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Dual regulation of mitochondrial fusion by Parkin–PINK1 and OMA1

Abstract

Mitochondrial stress pathways protect mitochondrial health from cellular insults1,2,3,4,5,6,7,8. However, their role under physiological conditions is largely unknown. Here, using 18 single, double and triple whole-body and tissue-specific knockout and mutant mice, along with systematic mitochondrial morphology analysis, untargeted metabolomics and RNA sequencing, we discovered that the synergy between two stress-responsive systems—the ubiquitin E3 ligase Parkin and the metalloprotease OMA1—safeguards mitochondrial structure and genome by mitochondrial fusion, mediated by the outer membrane GTPase MFN1 and the inner membrane GTPase OPA1. Whereas the individual loss of Parkin or OMA1 does not affect mitochondrial integrity, their combined loss results in small body size, low locomotor activity, premature death, mitochondrial abnormalities and innate immune responses. Thus, our data show that Parkin and OMA1 maintain a dual regulatory mechanism that controls mitochondrial fusion at the two membranes, even in the absence of extrinsic stress.

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Fig. 1: Parkin–PINK1 and OMA1 ensure mouse fitness by suppression of mitochondrial fusion.
Fig. 2: Parkin and OMA1 prevent excess mitochondrial fusion.
Fig. 3: Parkin and OMA1 protect the mitochondrial genome.
Fig. 4: Parkin and OMA1 suppress stress-induced mitochondrial enlargement in the liver.

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Data availability

Supplementary Fig. 1 includes uncropped immunoblot images corresponding to Figs. 3g and 4l, as well as to Extended Data Figs. 6a,c,e, 8b and 10a, with molecular weight markers indicating how blots were cropped for the final figures. RNA-seq data generated in this study are available in Gene Expression Omnibus under accession code PRJNA1157386. Materials generated in this study are available from the corresponding authors on request. Source data are provided with this paper.

Code availability

We did not generate any custom code for the RNA-seq analyses in this study; we utilized software packages with prewritten code and default parameters. We performed pairwise differential gene expression analysis using the R package DESeq2 1.20.0 and applied the Benjamini–Hochberg method for false discovery rate correction through RNAseqChef 1.1.2.

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Acknowledgements

We thank N. Senoo and S. M. Claypool at Johns Hopkins University School of Medicine for assistance with measurement of OCR. We also thank past and present members of the Iijima and Sesaki laboratories for helpful discussions and technical assistance. We acknowledge the joint participation by the Adrienne Helis Malvin Medical Research Foundation Parkinsons Disease Program (no. M-2019), through its direct engagement in the continuous active conduct of medical research, in conjunction with Johns Hopkins Hospital and Johns Hopkins University School of Medicine. T.M.D. is the Leonard and Madlyn Abramson Professor in Neurodegenerative Diseases. H.S. is the Ethan and Karen Leder CIM/HAP Scholar. This work was supported by NIH grants to H.S. (no. R35GM144103), M.I. (no. R35GM131768) and T.Y. (no. P20GM104320), as well as by grants from the Human Aging Project and Adrienne Helis Malvin Medical Research Foundation to H.S.

Author information

Authors and Affiliations

Authors

Contributions

T.Y., A.I., M.I. and H.S. conceived the study. T.Y. and A.I. performed most experiments, with assistance from Y.A. D.M. conducted immunoblot analysis, qPCR and the mitochondrial fusion assay. H.W. analysed dopaminergic neurons, dopamine metabolites and motor neurons. C.Z. and P.K. performed metabolomics. F.I. purified RNA for RNA-seq. A.I., M.I. and H.S. analysed most RNA-seq data, with assistance from S.B. M.I., H.S., D.C.C., T.L., T.M.D., P.M.Q. and C.L.-O. provided reagents and animals. H.S., M.I., T.M.D., V.L.D. and A.L. supervised the study. H.S., M.I., T.Y., A.I., H.W. and A.L. wrote and edited the manuscript. All authors participated in discussing and finalizing the manuscript.

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Correspondence to Miho Iijima or Hiromi Sesaki.

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Extended data figures and tables

Extended Data Fig. 1 Generation of Dele1−/− mice.

(a) To delete the Dele1 gene in the mouse genome, exon 2 was targeted using the CRISPR-Cas9 editing system with the indicated gRNA. (b) The location of the targeted site in the Dele1 gene is shown. (c) DNA sequencing confirmed that the genome editing removed 10 nucleotides at the position from 45 to 54 and introduced a stop codon after adding four amino acids.

Extended Data Fig. 2 Representative images of mitochondria in the zona incerta, midbrain, dorsal pallidum, lateral cortex, hippocampus, olfactory bulb, striatum, and cerebellum.

Brain sections from the indicated mouse lines were analyzed by laser confocal immunofluorescence microscopy with anti-PDH antibodies. Mice were analyzed at 6 weeks of age.

Extended Data Fig. 3 Representative images of mitochondria in the kidney, brown adipose tissue (BAT), skeletal muscle, lung, intestine, and spleen.

