Dynamic regulation of inter-organelle communication by ubiquitylation controls skeletal muscle development and disease onset

  1. Arian Mansur
  2. Remi Joseph
  3. Euri Kim
  4. Pierre M Jean-Beltran
  5. Namrata D Udeshi
  6. Cadence Pearce
  7. Hanjie Jiang
  8. Reina Iwase
  9. Miroslav P Milev
  10. Hashem A Almousa
  11. Elyshia McNamara
  12. Jeffrey Widrick
  13. Claudio Perez
  14. Gianina Ravenscroft
  15. Michael Sacher
  16. Philip A Cole
  17. Steven A Carr
  18. Vandana A Gupta  Is a corresponding author
  1. Brigham and Women's Hospital, United States
  2. Broad Institute, United States
  3. Concordia University of Edmonton, Canada
  4. University of Western Australia, Australia
  5. Boston Children's Hospital, United States

Abstract

Ubiquitin-proteasome system (UPS) dysfunction is associated with the pathology of a wide range of human diseases, including myopathies and muscular atrophy. However, the mechanistic understanding of specific components of the regulation of protein turnover during development and disease progression in skeletal muscle is unclear. Mutations in KLHL40, an E3 ubiquitin ligase cullin3 (CUL3) substrate-specific adapter protein, result in severe congenital nemaline myopathy, but the events that initiate the pathology and the mechanism through which it becomes pervasive remain poorly understood. To characterize the KLHL40-regulated ubiquitin-modified proteome during skeletal muscle development and disease onset, we used global, quantitative mass spectrometry-based ubiquitylome and global proteome analyses of klhl40a mutant zebrafish during disease progression. Global proteomics during skeletal muscle development revealed extensive remodeling of functional modules linked with sarcomere formation, energy, biosynthetic metabolic processes, and vesicle trafficking. Combined analysis of klh40 mutant muscle proteome and ubiquitylome identified thin filament proteins, metabolic enzymes, and ER-Golgi vesicle trafficking pathway proteins regulated by ubiquitylation during muscle development. Our studies identified a role for KLHL40 as a regulator of ER-Golgi anterograde trafficking through ubiquitin-mediated protein degradation of secretion-associated Ras-related GTPase1a (Sar1a). In KLHL40 deficient muscle, defects in ER exit site vesicle formation and downstream transport of extracellular cargo proteins result in structural and functional abnormalities. Our work reveals that the muscle proteome is dynamically fine-tuned by ubiquitylation to regulate skeletal muscle development and uncovers new disease mechanisms for therapeutic development in patients.

Data availability

The data is publicly available via Sequence Read Archive (SRA) (Accession Number: PRJNA861969) and MassIVE (http://massive.ucsd.edu) and are accessible at ftp://MSV000090018@massive.ucsd.edu.

The following data sets were generated

Article and author information

Author details

  1. Arian Mansur

    Department of Medicine, Brigham and Women's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Remi Joseph

    Department of Medicine, Brigham and Women's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Euri Kim

    Department of Medicine, Brigham and Women's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Pierre M Jean-Beltran

    Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5106-0992
  5. Namrata D Udeshi

    Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Cadence Pearce

    Proteomics Platform, Broad Institute, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Hanjie Jiang

    Department of Medicine, Brigham and Women's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Reina Iwase

    Department of Medicine, Brigham and Women's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3703-2511
  9. Miroslav P Milev

    Department of Biology, Concordia University of Edmonton, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  10. Hashem A Almousa

    Department of Biology, Concordia University of Edmonton, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  11. Elyshia McNamara

    Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
    Competing interests
    The authors declare that no competing interests exist.
  12. Jeffrey Widrick

    Division of Genetics, Boston Children's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Claudio Perez

    Department of Anesthesiology, Brigham and Women's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Gianina Ravenscroft

    Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
    Competing interests
    The authors declare that no competing interests exist.
  15. Michael Sacher

    Department of Biology, Concordia University of Edmonton, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  16. Philip A Cole

    Department of Medicine, Brigham and Women's Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6873-7824
  17. Steven A Carr

    Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Vandana A Gupta

    Department of Medicine, Brigham and Women's Hospital, Boston, United States
    For correspondence
    vgupta@research.bwh.harvard.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4057-8451

Funding

A foundation Building Strength

  • Vandana A Gupta

National Institute of Arthritis and Musculoskeletal and Skin Diseases (R56AR077017)

  • Vandana A Gupta

National Institute of Health (R37GM62437)

  • Philip A Cole

National Cancer Institute (R01CA74305)

  • Philip A Cole

Brigham and Women's Hospital

  • Vandana A Gupta

National Heart, Lung, and Blood Institute (F32HL154711)

  • Pierre M Jean-Beltran

National Health and Medical Research Council (APP2002640)

  • Gianina Ravenscroft

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

Reviewing Editor

  1. Meir Aridor

Ethics

Animal experimentation: Zebrafish were maintained and bred using standard methods as described (Westerfield,2000). All experiments and procedures were approved by the Institutional Animal Care and Use Committee at Brigham and Women's Hospital. (2016000304).

