GFPT2/GFAT2 and AMDHD2 act in tandem to control the hexosamine pathway

  1. Virginia Kroef
  2. Sabine Ruegenberg
  3. Moritz Horn
  4. Kira Allmeroth
  5. Lena Ebert
  6. Seyma Bozkus
  7. Stephan Miethe
  8. Ulrich Elling
  9. Bernhard Schermer
  10. Ulrich Baumann
  11. Martin Sebastian Denzel  Is a corresponding author
  1. Max Planck Institute for Biology of Ageing, Germany
  2. JLP Health GmbH, Austria
  3. University of Cologne, Germany
  4. Austrian Academy of Sciences, Austria
  5. Altos Labs, United Kingdom

Abstract

The hexosamine biosynthetic pathway (HBP) produces the essential metabolite UDP-GlcNAc and plays a key role in metabolism, health, and aging. The HBP is controlled by its rate-limiting enzyme glutamine fructose-6-phosphate amidotransferase (GFPT/GFAT) that is directly inhibited by UDP-GlcNAc in a feedback loop. HBP regulation by GFPT is well studied but other HBP regulators have remained obscure. Elevated UDP‑GlcNAc levels counteract the glycosylation toxin tunicamycin (TM) and thus we screened for TM resistance in haploid mouse embryonic stem cells (mESCs) using random chemical mutagenesis to determine alternative HBP regulation. We identified the N‑acetylglucosamine deacetylase AMDHD2 that catalyzes a reverse reaction in the HBP and its loss strongly elevated UDP-GlcNAc. To better understand AMDHD2, we solved the crystal structure and found that loss-of-function is caused by protein destabilization or interference with its catalytic activity. Finally, we show that mESCs express AMDHD2 together with GFPT2 instead of the more common paralog GFPT1. Compared with GFPT1, GFPT2 had a much lower sensitivity to UDP-GlcNAc inhibition, explaining how AMDHD2 loss-of-function resulted in HBP activation. This HBP configuration in which AMDHD2 serves to balance GFPT2 activity was also observed in other mESCs and, consistently, the GFPT2:GFPT1 ratio decreased with differentiation of human embryonic stem cells. Together, our data reveal a critical function of AMDHD2 in limiting UDP‑GlcNAc production in cells that use GFPT2 for metabolite entry into the HBP.

Data availability

Structural data reported in this study have been deposited in the Protein Data Bank with the accession codes 7NUT [https://doi.org/10.2210/pdb7NUT/pdb] and 7NUU [https://doi.org/10.2210/pdb7NUU/pdb].

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Virginia Kroef

    Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3695-911X
  2. Sabine Ruegenberg

    Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5292-9610
  3. Moritz Horn

    JLP Health GmbH, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  4. Kira Allmeroth

    Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2659-6776
  5. Lena Ebert

    University of Cologne, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Seyma Bozkus

    University of Cologne, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Stephan Miethe

    Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Ulrich Elling

    Vienna Biocenter, Austrian Academy of Sciences, Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  9. Bernhard Schermer

    University of Cologne, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. Ulrich Baumann

    University of Cologne, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  11. Martin Sebastian Denzel

    Altos Labs, Cambridge, United Kingdom
    For correspondence
    mdenzel@altoslabs.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5691-3349

Funding

Bundesministerium für Bildung und Forschung (01GQ1423A EndoProtect)

  • Sabine Ruegenberg

Bundesministerium für Bildung und Forschung (01GQ1423A EndoProtect)

  • Stephan Miethe

Bundesministerium für Bildung und Forschung (01GQ1423A EndoProtect)

  • Martin Sebastian Denzel

Deutsche Forschungsgemeinschaft (73111208-SFB 829)

  • Ulrich Baumann

Deutsche Forschungsgemeinschaft (73111208-SFB 829)

  • Martin Sebastian Denzel

H2020 European Research Council (ERC-2014-StG-640254-MetAGEn)

  • Martin Sebastian Denzel

Max Planck Institute for Biology of Ageing (Open Access Funding)

  • Virginia Kroef

Deutsche Forschungsgemeinschaft (SCHE1562/8-1)

  • Bernhard Schermer

Deutsche Forschungsgemeinschaft (SFB1403, project number 414786233, A09)

  • Bernhard Schermer

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

Ethics

Animal experimentation: All procedures have been performed in our specialized facility, followed all relevant animal welfare guidelines and regulations, and were approved by LANUV NRW 84-02.04.2015.A025.

Copyright

© 2022, Kroef 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

  • 1,875
    views
  • 316
    downloads
  • 23
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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. Virginia Kroef
  2. Sabine Ruegenberg
  3. Moritz Horn
  4. Kira Allmeroth
  5. Lena Ebert
  6. Seyma Bozkus
  7. Stephan Miethe
  8. Ulrich Elling
  9. Bernhard Schermer
  10. Ulrich Baumann
  11. Martin Sebastian Denzel
(2022)
GFPT2/GFAT2 and AMDHD2 act in tandem to control the hexosamine pathway
eLife 11:e69223.
https://doi.org/10.7554/eLife.69223

Share this article

https://doi.org/10.7554/eLife.69223

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.