Tissue sections from the indicated mouse lines were analyzed by laser confocal immunofluorescence microscopy with anti-PDH antibodies. Mice were analyzed at 6 weeks of age.

Extended Data Fig. 4 Quantification of cells that contain enlarged mitochondria.

Values are mean ± SD (n = 4 for all tissues in the mouse lines, except for the following: zona incerta, midbrain, dorsal pallidum, and lateral cortex in 5 Parkin−/−Oma1−/−Mfn1+/− mice; BAT in 3 Oma1−/− mice; and lung in 3 WT, 3 Parkin−/−Oma1−/−, and 3 Parkin−/−Oma1−/−Mfn1+/− mice). Significance was calculated using one-way ANOVA with post-hoc Tukey: *p < 0.05, **p < 0.01, ***p < 0.001. Mice were analyzed at 6 weeks of age.

Source data

Extended Data Fig. 5 Megamitochondria are formed in neurons of Parkin−/−Oma1−/− mice.

(a) Quantification of cells that contain enlarged mitochondria in the pons and medulla in Parkin−/−Oma1−/− mice (mean ± SD, n = 3 mice). (b) Frozen sections of the pons/medulla from WT and Parkin−/−Oma1−/− mice were analyzed using laser confocal immunofluorescence microscopy with anti-PDH antibodies alongside cell type markers: NeuN (neurons), Iba1 (microglia), GFAP (astrocytes), and PECAM1 (vascular cells). (c) Megamitochondria-containing cells positive for each marker were quantified (mean ± SD, n = 3 mice). (d and e) Frozen sections of WT pons/medulla were analyzed using laser confocal immunofluorescence microscopy with antibodies against PDH and NeuN, with or without antigen retrieval using 1 mM EDTA. Two NeuN antibodies were used: 26975-1-AP from Proteintech in (d) and 24307 from Cell Signaling in (e). DNA was co-stained with DAPI. Significance was calculated using two-tailed Student’s t-test in (a) and one-way ANOVA with post-hoc Tukey (c): ***p < 0.001. Mice were analyzed at 6 weeks of age.

Source data

Extended Data Fig. 6 Western blotting analysis.

(a) The pons/medulla, cerebellum, and liver from WT and Parkin−/− mice were analyzed by Western blotting with the indicated antibodies. The asterisk indicates non-specific bands detected by the anti-Mfn1 antibodies. (b) Quantification of band intensity (mean ± SD, n = 3). (c) Confirmation of the specificity of the anti-Mfn1 antibodies was performed. Mfn1 was knocked down in mouse embryonic fibroblasts using two distinct siRNAs and subjected to Western blotting with the specified antibodies. (d) Quantification of band intensity (mean ± SD, n = 3). (e) The tissues from WT and Oma1−/− mice were analyzed by Western blotting with the specified antibodies. For Pgam5, P indicates the precursor form, and M in the mature form. (f) Quantification of band intensity (mean ± SD, n = 3). Significance was determined using two-tailed Student’s t-test in (b, f) and one-way ANOVA with post-hoc Tukey (d): *p < 0.05, **p < 0.01, ***p < 0.001. Mice were analyzed at 6 weeks of age.

Source data

Extended Data Fig. 7 Comparison of the metabolomic landscapes.

(a) Volcano plot of metabolomic data from WT and Parkin−/−Oma1−/− pons/medulla. None of the 188 metabolites identified showed significant changes in the Parkin−/−Oma1−/− pons/medulla compared to WT, using an FDR threshold of 0.05 indicated by the dotted line (n = 4 WT and 5 Parkin−/−Oma1−/− mice). (b) Log2 fold change and FDR of each metabolite involved in the TCA cycle, energy metabolism, glycolysis/gluconeogenesis, purine/pyrimidine metabolism, and amino acids. (c) Activity of each of the nine TCA cycle enzymes: aconitase (ACO), isocitrate dehydrogenase (IDH), oxoglutarate dehydrogenase (OGDH), succinyl-CoA ligase (SUCLG), fumarase (FUMH), malate dehydrogenase (MDH), citrate synthase (CS), succinate dehydrogenase (SDH), and pyruvate dehydrogenase (PDH) in WT and Parkin−/−Oma1−/− pons/medulla (mean ± SD, n = 3 mice). (d) Oxygen consumption rates (OCRs) in WT and Parkin−/−Oma1−/− brain (mean ± SD, n = 3 mice). Mice were analyzed at 6 weeks of age.

Source data

Extended Data Fig. 8 Principal component analysis and Western blotting.

(a) Principal component analysis of bulk RNA-seq data. (b) Postnuclear supernatants and mitochondrial fractions from WT and Parkin−/−Oma1−/− pons/medulla were analyzed by Western blotting using antibodies against Tim23 and α-tubulin. (c) qPCR analysis of the mitochondrial fraction from WT and Parkin−/−Oma1−/− pons/medulla (mean ± SD, n = 3). Significance was determined using two-tailed Student’s t-test.

