Defining mitochondrial protein functions through deep multiomic profiling

• Published in: Nature (London) Vol. 606; no. 7913; pp. 382 - 388
• Main Authors: Rensvold, Jarred W., Shishkova, Evgenia, Sverchkov, Yuriy, Miller, Ian J., Cetinkaya, Arda, Pyle, Angela, Manicki, Mateusz, Brademan, Dain R., Alanay, Yasemin, Raiman, Julian, Jochem, Adam, Hutchins, Paul D., Peters, Sean R., Linke, Vanessa, Overmyer, Katherine A., Salome, Austin Z., Hebert, Alexander S., Vincent, Catherine E., Kwiecien, Nicholas W., Rush, Matthew J. P., Westphall, Michael S., Craven, Mark, Akarsu, Nurten A., Taylor, Robert W., Coon, Joshua J., Pagliarini, David J.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 09-06-2022; Nature Publishing Group
• Subjects: 13/106; 38; 45; 45/41; 631/45/475; 631/553/2710; 631/80/642/333; 692/699/317; 82; 82/1; 82/16; 82/29; 82/47; 82/58; 82/80; 82/83; Adenosylmethionine; Biology; Biosynthesis; Cation Transport Proteins; Cell Cycle Proteins; Chromatography; Coenzyme Q; CRISPR; Depth profiling; Electron microscopy; Energy Metabolism; Functionals; Genes; Humanities and Social Sciences; Humans; Kinases; Lipids; Mass Spectrometry; Mass spectroscopy; Metabolism; Metabolites; Methyltransferase; Mitochondria; Mitochondria - genetics; Mitochondria - metabolism; Mitochondrial Diseases - genetics; Mitochondrial Diseases - metabolism; Mitochondrial DNA; Mitochondrial Proteins - genetics; Mitochondrial Proteins - metabolism; mRNA; multidisciplinary; Mutation; Proteins; Proteomics; rab5 GTP-Binding Proteins; S-Adenosylmethionine; Science; Science (multidisciplinary); Scientific imaging; Transcription Factors
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/s41586-022-04765-3

Mitochondria are epicentres of eukaryotic metabolism and bioenergetics. Pioneering efforts in recent decades have established the core protein componentry of these organelles
1
and have linked their dysfunction to more than 150 distinct disorders
2
,
3
. Still, hundreds of mitochondrial proteins lack clear functions
4
, and the underlying genetic basis for approximately 40% of mitochondrial disorders remains unresolved
5
. Here, to establish a more complete functional compendium of human mitochondrial proteins, we profiled more than 200 CRISPR-mediated HAP1 cell knockout lines using mass spectrometry-based multiomics analyses. This effort generated approximately 8.3 million distinct biomolecule measurements, providing a deep survey of the cellular responses to mitochondrial perturbations and laying a foundation for mechanistic investigations into protein function. Guided by these data, we discovered that
PIGY
upstream open reading frame (PYURF) is an
S
-adenosylmethionine-dependent methyltransferase chaperone that supports both complex I assembly and coenzyme Q biosynthesis and is disrupted in a previously unresolved multisystemic mitochondrial disorder. We further linked the putative zinc transporter SLC30A9 to mitochondrial ribosomes and OxPhos integrity and established
RAB5IF
as the second gene harbouring pathogenic variants that cause cerebrofaciothoracic dysplasia. Our data, which can be explored through the interactive online MITOMICS.app resource, suggest biological roles for many other orphan mitochondrial proteins that still lack robust functional characterization and define a rich cell signature of mitochondrial dysfunction that can support the genetic diagnosis of mitochondrial diseases.
A multiomics resource characterizing human mitochondrial proteins enables identification of biological functions and supports genetic diagnosis of mitochondrial pathologies.