Modular metabolite assembly in C. elegans depends on carboxylesterases and formation of lysosome-related organelles

  1. Henry H Le
  2. Chester JJ Wrobel
  3. Sarah M Cohen
  4. Jingfang Yu
  5. Heenam Park
  6. Maximilian J Helf
  7. Brian J Curtis
  8. Joseph C Kruempel
  9. Pedro Reis Rodrigues
  10. Patrick J Hu
  11. Paul W Sternberg  Is a corresponding author
  12. Frank C Schroeder  Is a corresponding author
  1. BTI/Cornell University, United States
  2. Caltech, United States
  3. University of Michigan Medical School, United States
  4. Vanderbilt University School of Medicine, United States
  5. Howard Hughes Medical Institute, California Institute of Technology, United States

Abstract

Signaling molecules derived from attachment of diverse metabolic building blocks to ascarosides play a central role in the life history of C. elegans and other nematodes; however, many aspects of their biogenesis remain unclear. Using comparative metabolomics, we show that a pathway mediating formation of intestinal lysosome-related organelles (LROs) is required for biosynthesis of most modular ascarosides as well as previously undescribed modular glucosides. Similar to modular ascarosides, the modular glucosides are derived from highly selective assembly of moieties from nucleoside, amino acid, neurotransmitter, and lipid metabolism, suggesting that modular glucosides, like the ascarosides, may serve signaling functions. We further show that carboxylesterases that localize to intestinal organelles are required for the assembly of both modular ascarosides and glucosides via ester and amide linkages. Further exploration of LRO function and carboxylesterase homologs in C. elegans and other animals may reveal additional new compound families and signaling paradigms.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. MS/MS data is available via MassIVE under accession number: MSV000086293.

The following data sets were generated

Article and author information

Author details

  1. Henry H Le

    Chemistry and Chemical Biology, BTI/Cornell University, Ithaca, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2942-2357
  2. Chester JJ Wrobel

    Chemistry and Chemical Biology, BTI/Cornell University, Ithaca, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Sarah M Cohen

    Division of Biology and Biological Engineering, Caltech, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Jingfang Yu

    Chemistry and Chemical Biology, BTI/Cornell University, Ithaca, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1770-5368
  5. Heenam Park

    Division of Biology and Biological Engineering, Caltech, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Maximilian J Helf

    Chemistry and Chemical Biology, BTI/Cornell University, Ithaca, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Brian J Curtis

    Chemistry and Chemical Biology, BTI/Cornell University, Ithaca, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Joseph C Kruempel

    Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Pedro Reis Rodrigues

    Chemistry and Chemical Biology, BTI/Cornell University, Ithaca, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Patrick J Hu

    Departments of Medicine and Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Paul W Sternberg

    Division of Biology & BIological Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
    For correspondence
    pws@caltech.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7699-0173
  12. Frank C Schroeder

    Chemistry and Chemical Biology, BTI/Cornell University, Ithaca, United States
    For correspondence
    fs31@cornell.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4420-0237

Funding

National Institutes of Health (R35 GM131877)

  • Frank C Schroeder

National Institutes of Health (R24 OD023041)

  • Paul W Sternberg

National Institutes of Health (5T32GM008500)

  • Brian J Curtis

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

Reviewing Editor

  1. Michael A Marletta, University of California, Berkeley, United States

Version history

  1. Received: August 7, 2020
  2. Accepted: October 14, 2020
  3. Accepted Manuscript published: October 16, 2020 (version 1)
  4. Version of Record published: November 4, 2020 (version 2)

Copyright

© 2020, Le 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

  • 2,064
    views
  • 319
    downloads
  • 17
    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. Henry H Le
  2. Chester JJ Wrobel
  3. Sarah M Cohen
  4. Jingfang Yu
  5. Heenam Park
  6. Maximilian J Helf
  7. Brian J Curtis
  8. Joseph C Kruempel
  9. Pedro Reis Rodrigues
  10. Patrick J Hu
  11. Paul W Sternberg
  12. Frank C Schroeder
(2020)
Modular metabolite assembly in C. elegans depends on carboxylesterases and formation of lysosome-related organelles
eLife 9:e61886.
https://doi.org/10.7554/eLife.61886

Share this article

https://doi.org/10.7554/eLife.61886

Further reading

    1. Biochemistry and Chemical Biology
    Ornella Bimai, Ipsita Banerjee ... Derek T Logan
    Research Article

    A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding adenosine triphosphate (ATP) or deoxyadenosine triphosphate (dATP) it regulates the enzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs has revealed a plethora of ways in which dATP inhibits activity by inducing oligomerisation and preventing a productive radical transfer from one subunit to the active site in the other. Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and the basis for their dATP-dependent inhibition is completely unknown. We present biochemical, biophysical, and structural information on the effects of ATP and dATP binding to the anaerobic RNR from Prevotella copri. The enzyme exists in a dimer–tetramer equilibrium biased towards dimers when two ATP molecules are bound to the ATP-cone and tetramers when two dATP molecules are bound. In the presence of ATP, P. copri NrdD is active and has a fully ordered glycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-cone results in loss of activity and increased dynamics of the GRD, such that it cannot be detected in the cryo-EM structures. The glycyl radical is formed even in the dATP-bound form, but the substrate does not bind. The structures implicate a complex network of interactions in activity regulation that involve the GRD more than 30 Å away from the dATP molecules, the allosteric substrate specificity site and a conserved but previously unseen flap over the active site. Taken together, the results suggest that dATP inhibition in anaerobic RNRs acts by increasing the flexibility of the flap and GRD, thereby preventing both substrate binding and radical mobilisation.

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Ya-Juan Wang, Xiao-Jing Di ... Ting-Wei Mu
    Research Article

    Protein homeostasis (proteostasis) deficiency is an important contributing factor to neurological and metabolic diseases. However, how the proteostasis network orchestrates the folding and assembly of multi-subunit membrane proteins is poorly understood. Previous proteomics studies identified Hsp47 (Gene: SERPINH1), a heat shock protein in the endoplasmic reticulum lumen, as the most enriched interacting chaperone for gamma-aminobutyric type A (GABAA) receptors. Here, we show that Hsp47 enhances the functional surface expression of GABAA receptors in rat neurons and human HEK293T cells. Furthermore, molecular mechanism study demonstrates that Hsp47 acts after BiP (Gene: HSPA5) and preferentially binds the folded conformation of GABAA receptors without inducing the unfolded protein response in HEK293T cells. Therefore, Hsp47 promotes the subunit-subunit interaction, the receptor assembly process, and the anterograde trafficking of GABAA receptors. Overexpressing Hsp47 is sufficient to correct the surface expression and function of epilepsy-associated GABAA receptor variants in HEK293T cells. Hsp47 also promotes the surface trafficking of other Cys-loop receptors, including nicotinic acetylcholine receptors and serotonin type 3 receptors in HEK293T cells. Therefore, in addition to its known function as a collagen chaperone, this work establishes that Hsp47 plays a critical and general role in the maturation of multi-subunit Cys-loop neuroreceptors.