Dynamic regulation of inter-organelle communication by ubiquitylation controls skeletal muscle development and disease onset
- Brigham and Women's Hospital, United States
- Broad Institute, United States
- Concordia University of Edmonton, Canada
- University of Western Australia, Australia
- 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.
Article and author information
Author details
Pierre M Jean-Beltran
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
- 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
- Received: July 18, 2022
- Preprint posted: July 22, 2022 (view preprint)
- Accepted: June 16, 2023
- Accepted Manuscript published: July 11, 2023 (version 1)
- 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.
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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
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