient-sensing enzyme OGT, suggesting a connection between metabolism and the epigenome. Here, we show for the first time that modification by OGT enhances TET1 activity in vitro. We identify a TET1 domain that is necessary and sufficient for binding to OGT and report a point mutation that disrupts the TET1-OGT interaction. We show that this interaction is necessary for TET1 to rescue hematopoetic stem cell production in tet mutant zebrafish embryos, suggesting that OGT promotes TET1's function during development. Finally, we show that disrupting the TET1-OGT interaction in mouse embryonic stem cells changes the abundance of TET2 and 5-methylcytosine, which is accompanied by alterations in gene expression. These results link metabolism and epigenetic control, which may be relevant to the developmental and disease processes regulated by these two enzymes.

Data availability

5hmC-Seal data has been uploaded to GEO under accession GSE119500.High throughput RNA-seq and WGBS data has been uploaded to GEO under accession GSE119666.

The following data sets were generated

Article and author information

Author details

  1. Joel Hrit

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Leeanne Goodrich

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Cheng Li

    Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Bang-An Wang

    Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Ji Nie

    Departments of Chemistry, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Xiaolong Cui

    Departments of Chemistry, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Elizabeth Allene Martin

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Eric Simental

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Jenna Fernandez

    Department of Medicinal Chemistry, University of Minnesota, Minneapolis, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Monica Y Liu

    Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Joseph R Nery

    Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Rosa Castanon

    Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Rahul M Kohli

    Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Natalia Tretyakova

    Department of Medicinal Chemistry, University of Minnesota, Minneapolis, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Chuan He

    Department of Chemistry, University of 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:" 0000-0003-4319-7424
  16. Joseph R Ecker

    Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5799-5895
  17. Mary Goll

    Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Barbara Panning

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    For correspondence
    barbara.panning@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8301-1172

Funding

National Cancer Institute (P30 CA008748)

  • Cheng Li
  • Mary Goll

California Institute for Regenerative Medicine (TG2-01153)

  • Joel Hrit
  • Barbara Panning

National Institutes of Health (R01 GM088506)

  • Joel Hrit
  • Leeanne Goodrich
  • Barbara Panning

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

Reviewing Editor

  1. Daniel Zilberman, John Innes Centre, United Kingdom

Publication history

  1. Received: January 6, 2018
  2. Accepted: October 15, 2018
  3. Accepted Manuscript published: October 16, 2018 (version 1)
  4. Version of Record published: November 2, 2018 (version 2)

Copyright

© 2018, Hrit 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

  • 3,390
    Page views
  • 600
    Downloads
  • 26
    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. Joel Hrit
  2. Leeanne Goodrich
  3. Cheng Li
  4. Bang-An Wang
  5. Ji Nie
  6. Xiaolong Cui
  7. Elizabeth Allene Martin
  8. Eric Simental
  9. Jenna Fernandez
  10. Monica Y Liu
  11. Joseph R Nery
  12. Rosa Castanon
  13. Rahul M Kohli
  14. Natalia Tretyakova
  15. Chuan He
  16. Joseph R Ecker
  17. Mary Goll
  18. Barbara Panning
(2018)
OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development
eLife 7:e34870.
https://doi.org/10.7554/eLife.34870

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Morgane Boone et al.
    Research Advance Updated

    In eukaryotic cells, stressors reprogram the cellular proteome by activating the integrated stress response (ISR). In its canonical form, stress-sensing kinases phosphorylate the eukaryotic translation initiation factor eIF2 (eIF2-P), which ultimately leads to reduced levels of ternary complex required for initiation of mRNA translation. Previously we showed that translational control is primarily exerted through a conformational switch in eIF2’s nucleotide exchange factor, eIF2B, which shifts from its active A-State conformation to its inhibited I-State conformation upon eIF2-P binding, resulting in reduced nucleotide exchange on eIF2 (Schoof et al. 2021). Here, we show functionally and structurally how a single histidine to aspartate point mutation in eIF2B’s β subunit (H160D) mimics the effects of eIF2-P binding by promoting an I-State like conformation, resulting in eIF2-P independent activation of the ISR. These findings corroborate our previously proposed A/I-State model of allosteric ISR regulation.

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Florian Bleffert et al.
    Research Article Updated

    Cells steadily adapt their membrane glycerophospholipid (GPL) composition to changing environmental and developmental conditions. While the regulation of membrane homeostasis via GPL synthesis in bacteria has been studied in detail, the mechanisms underlying the controlled degradation of endogenous GPLs remain unknown. Thus far, the function of intracellular phospholipases A (PLAs) in GPL remodeling (Lands cycle) in bacteria is not clearly established. Here, we identified the first cytoplasmic membrane-bound phospholipase A1 (PlaF) from Pseudomonas aeruginosa, which might be involved in the Lands cycle. PlaF is an important virulence factor, as the P. aeruginosa ΔplaF mutant showed strongly attenuated virulence in Galleria mellonella and macrophages. We present a 2.0-Å-resolution crystal structure of PlaF, the first structure that reveals homodimerization of a single-pass transmembrane (TM) full-length protein. PlaF dimerization, mediated solely through the intermolecular interactions of TM and juxtamembrane regions, inhibits its activity. The dimerization site and the catalytic sites are linked by an intricate ligand-mediated interaction network, which might explain the product (fatty acid) feedback inhibition observed with the purified PlaF protein. We used molecular dynamics simulations and configurational free energy computations to suggest a model of PlaF activation through a coupled monomerization and tilting of the monomer in the membrane, which constrains the active site cavity into contact with the GPL substrates. Thus, these data show the importance of the PlaF-mediated GPL remodeling pathway for virulence and could pave the way for the development of novel therapeutics targeting PlaF.