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Venkatraman K, Lee CT, Garcia GC, Mahapatra A, Milshteyn D, Perkins G, Kim K, Pasolli HA, Phan S, Lippincott‐Schwartz J, Ellisman MH, Rangamani P, Budin I. Cristae formation is a mechanical buckling event controlled by the inner mitochondrial membrane lipidome. EMBO J 2023; 42:e114054. [PMID: 37933600 PMCID: PMC10711667 DOI: 10.15252/embj.2023114054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023] Open
Abstract
Cristae are high-curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae-shaping proteins have been defined, analogous lipid-based mechanisms have yet to be elucidated. Here, we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the inner mitochondrial membrane against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein-mediated curvatures. This model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that cardiolipin is essential in low-oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of cardiolipin is dependent on the surrounding lipid and protein components of the IMM.
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Affiliation(s)
- Kailash Venkatraman
- Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaCAUSA
| | - Christopher T Lee
- Department of Mechanical and Aerospace EngineeringUniversity of California San DiegoLa JollaCAUSA
| | - Guadalupe C Garcia
- Computational Neurobiology LaboratorySalk Institute for Biological StudiesLa JollaCAUSA
| | - Arijit Mahapatra
- Department of Mechanical and Aerospace EngineeringUniversity of California San DiegoLa JollaCAUSA
- Present address:
Applied Physical SciencesUniversity of North Carolina Chapel HillChapel HillNCUSA
| | - Daniel Milshteyn
- Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaCAUSA
| | - Guy Perkins
- National Center for Microscopy and Imaging Research, Center for Research in Biological SystemsUniversity of California San DiegoLa JollaCAUSA
| | - Keun‐Young Kim
- National Center for Microscopy and Imaging Research, Center for Research in Biological SystemsUniversity of California San DiegoLa JollaCAUSA
| | - H Amalia Pasolli
- Howard Hughes Medical InstituteAshburnVAUSA
- Present address:
Electron Microscopy Resource CenterThe Rockefeller UniversityNew YorkNYUSA
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological SystemsUniversity of California San DiegoLa JollaCAUSA
| | | | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological SystemsUniversity of California San DiegoLa JollaCAUSA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace EngineeringUniversity of California San DiegoLa JollaCAUSA
| | - Itay Budin
- Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaCAUSA
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Venkatraman K, Lee CT, Garcia GC, Mahapatra A, Milshteyn D, Perkins G, Kim KY, Pasolli HA, Phan S, Lippincott-Schwartz J, Ellisman MH, Rangamani P, Budin I. Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532310. [PMID: 36993370 PMCID: PMC10054968 DOI: 10.1101/2023.03.13.532310] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Cristae are high curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae-shaping proteins have been defined, analogous mechanisms for lipids have yet to be elucidated. Here we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the IMM against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein-mediated curvatures. The model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that CL is essential in low oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of CL is dependent on the surrounding lipid and protein components of the IMM.
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Affiliation(s)
- Kailash Venkatraman
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093
| | - Guadalupe C Garcia
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla CA 92097
| | - Arijit Mahapatra
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093
| | - Daniel Milshteyn
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Guy Perkins
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093
| | - Keun-Young Kim
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093
| | - H Amalia Pasolli
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn VA 20147
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093
| | | | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093
| | - Itay Budin
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
- Lead contact
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Galber C, Fabbian S, Gatto C, Grandi M, Carissimi S, Acosta MJ, Sgarbi G, Tiso N, Argenton F, Solaini G, Baracca A, Bellanda M, Giorgio V. The mitochondrial inhibitor IF1 binds to the ATP synthase OSCP subunit and protects cancer cells from apoptosis. Cell Death Dis 2023; 14:54. [PMID: 36690622 PMCID: PMC9870916 DOI: 10.1038/s41419-023-05572-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/29/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023]
Abstract
The mitochondrial protein IF1 binds to the catalytic domain of the ATP synthase and inhibits ATP hydrolysis in ischemic tissues. Moreover, IF1 is overexpressed in many tumors and has been shown to act as a pro-oncogenic protein, although its mechanism of action is still debated. Here, we show that ATP5IF1 gene disruption in HeLa cells decreases colony formation in soft agar and tumor mass development in xenografts, underlining the role of IF1 in cancer. Notably, the lack of IF1 does not affect proliferation or oligomycin-sensitive mitochondrial respiration, but it sensitizes the cells to the opening of the permeability transition pore (PTP). Immunoprecipitation and proximity ligation analysis show that IF1 binds to the ATP synthase OSCP subunit in HeLa cells under oxidative phosphorylation conditions. The IF1-OSCP interaction is confirmed by NMR spectroscopy analysis of the recombinant soluble proteins. Overall, our results suggest that the IF1-OSCP interaction protects cancer cells from PTP-dependent apoptosis under normoxic conditions.