Source data

Extended Data Fig. 9 qRT-PCR analysis.

qRT-PCR analysis of Ifit3, Usp18, Oasl2, Ddx60, Bst2, and Sting1 in the pons/medulla of WT and Parkin−/−Oma1−/− mice (mean ± SD, n = 5). Significance was determined using two-tailed Student’s t-test: *p < 0.05, **p < 0.01, ***p < 0.001.

Source data

Extended Data Fig. 10 Measurement of mitochondrial fusion status.

(a) Western blotting of Drp1 KO MEFs transduced with lentiviruses carrying Opa1 and/or Mfn1. The asterisk indicates non-specific bands of anti-Mfn1 antibodies. Quantification of band intensity is shown (mean ± SD, n = 3). (b) Drp1 KO MEFs carrying matrix-targeted photoactivatable GFP (mito-PA-GFP), along with Opa1 and/or Mfn1, were stained with tetramethylrhodamine ethyl ester (TMRE). mito-PA-GFP in a single mitochondrion (indicated by the boxes) in the cell periphery was photoactivated, and images were obtained every 1 min at a single focal plane. Photoactivation was performed every 1 min on the same mitochondrion to maintain signal intensity. Representative images before and after (0 and 15 min) photoactivation are shown. (c) The mitochondrial fusion status was calculated based on the relative area containing photoactivated mito-PA-GFP signals over the total mitochondria stained with TMRE at 15 min (mean ± SD, n = 35 cells for Drp1 KO, 32 cells for Drp1 KO + Opa1, 34 cells for Drp1 KO + Mfn1, and 31 cells for Drp1 KO + Opa1 + Mfn1). Statistical analysis was performed using one-way ANOVA with post-hoc Tukey test: *p < 0.05, ***p < 0.001.

Source data

Extended Data Fig. 11 Analysis of dopaminergic and motor neurons.

(a) Tyrosine hydroxylase (TH) immunohistochemistry images of dopaminergic neurons in the substantia nigra pars compacta (SN) and striatum (STR) of WT and Parkin−/−Oma1−/− mice are shown. Nissl staining was included for the SN. (b, c) Stereological counting of TH-positive neurons (b) and Nissl-positive neurons (c) in the SN (mean ± SD, n = 3 mice). (d) Quantification of TH-positive fiber density in the STR (mean ± SD, n = 9 from 3 mice). (e–h) Measurements of dopamine (e), 3,4-dihydroxyphenylacetic acid (f), homovanillic acid (g), and 3-methoxytyramine (h) (mean ± SD, n = 4 mice). (i) Immunofluorescence microscopy of the spinal cord using anti-choline acetyltransferase antibodies. The cervical, thoracic, and lumbar regions were analyzed. Boxed areas are enlarged. (j) The number of motor neurons per 2,500 µm length of each spinal cord region is shown (mean ± SD, n = 4 mice). Significance was determined using two-tailed Student’s t-test in (b–h, j): **p < 0.01, ***p < 0.001.

Source data

Supplementary information

Supplementary Information (download PDF )

Supplementary Fig. 1. Uncropped immunoblot images for Figs. 3g and 4l, and for Extended Data Figs. 6a,c,e, 8b and 10a, are shown with molecular weight markers, indicating how blots were cropped for the final figures.

Reporting Summary (download PDF )

Supplementary Table 1 (download XLSX )

Comparison of amounts of metabolites in WT and Parkin−/−Oma1−/− pons/medulla. Values are normalized to the mean of WT for each metabolite (n = 4 WT and 5 Parkin−/−Oma1−/− mice). Significance was calculated using the two-tailed Student’s t-test with Benjamini–Hochberg multiple testing corrections.

Supplementary Table 2 (download XLSX )

RNA-seq gene count data and the results of GSEA and DEG analysis using RNAseqChef (n = 3 mice).

Supplementary Video 1 (download MOV )

A representative example of general locomotor activity of WT, Parkin−/−, Oma1−/− and Parkin−/−Oma1−/− mice at 6 weeks of age. The three larger, active mice are WT, Parkin−/− and Oma1−/−; the small, inactive mouse is Parkin−/−Oma1−/−.

Supplementary Video 2 (download MOV )

A representative example of general locomotor activity of Parkin−/−Oma1−/− and Parkin−/−Oma1−/−Opa1+/− mice at 6 weeks of age. The smaller, inactive mouse is Parkin−/−Oma1−/−; the larger, active mouse is Parkin−/−Oma1−/−Opa1+/−.

Source data

41586_2025_8590_MOESM7_ESM.xlsx (download XLSX )

Source Data Figs. 1–4 and Extended Data Figs. 4–11

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Yamada, T., Ikeda, A., Murata, D. et al. Dual regulation of mitochondrial fusion by Parkin–PINK1 and OMA1. Nature 639, 776–783 (2025). https://doi.org/10.1038/s41586-025-08590-2

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