1
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Raimi OG, Ojha H, Ehses K, Dederer V, Lange SM, Rivera CP, Deegan TD, Chen Y, Wightman M, Toth R, Labib KPM, Mathea S, Ranson N, Fernández-Busnadiego R, Muqit MMK. Mechanism of human PINK1 activation at the TOM complex in a reconstituted system. SCIENCE ADVANCES 2024; 10:eadn7191. [PMID: 38848361 PMCID: PMC11160474 DOI: 10.1126/sciadv.adn7191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 05/02/2024] [Indexed: 06/09/2024]
Abstract
Loss-of-function mutations in PTEN-induced kinase 1 (PINK1) are a frequent cause of early-onset Parkinson's disease (PD). Stabilization of PINK1 at the translocase of outer membrane (TOM) complex of damaged mitochondria is critical for its activation. The mechanism of how PINK1 is activated in the TOM complex is unclear. Here, we report that co-expression of human PINK1 and all seven TOM subunits in Saccharomyces cerevisiae is sufficient for PINK1 activation. We use this reconstitution system to systematically assess the role of each TOM subunit toward PINK1 activation. We unambiguously demonstrate that the TOM20 and TOM70 receptor subunits are required for optimal PINK1 activation and map their sites of interaction with PINK1 using AlphaFold structural modeling and mutagenesis. We also demonstrate an essential role of the pore-containing subunit TOM40 and its structurally associated subunits TOM7 and TOM22 for PINK1 activation. These findings will aid in the development of small-molecule activators of PINK1 as a therapeutic strategy for PD.
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Affiliation(s)
- Olawale G. Raimi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Hina Ojha
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Kenneth Ehses
- Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
| | - Verena Dederer
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Institute of Pharmaceutical Chemistry, Goethe-Universität, 60438 Frankfurt, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Goethe-Universität, 60438 Frankfurt, Germany
| | - Sven M. Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Cristian Polo Rivera
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Tom D. Deegan
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Yinchen Chen
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Melanie Wightman
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Karim P. M. Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Sebastian Mathea
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Institute of Pharmaceutical Chemistry, Goethe-Universität, 60438 Frankfurt, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Goethe-Universität, 60438 Frankfurt, Germany
| | - Neil Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Rubén Fernández-Busnadiego
- Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Faculty of Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Miratul M. K. Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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2
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Borgert L, Becker T, den Brave F. Conserved quality control mechanisms of mitochondrial protein import. J Inherit Metab Dis 2024. [PMID: 38790152 DOI: 10.1002/jimd.12756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]
Abstract
Mitochondria carry out essential functions for the cell, including energy production, various biosynthesis pathways, formation of co-factors and cellular signalling in apoptosis and inflammation. The functionality of mitochondria requires the import of about 900-1300 proteins from the cytosol in baker's yeast Saccharomyces cerevisiae and human cells, respectively. The vast majority of these proteins pass the outer membrane in a largely unfolded state through the translocase of the outer mitochondrial membrane (TOM) complex. Subsequently, specific protein translocases sort the precursor proteins into the outer and inner membranes, the intermembrane space and matrix. Premature folding of mitochondrial precursor proteins, defects in the mitochondrial protein translocases or a reduction of the membrane potential across the inner mitochondrial membrane can cause stalling of precursors at the protein import apparatus. Consequently, the translocon is clogged and non-imported precursor proteins accumulate in the cell, which in turn leads to proteotoxic stress and eventually cell death. To prevent such stress situations, quality control mechanisms remove non-imported precursor proteins from the TOM channel. The highly conserved ubiquitin-proteasome system of the cytosol plays a critical role in this process. Thus, the surveillance of protein import via the TOM complex involves the coordinated activity of mitochondria-localized and cytosolic proteins to prevent proteotoxic stress in the cell.
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Affiliation(s)
- Lion Borgert
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Thomas Becker
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Fabian den Brave
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
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3
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Krakowczyk M, Lenkiewicz AM, Sitarz T, Malinska D, Borrero M, Mussulini BHM, Linke V, Szczepankiewicz AA, Biazik JM, Wydrych A, Nieznanska H, Serwa RA, Chacinska A, Bragoszewski P. OMA1 protease eliminates arrested protein import intermediates upon mitochondrial depolarization. J Cell Biol 2024; 223:e202306051. [PMID: 38530280 DOI: 10.1083/jcb.202306051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/28/2023] [Accepted: 02/16/2024] [Indexed: 03/27/2024] Open
Abstract
Most mitochondrial proteins originate from the cytosol and require transport into the organelle. Such precursor proteins must be unfolded to pass through translocation channels in mitochondrial membranes. Misfolding of transported proteins can result in their arrest and translocation failure. Arrested proteins block further import, disturbing mitochondrial functions and cellular proteostasis. Cellular responses to translocation failure have been defined in yeast. We developed the cell line-based translocase clogging model to discover molecular mechanisms that resolve failed import events in humans. The mechanism we uncover differs significantly from these described in fungi, where ATPase-driven extraction of blocked protein is directly coupled with proteasomal processing. We found human cells to rely primarily on mitochondrial factors to clear translocation channel blockage. The mitochondrial membrane depolarization triggered proteolytic cleavage of the stalled protein, which involved mitochondrial protease OMA1. The cleavage allowed releasing the protein fragment that blocked the translocase. The released fragment was further cleared in the cytosol by VCP/p97 and the proteasome.