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Affiliation(s)
- Chiara Galber
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, I-40126, Italy
- Consiglio Nazionale delle Ricerche Institute of Neuroscience, Padova, I-35121, Italy
| | - Simone Fabbian
- Department of Chemical Science, University of Padova, Padova, I-35121, Italy
| | - Cristina Gatto
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, I-40126, Italy
| | - Martina Grandi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, I-40126, Italy
| | - Stefania Carissimi
- Consiglio Nazionale delle Ricerche Institute of Neuroscience, Padova, I-35121, Italy
| | - Manuel Jesus Acosta
- Consiglio Nazionale delle Ricerche Institute of Neuroscience, Padova, I-35121, Italy
| | - Gianluca Sgarbi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, I-40126, Italy
| | - Natascia Tiso
- Department of Biology, University of Padova, Padova, I-35131, Italy
| | | | - Giancarlo Solaini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, I-40126, Italy
| | - Alessandra Baracca
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, I-40126, Italy
| | - Massimo Bellanda
- Department of Chemical Science, University of Padova, Padova, I-35121, Italy
- Consiglio Nazionale delle Ricerche Institute of Biomolecular Chemistry, Padova, I-35131, Italy
| | - Valentina Giorgio
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, I-40126, Italy.
- Consiglio Nazionale delle Ricerche Institute of Neuroscience, Padova, I-35121, Italy.
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Galber C, Minervini G, Cannino G, Boldrin F, Petronilli V, Tosatto S, Lippe G, Giorgio V. The f subunit of human ATP synthase is essential for normal mitochondrial morphology and permeability transition. Cell Rep 2021; 35:109111. [PMID: 33979610 DOI: 10.1016/j.celrep.2021.109111] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/11/2021] [Accepted: 04/20/2021] [Indexed: 01/03/2023] Open
Abstract
The f subunit is localized at the base of the ATP synthase peripheral stalk. Its function in the human enzyme is poorly characterized. Because full disruption of its ATP5J2 gene with the CRISPR-Cas9 strategy in the HAP1 human model has been shown to cause alterations in the amounts of other ATP synthase subunits, here we investigated the role of the f subunit in HeLa cells by regulating its levels through RNA interference. We confirm the role of the f subunit in ATP synthase dimer stability and observe that its downregulation per se does not alter the amounts of the other enzyme subunits or ATP synthase synthetic/hydrolytic activity. We show that downregulation of the f subunit causes abnormal crista organization and decreases permeability transition pore (PTP) size, whereas its re-expression in f subunit knockdown cells rescues mitochondrial morphology and PTP-dependent swelling.
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Affiliation(s)
- Chiara Galber
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy; Consiglio Nazionale delle Ricerche Institute of Neuroscience, Padova 35121, Italy
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Giuseppe Cannino
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | | | - Valeria Petronilli
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy; Consiglio Nazionale delle Ricerche Institute of Neuroscience, Padova 35121, Italy
| | - Silvio Tosatto
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy
| | - Giovanna Lippe
- Department of Medicine, University of Udine, Udine 33100, Italy
| | - Valentina Giorgio
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy; Consiglio Nazionale delle Ricerche Institute of Neuroscience, Padova 35121, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy.
