GNPS - MITOMICS: defining mitochondrial protein functions through deep multi-omic profiling

Mitochondria are epicenters of eukaryotic metabolism and bioenergetics. Pioneering
efforts in recent decades have established the core protein componentry of these organelles
and have linked their dysfunction to over 150 distinct disorders. However, hundreds of
mitochondrial proteins still lack clear functions, and ~40% of mitochondrial disorders
remain unresolved. To establish a more complete functional compendium of human
mitochondrial proteins, we profiled 203 CRISPR-mediated HAP1 cell knockout lines
using mass spectrometry-based multi-omics analyses. This effort generated ~8.2 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 PYURF is a SAM-dependent
methyltransferase chaperone that supports both complex I assembly and coenzyme Q
biosynthesis, and that is disrupted in a previously unresolved multisystemic mitochondrial
disorder. We further linked the putative zinc transporter SLC30A9 to mitoribosome and
OxPhos integrity and established RAB5IF as the second gene harboring pathogenic
variants causing cerebrofaciothoracic dysplasia. Our data - which can be explored through
an interactive online resource - suggest biological roles for many other orphan
mitochondrial proteins still lacking robust functional characterization, and define a rich
cell signature of mitochondrial dysfunction that can support the genetic diagnosis of
mitochondrial diseases.