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Affiliation(s)
- Magda Krakowczyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences , Warsaw, Poland
| | - Anna M Lenkiewicz
- Nencki Institute of Experimental Biology, Polish Academy of Sciences , Warsaw, Poland
| | - Tomasz Sitarz
- Centre of New Technologies, University of Warsaw , Warsaw, Poland
| | - Dominika Malinska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences , Warsaw, Poland
| | - Mayra Borrero
- IMol Polish Academy of Sciences , Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences , Warsaw, Poland
| | - Ben Hur Marins Mussulini
- IMol Polish Academy of Sciences , Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences , Warsaw, Poland
| | - Vanessa Linke
- IMol Polish Academy of Sciences , Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences , Warsaw, Poland
| | | | - Joanna M Biazik
- Nencki Institute of Experimental Biology, Polish Academy of Sciences , Warsaw, Poland
- University of New South Wales , Sydney, Australia
| | - Agata Wydrych
- Nencki Institute of Experimental Biology, Polish Academy of Sciences , Warsaw, Poland
| | - Hanna Nieznanska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences , Warsaw, Poland
| | - Remigiusz A Serwa
- IMol Polish Academy of Sciences , Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences , Warsaw, Poland
| | - Agnieszka Chacinska
- IMol Polish Academy of Sciences , Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences , Warsaw, Poland
| | - Piotr Bragoszewski
- Nencki Institute of Experimental Biology, Polish Academy of Sciences , Warsaw, Poland
- Centre of New Technologies, University of Warsaw , Warsaw, Poland
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4
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Nussberger S, Ghosh R, Wang S. New insights into the structure and dynamics of the TOM complex in mitochondria. Biochem Soc Trans 2024; 52:911-922. [PMID: 38629718 PMCID: PMC11088910 DOI: 10.1042/bst20231236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/21/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
To date, there is no general physical model of the mechanism by which unfolded polypeptide chains with different properties are imported into the mitochondria. At the molecular level, it is still unclear how transit polypeptides approach, are captured by the protein translocation machinery in the outer mitochondrial membrane, and how they subsequently cross the entropic barrier of a protein translocation pore to enter the intermembrane space. This deficiency has been due to the lack of detailed structural and dynamic information about the membrane pores. In this review, we focus on the recently determined sub-nanometer cryo-EM structures and our current knowledge of the dynamics of the mitochondrial two-pore outer membrane protein translocation machinery (TOM core complex), which provide a starting point for addressing the above questions. Of particular interest are recent discoveries showing that the TOM core complex can act as a mechanosensor, where the pores close as a result of interaction with membrane-proximal structures. We highlight unusual and new correlations between the structural elements of the TOM complexes and their dynamic behavior in the membrane environment.
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Affiliation(s)
- Stephan Nussberger
- Department of Biophysics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Robin Ghosh
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Shuo Wang
- Department of Biophysics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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5
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Li D, Rocha-Roa C, Schilling MA, Reinisch KM, Vanni S. Lipid scrambling is a general feature of protein insertases. Proc Natl Acad Sci U S A 2024; 121:e2319476121. [PMID: 38621120 PMCID: PMC11047089 DOI: 10.1073/pnas.2319476121] [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: 11/07/2023] [Accepted: 03/13/2024] [Indexed: 04/17/2024] Open
Abstract
Glycerophospholipids are synthesized primarily in the cytosolic leaflet of the endoplasmic reticulum (ER) membrane and must be equilibrated between bilayer leaflets to allow the ER and membranes derived from it to grow. Lipid equilibration is facilitated by integral membrane proteins called "scramblases." These proteins feature a hydrophilic groove allowing the polar heads of lipids to traverse the hydrophobic membrane interior, similar to a credit card moving through a reader. Nevertheless, despite their fundamental role in membrane expansion and dynamics, the identity of most scramblases has remained elusive. Here, combining biochemical reconstitution and molecular dynamics simulations, we show that lipid scrambling is a general feature of protein insertases, integral membrane proteins which insert polypeptide chains into membranes of the ER and organelles disconnected from vesicle trafficking. Our data indicate that lipid scrambling occurs in the same hydrophilic channel through which protein insertion takes place and that scrambling is abolished in the presence of nascent polypeptide chains. We propose that protein insertases could have a so-far-overlooked role in membrane dynamics as scramblases.
