PXD026793-2

PXD026793 is an original dataset announced via ProteomeXchange.

Title	Tissue-specific in vivo mitochondrial matrix proteome profiling in mouse
Description	Targeting proximity labeling enzymes to specific cellular locations is a viable strategy for profiling subcellular proteomes with minimal perturbance to normal physiology. Here, we generate transgenic mice expressing a mitochondrial matrix-targeted ascorbate peroxidase (MTS-APEX2) to enable analysis of tissue-specific matrix proteomes. Desthiobiotin-phenol labeling of the mitochondrial proteome revealed 263 mitochondrial-localized proteins in mouse muscle tissues. Comparison with the MTS-APEX2-labeled proteome in HEK293T cells revealed enrichment in mitochondrial proteins related to energy production in the muscle tissues of transgenic mice. We found Reticulon 4 Interacting Protein 1(RTN4IP1) or Optic Atrophhy-10 (OPA10) was highly enriched in cardiac and soleus muscle and contained a strong mitochondrial matrix-targeting sequence. Structural analysis shows RTN4IP1 is an NADPH oxidoreductase with protein structure resembling quinone oxidoreductase (QOR) in bacterial species. Enzymatic activity assays, interactome analysis, and metabolite profiling confirmed that RTN4IP1 functions in coenzyme Q biosynthesis in the mitochondria. Due to reduced CoQ9 levels, Rtn4ip1-knockout C2C12 cells were vulnerable to oxidative stress and had decreased oxygen consumption rates and ATP production.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:02:14.788.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD026793
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jong-Seo Kim
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	biotinylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-18 03:51:34	ID requested
1	2023-08-30 19:21:56	announced
⏵ 2	2024-10-22 06:02:15	announced	2024-10-22: Updated project metadata.

10.6019/PXD026793;

submitter keyword: coenzyme Q, proximity labeling, mitochondrial proteome,APEX, RTN4IP1, NADPH, muscle, LC-MS/MS

Jong-Seo Kim
contact affiliation	Assistant professor, School of Biological Sciences, Seoul National University
contact email	jongseokim@snu.ac.kr
lab head
Jong-Seo Kim
contact affiliation	School of Biological Sciences, Seoul National University
contact email	jongseokim@snu.ac.kr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD026793
     1. Label: PRIDE project
     2. Name: Tissue-specific in vivo mitochondrial matrix proteome profiling in mouse