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Rossi A, Rigotto G, Valente G, Giorgio V, Basso E, Filadi R, Pizzo P. Defective Mitochondrial Pyruvate Flux Affects Cell Bioenergetics in Alzheimer's Disease-Related Models. Cell Rep 2021; 30:2332-2348.e10. [PMID: 32075767 DOI: 10.1016/j.celrep.2020.01.060] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/04/2019] [Accepted: 01/17/2020] [Indexed: 12/20/2022] Open
Abstract
Mitochondria are key organelles for brain health. Mitochondrial alterations have been reported in several neurodegenerative disorders, including Alzheimer's disease (AD), and the comprehension of the underlying mechanisms appears crucial to understand their relationship with the pathology. Using multiple genetic, pharmacological, imaging, and biochemical approaches, we demonstrate that, in different familial AD cell models, mitochondrial ATP synthesis is affected. The defect depends on reduced mitochondrial pyruvate oxidation, due to both lower Ca2+-mediated stimulation of the Krebs cycle and dampened mitochondrial pyruvate uptake. Importantly, this latter event is linked to glycogen-synthase-kinase-3β (GSK-3β) hyper-activation, leading, in turn, to impaired recruitment of hexokinase 1 (HK1) to mitochondria, destabilization of mitochondrial-pyruvate-carrier (MPC) complexes, and decreased MPC2 protein levels. Remarkably, pharmacological GSK-3β inhibition in AD cells rescues MPC2 expression and improves mitochondrial ATP synthesis and respiration. The defective mitochondrial bioenergetics influences glutamate-induced neuronal excitotoxicity, thus representing a possible target for future therapeutic interventions.
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Affiliation(s)
- Alice Rossi
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35121 Padua, Italy
| | - Giulia Rigotto
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35121 Padua, Italy
| | - Giulia Valente
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35121 Padua, Italy; Neuroscience Institute - Italian National Research Council (CNR), Padua 35121, Italy
| | - Valentina Giorgio
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35121 Padua, Italy; Neuroscience Institute - Italian National Research Council (CNR), Padua 35121, Italy
| | - Emy Basso
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35121 Padua, Italy; Neuroscience Institute - Italian National Research Council (CNR), Padua 35121, Italy
| | - Riccardo Filadi
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35121 Padua, Italy; Neuroscience Institute - Italian National Research Council (CNR), Padua 35121, Italy.
| | - Paola Pizzo
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35121 Padua, Italy; Neuroscience Institute - Italian National Research Council (CNR), Padua 35121, Italy.
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Zhang Y, Fernie AR. On the Detection and Functional Significance of the Protein-Protein Interactions of Mitochondrial Transport Proteins. Biomolecules 2020; 10:E1107. [PMID: 32722450 PMCID: PMC7464641 DOI: 10.3390/biom10081107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/23/2022] Open
Abstract
Protein-protein assemblies are highly prevalent in all living cells. Considerable evidence has recently accumulated suggesting that particularly transient association/dissociation of proteins represent an important means of regulation of metabolism. This is true not only in the cytosol and organelle matrices, but also at membrane surfaces where, for example, receptor complexes, as well as those of key metabolic pathways, are common. Transporters also frequently come up in lists of interacting proteins, for example, binding proteins that catalyze the production of their substrates or that act as relays within signal transduction cascades. In this review, we provide an update of technologies that are used in the study of such interactions with mitochondrial transport proteins, highlighting the difficulties that arise in their use for membrane proteins and discussing our current understanding of the biological function of such interactions.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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05SAR-PAGE: Separation of protein dimerization and modification using a gel with 0.05% sarkosyl. Anal Chim Acta 2020; 1101:193-198. [DOI: 10.1016/j.aca.2019.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 11/19/2022]
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