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Affiliation(s)
- Dazhi Li
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Cristian Rocha-Roa
- Department of Biology, University of Fribourg, FribourgCH-1700, Switzerland
| | - Matthew A. Schilling
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Karin M. Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Stefano Vanni
- Department of Biology, University of Fribourg, FribourgCH-1700, Switzerland
- Swiss National Center for Competence in Research Bio-Inspired Materials, University of Fribourg, FribourgCH-1700, Switzerland
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6
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Busto JV, Ganesan I, Mathar H, Steiert C, Schneider EF, Straub SP, Ellenrieder L, Song J, Stiller SB, Lübbert P, Chatterjee R, Elsaesser J, Melchionda L, Schug C, den Brave F, Schulte U, Klecker T, Kraft C, Fakler B, Becker T, Wiedemann N. Role of the small protein Mco6 in the mitochondrial sorting and assembly machinery. Cell Rep 2024; 43:113805. [PMID: 38377000 DOI: 10.1016/j.celrep.2024.113805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
The majority of mitochondrial precursor proteins are imported through the Tom40 β-barrel channel of the translocase of the outer membrane (TOM). The sorting and assembly machinery (SAM) is essential for β-barrel membrane protein insertion into the outer membrane and thus required for the assembly of the TOM complex. Here, we demonstrate that the α-helical outer membrane protein Mco6 co-assembles with the mitochondrial distribution and morphology protein Mdm10 as part of the SAM machinery. MCO6 and MDM10 display a negative genetic interaction, and a mco6-mdm10 yeast double mutant displays reduced levels of the TOM complex. Cells lacking Mco6 affect the levels of Mdm10 and show assembly defects of the TOM complex. Thus, this work uncovers a role of the SAMMco6 complex for the biogenesis of the mitochondrial outer membrane.
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Affiliation(s)
- Jon V Busto
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Iniyan Ganesan
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hannah Mathar
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Conny Steiert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eva F Schneider
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian P Straub
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Lars Ellenrieder
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jiyao Song
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Sebastian B Stiller
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp Lübbert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ritwika Chatterjee
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Jana Elsaesser
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Laura Melchionda
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christina Schug
- Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany
| | - Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Till Klecker
- Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany; Center for Basics in NeuroModulation, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany.
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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7
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Muthukumar G, Stevens TA, Inglis AJ, Esantsi TK, Saunders RA, Schulte F, Voorhees RM, Guna A, Weissman JS. Triaging of α-helical proteins to the mitochondrial outer membrane by distinct chaperone machinery based on substrate topology. Mol Cell 2024; 84:1101-1119.e9. [PMID: 38428433 DOI: 10.1016/j.molcel.2024.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/08/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
Mitochondrial outer membrane ⍺-helical proteins play critical roles in mitochondrial-cytoplasmic communication, but the rules governing the targeting and insertion of these biophysically diverse proteins remain unknown. Here, we first defined the complement of required mammalian biogenesis machinery through genome-wide CRISPRi screens using topologically distinct membrane proteins. Systematic analysis of nine identified factors across 21 diverse ⍺-helical substrates reveals that these components are organized into distinct targeting pathways that act on substrates based on their topology. NAC is required for the efficient targeting of polytopic proteins, whereas signal-anchored proteins require TTC1, a cytosolic chaperone that physically engages substrates. Biochemical and mutational studies reveal that TTC1 employs a conserved TPR domain and a hydrophobic groove in its C-terminal domain to support substrate solubilization and insertion into mitochondria. Thus, the targeting of diverse mitochondrial membrane proteins is achieved through topological triaging in the cytosol using principles with similarities to ER membrane protein biogenesis systems.
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Affiliation(s)
- Gayathri Muthukumar
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Taylor A Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alison J Inglis
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Reuben A Saunders
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alina Guna
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA.
