PXD061050

PXD061050 is an original dataset announced via ProteomeXchange.

Title	Time-resolved mitochondrial-focused screening identifies regulatory components of oxidative metabolism
Description	Defects in mitochondrial oxidative metabolism contribute to various genetic inherited disorders, termed mitochondrial diseases, with limited treatment options. Given the lack of functional annotation for numerous mitochondrial proteins, there is a necessity for an extensive gene inventory related to mitochondrial function, with special interest in Oxidative Phosphorylation (OXPHOS). To address this gap, we developed a CRISPR/Cas9 loss-of-function library targeting nuclear-encoded mitochondrial genes and conducted galactose-based screenings at various time points to uncover novel regulators of mitochondrial function. Our study resulted in a gene catalog essential for mitochondrial oxidative metabolism, and constructed a dynamic timeline mapping a broad network of mitochondrial pathways, with a particular focus on the OXPHOS complexes. Computational analysis pinpointed RTN4IP1 and ECHS1 as key genes strongly associated with OXPHOS and whose mutations are associated with mitochondrial diseases in humans. RTN4IP1 was found to be crucial for mitochondrial respiration, with complexome profiling revealing its role as an assembly factor required for the complete assembly of complex I. Furthermore, we discovered that ECHS1 controls oxidative metabolism independently of its canonical function in fatty acid oxidation. Deletion of ECHS1 leads to reduced catabolism of branched-chain amino acids (BCAAs), which impairs the activity of lipoic acid-dependent enzymes such as pyruvate dehydrogenase (PDH). This deleterious phenotype can be rescued by restricting valine intake or catabolism in ECHS1-deficient cells
HostingRepository	PRIDE
AnnounceDate	2025-06-30
AnnouncementXML	Submission_2025-06-29_16:09:51.028.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD061050
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alberto Paradela
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-21 06:26:36	ID requested
⏵ 1	2025-06-29 16:09:51	announced

10.1038/s44319-025-00459-9;

Zamora-Dorta M, Laine-Men, é, ndez S, Abia D, Gonz, á, lez-Garc, í, a P, L, ó, pez LC, Fern, á, ndez-Montes P, Calvo E, V, á, zquez J, Enr, í, quez JA, Balsa E, Time-resolved mitochondrial screen identifies regulatory components of oxidative metabolism. EMBO Rep, 26(12):3045-3074(2025) [pubmed]

10.6019/PXD061050;

submitter keyword: mitochondrial diseases

oxidative metabolism

oxidative phosphorylation

Eduardo Balsa
contact affiliation	Head of Mitochondrial dysfunction in metabolic diseases lab. ERC Researcher. CBMSO-UAM C/ Nicolas Cabrera, 1 28049 Madrid, Spain.
contact email	ebalsa@cbm.csic.es
lab head
Alberto Paradela
contact affiliation	Proteomics Lab CNB-CSIC
contact email	alberto.paradela@cnb.csic.es
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/06/PXD061050

PRIDE project URI

• PRIDE
  1. PXD061050
     1. Label: PRIDE project
     2. Name: Time-resolved mitochondrial-focused screening identifies regulatory components of oxidative metabolism