IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-28391-9.html
   My bibliography  Save this article

Comparative metabolomics with Metaboseek reveals functions of a conserved fat metabolism pathway in C. elegans

Author

Listed:
  • Maximilian J. Helf

    (Cornell University)

  • Bennett W. Fox

    (Cornell University)

  • Alexander B. Artyukhin

    (State University of New York)

  • Ying K. Zhang

    (Cornell University)

  • Frank C. Schroeder

    (Cornell University)

Abstract

Untargeted metabolomics via high-resolution mass spectrometry can reveal more than 100,000 molecular features in a single sample, many of which may represent unidentified metabolites, posing significant challenges to data analysis. We here introduce Metaboseek, an open-source analysis platform designed for untargeted comparative metabolomics and demonstrate its utility by uncovering biosynthetic functions of a conserved fat metabolism pathway, α-oxidation, using C. elegans as a model. Metaboseek integrates modules for molecular feature detection, statistics, molecular formula prediction, and fragmentation analysis, which uncovers more than 200 previously uncharacterized α-oxidation-dependent metabolites in an untargeted comparison of wildtype and α-oxidation-defective hacl-1 mutants. The identified metabolites support the predicted enzymatic function of HACL-1 and reveal that α-oxidation participates in metabolism of endogenous β-methyl-branched fatty acids and food-derived cyclopropane lipids. Our results showcase compound discovery and feature annotation at scale via untargeted comparative metabolomics applied to a conserved primary metabolic pathway and suggest a model for the metabolism of cyclopropane lipids.

Suggested Citation

  • Maximilian J. Helf & Bennett W. Fox & Alexander B. Artyukhin & Ying K. Zhang & Frank C. Schroeder, 2022. "Comparative metabolomics with Metaboseek reveals functions of a conserved fat metabolism pathway in C. elegans," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28391-9
    DOI: 10.1038/s41467-022-28391-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-28391-9
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-28391-9?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Masanori Funabashi & Tyler L. Grove & Min Wang & Yug Varma & Molly E. McFadden & Laura C. Brown & Chunjun Guo & Steven Higginbottom & Steven C. Almo & Michael A. Fischbach, 2020. "A metabolic pathway for bile acid dehydroxylation by the gut microbiome," Nature, Nature, vol. 582(7813), pages 566-570, June.
    2. Michael P. O’Donnell & Bennett W. Fox & Pin-Hao Chao & Frank C. Schroeder & Piali Sengupta, 2020. "A neurotransmitter produced by gut bacteria modulates host sensory behaviour," Nature, Nature, vol. 583(7816), pages 415-420, July.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Russell N. Burkhardt & Alexander B. Artyukhin & Erin Z. Aprison & Brian J. Curtis & Bennett W. Fox & Andreas H. Ludewig & Diana Fajardo Palomino & Jintao Luo & Amaresh Chaturbedi & Oishika Panda & Che, 2023. "Sex-specificity of the C. elegans metabolome," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    2. Tae Hyung Won & Jin Woo Bok & Nischala Nadig & Nandhitha Venkatesh & Grant Nickles & Claudio Greco & Fang Yun Lim & Jennifer B. González & B. Gillian Turgeon & Nancy P. Keller & Frank C. Schroeder, 2022. "Copper starvation induces antimicrobial isocyanide integrated into two distinct biosynthetic pathways in fungi," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. Bennett W. Fox & Maximilian J. Helf & Russell N. Burkhardt & Alexander B. Artyukhin & Brian J. Curtis & Diana Fajardo Palomino & Allen F. Schroeder & Amaresh Chaturbedi & Arnaud Tauffenberger & Cheste, 2024. "Evolutionarily related host and microbial pathways regulate fat desaturation in C. elegans," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Tripti Nair & Brandy A. Weathers & Nicole L. Stuhr & James D. Nhan & Sean P. Curran, 2024. "Serotonin deficiency from constitutive SKN-1 activation drives pathogen apathy," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Bennett W. Fox & Maximilian J. Helf & Russell N. Burkhardt & Alexander B. Artyukhin & Brian J. Curtis & Diana Fajardo Palomino & Allen F. Schroeder & Amaresh Chaturbedi & Arnaud Tauffenberger & Cheste, 2024. "Evolutionarily related host and microbial pathways regulate fat desaturation in C. elegans," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Elvin Koh & In Young Hwang & Hui Ling Lee & Ryan De Sotto & Jonathan Wei Jie Lee & Yung Seng Lee & John C. March & Matthew Wook Chang, 2022. "Engineering probiotics to inhibit Clostridioides difficile infection by dynamic regulation of intestinal metabolism," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    4. Mengci Li & Shouli Wang & Yitao Li & Mingliang Zhao & Junliang Kuang & Dandan Liang & Jieyi Wang & Meilin Wei & Cynthia Rajani & Xinran Ma & Yajun Tang & Zhenxing Ren & Tianlu Chen & Aihua Zhao & Chen, 2022. "Gut microbiota-bile acid crosstalk contributes to the rebound weight gain after calorie restriction in mice," Nature Communications, Nature, vol. 13(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28391-9. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.