Human subjects: Human Research Ethics Committee of the University of Western Australia (RA/4/20/1008). Written informed consent was provided by all families.

Version history

  1. Received: July 18, 2022
  2. Preprint posted: July 22, 2022 (view preprint)
  3. Accepted: June 16, 2023
  4. Accepted Manuscript published: July 11, 2023 (version 1)
  5. Version of Record published: July 19, 2023 (version 2)

Copyright

© 2023, Mansur 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

  • 955
    views
  • 159
    downloads
  • 3
    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. Arian Mansur
  2. Remi Joseph
  3. Euri Kim
  4. Pierre M Jean-Beltran
  5. Namrata D Udeshi
  6. Cadence Pearce
  7. Hanjie Jiang
  8. Reina Iwase
  9. Miroslav P Milev
  10. Hashem A Almousa
  11. Elyshia McNamara
  12. Jeffrey Widrick
  13. Claudio Perez
  14. Gianina Ravenscroft
  15. Michael Sacher
  16. Philip A Cole
  17. Steven A Carr
  18. Vandana A Gupta
(2023)
Dynamic regulation of inter-organelle communication by ubiquitylation controls skeletal muscle development and disease onset
eLife 12:e81966.
https://doi.org/10.7554/eLife.81966

Share this article

https://doi.org/10.7554/eLife.81966

Further reading

    1. Cell Biology
    2. Developmental Biology
    Corey D Holman, Alexander P Sakers ... Patrick Seale
    Research Article

    The energy-burning capability of beige adipose tissue is a potential therapeutic tool for reducing obesity and metabolic disease, but this capacity is decreased by aging. Here, we evaluate the impact of aging on the profile and activity of adipocyte stem and progenitor cells (ASPCs) and adipocytes during the beiging process in mice. We found that aging increases the expression of Cd9 and other fibro-inflammatory genes in fibroblastic ASPCs and blocks their differentiation into beige adipocytes. Fibroblastic ASPC populations from young and aged mice were equally competent for beige differentiation in vitro, suggesting that environmental factors suppress adipogenesis in vivo. Examination of adipocytes by single nucleus RNA-sequencing identified compositional and transcriptional differences in adipocyte populations with aging and cold exposure. Notably, cold exposure induced an adipocyte population expressing high levels of de novo lipogenesis (DNL) genes, and this response was severely blunted in aged animals. We further identified Npr3, which encodes the natriuretic peptide clearance receptor, as a marker gene for a subset of white adipocytes and an aging-upregulated gene in adipocytes. In summary, this study indicates that aging blocks beige adipogenesis and dysregulates adipocyte responses to cold exposure and provides a resource for identifying cold and aging-regulated pathways in adipose tissue.

    1. Cell Biology
    Tongtong Ma, Ruimin Ren ... Heng Wang
    Research Article

    Current studies on cultured meat mainly focus on the muscle tissue reconstruction in vitro, but lack the formation of intramuscular fat, which is a crucial factor in determining taste, texture, and nutritional contents. Therefore, incorporating fat into cultured meat is of superior value. In this study, we employed the myogenic/lipogenic transdifferentiation of chicken fibroblasts in 3D to produce muscle mass and deposit fat into the same cells without the co-culture or mixture of different cells or fat substances. The immortalized chicken embryonic fibroblasts were implanted into the hydrogel scaffold, and the cell proliferation and myogenic transdifferentiation were conducted in 3D to produce the whole-cut meat mimics. Compared to 2D, cells grown in 3D matrix showed elevated myogenesis and collagen production. We further induced fat deposition in the transdifferentiated muscle cells and the triglyceride content could be manipulated to match and exceed the levels of chicken meat. The gene expression analysis indicated that both lineage-specific and multifunctional signalings could contribute to the generation of muscle/fat matrix. Overall, we were able to precisely modulate muscle, fat, and extracellular matrix contents according to balanced or specialized meat preferences. These findings provide new avenues for customized cultured meat production with desired intramuscular fat contents that can be tailored to meet the diverse demands of consumers.