Mitochondrial phosphoproteomes are functionally specialized across tissues

Abstract

Mitochondria are essential organelles involved in critical biological processes such as energy metabolism and cell survival. Their dysfunction is linked to numerous human pathologies that often manifest in a tissue-specific manner. Accordingly, mitochondrial fitness depends on versatile proteomes specialized to meet diverse tissue-specific requirements. Furthermore, increasing evidence suggests that phosphorylation may also play an important role in regulating tissue-specific mitochondrial functions and pathophysiology. We hypothesized that recent advances in mass spectrometry (MS)-based proteomics would now enable in-depth measurement to quantitatively profile mitochondrial proteomes along with their matching phosphoproteomes across tissues. We isolated mitochondria from mouse heart, skeletal muscle, brown adipose tissue, kidney, liver, brain, and spleen by differential centrifugation followed by separation on Percoll gradients and high-resolution MS analysis of the proteomes and phosphoproteomes. This in-depth map substantially quantifies known and predicted mitochondrial proteins and provides a resource of core and tissue modulated mitochondrial proteins (mitophos.de). We also uncover tissue-specific repertoires of dozens of kinases and phosphatases. Predicting kinase substrate associations for different mitochondrial compartments indicates tissue-specific regulation at the phosphoproteome level. Illustrating the functional value of our resource, we reproduce mitochondrial phosphorylation events on DRP1 responsible for its mitochondrial recruitment and fission initiation and describe phosphorylation clusters on MIGA2 linked to mitochondrial fusion.

Systematic mapping of MCU-mediated mitochondrial calcium signaling networks

“…6H ). We observed the same phenotype in mitochondria isolated from the brain of MCUB KO mice, where we and others (Samaras et al , 2020; Hansen et al , 2024) could detect a clear expression of MCUB ( Fig. S6A-C ).…”

Bioorthogonal photocatalytic proximity labeling in primary living samples

“…Given that the spleen accommodates a huge quantity of immune cells (predominantly B cells and T cells), our observation indicated the elevated mitochondrial biogenesis and dynamics within this organ that might be required by immune cell development and migration 39 . Cross-analysis with the reported indepth tissue proteomic data 40 , showed that our captured "kidneyonly" and "spleen-only" proteomes were typically more significant in the reported dataset for the corresponding tissue (Supplementary Fig. 17), further supporting the proteomic characteristics observed by CAT-S.…”

“…For comparison and validation, the proteins detected only in postcutoff kidney and spleen proteomes (i.e., "kidney-only" and "spleenonly") were cross-analyzed with the published datasets 40 (https://www. ebi.ac.uk/pride/archive/projects/PXD030062) of high-coverage mitochondrial proteomics for mouse tissues by Mann group, which contained six samples for each tissue.…”

Pptc7 maintains mitochondrial protein content by suppressing receptor-mediated mitophagy

“…J.K.P and K.K. were supported by a Mito Foundation Incubator Grant (2022) and Mito Foundation Ph.D. scholarship, respectively. We would like to thank Kathy Krentz and C. Dustin Rubenstein from the Animal Models and Genome Editing Cores at the University of Wisconsin-Madison for generating of the Pptc7 floxed model.…”