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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8
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Eldeeb MA, Bayne AN, Fallahi A, Goiran T, MacDougall EJ, Soumbasis A, Zorca CE, Tabah JJ, Thomas RA, Karpilovsky N, Mathur M, Durcan TM, Trempe JF, Fon EA. Tom20 gates PINK1 activity and mediates its tethering of the TOM and TIM23 translocases upon mitochondrial stress. Proc Natl Acad Sci U S A 2024; 121:e2313540121. [PMID: 38416681 DOI: 10.1073/pnas.2313540121] [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: 08/13/2023] [Accepted: 01/08/2024] [Indexed: 03/01/2024] Open
Abstract
Mutations in PTEN-induced putative kinase 1 (PINK1) cause autosomal recessive early-onset Parkinson's disease (PD). PINK1 is a Ser/Thr kinase that regulates mitochondrial quality control by triggering mitophagy mediated by the ubiquitin (Ub) ligase Parkin. Upon mitochondrial damage, PINK1 accumulates on the outer mitochondrial membrane forming a high-molecular-weight complex with the translocase of the outer membrane (TOM). PINK1 then phosphorylates Ub, which enables recruitment and activation of Parkin followed by autophagic clearance of the damaged mitochondrion. Thus, Parkin-dependent mitophagy hinges on the stable accumulation of PINK1 on the TOM complex. Yet, the mechanism linking mitochondrial stressors to PINK1 accumulation and whether the translocases of the inner membrane (TIMs) are also involved remain unclear. Herein, we demonstrate that mitochondrial stress induces the formation of a PINK1-TOM-TIM23 supercomplex in human cultured cell lines, dopamine neurons, and midbrain organoids. Moreover, we show that PINK1 is required to stably tether the TOM to TIM23 complexes in response to stress such that the supercomplex fails to accumulate in cells lacking PINK1. This tethering is dependent on an interaction between the PINK1 N-terminal-C-terminal extension module and the cytosolic domain of the Tom20 subunit of the TOM complex, the disruption of which, by either designer or PD-associated PINK1 mutations, inhibits downstream mitophagy. Together, the findings provide key insight into how PINK1 interfaces with the mitochondrial import machinery, with important implications for the mechanisms of mitochondrial quality control and PD pathogenesis.
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Affiliation(s)
- Mohamed A Eldeeb
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
| | - Andrew N Bayne
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
- Centre de Recherche en Biologie Structurale, Montréal, QC H3G 0B1, Canada
| | - Armaan Fallahi
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
| | - Thomas Goiran
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
| | - Emma J MacDougall
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
| | - Andrea Soumbasis
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
| | - Cornelia E Zorca
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
| | - Jace-Jones Tabah
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
| | - Rhalena A Thomas
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
| | - Nathan Karpilovsky
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
| | - Meghna Mathur
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
| | - Thomas M Durcan
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
| | - Jean-François Trempe
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
- Centre de Recherche en Biologie Structurale, Montréal, QC H3G 0B1, Canada
| | - Edward A Fon
- McGill Parkinson Program and Neurodegenerative Disorders Research Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Structural Genomics Consortium - Neuro, McGill University, Montréal, QC H3A 2B4, Canada
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9
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Woods H, Leman JK, Meiler J. Modeling membrane geometries implicitly in Rosetta. Protein Sci 2024; 33:e4908. [PMID: 38358133 PMCID: PMC10868433 DOI: 10.1002/pro.4908] [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: 08/25/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
Interactions between membrane proteins (MPs) and lipid bilayers are critical for many cellular functions. In the Rosetta molecular modeling suite, the implicit membrane energy function is based on a "slab" model, which represent the membrane as a flat bilayer. However, in nature membranes often have a curvature that is important for function and/or stability. Even more prevalent, in structural biology research MPs are reconstituted in model membrane systems such as micelles, bicelles, nanodiscs, or liposomes. Thus, we have modified the existing membrane energy potentials within the RosettaMP framework to allow users to model MPs in different membrane geometries. We show that these modifications can be utilized in core applications within Rosetta such as structure refinement, protein-protein docking, and protein design. For MP structures found in curved membranes, refining these structures in curved, implicit membranes produces higher quality models with structures closer to experimentally determined structures. For MP systems embedded in multiple membranes, representing both membranes results in more favorable scores compared to only representing one of the membranes. Modeling MPs in geometries mimicking the membrane model system used in structure determination can improve model quality and model discrimination.
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Affiliation(s)
- Hope Woods
- Center of Structural Biology, Vanderbilt UniversityNashvilleTennesseeUSA
- Chemical and Physical Biology ProgramVanderbilt UniversityNashvilleTennesseeUSA
| | | | - Jens Meiler
- Center of Structural Biology, Vanderbilt UniversityNashvilleTennesseeUSA
- Department of ChemistryVanderbilt UniversityNashvilleTennesseeUSA
- Institute for Drug Discovery, Leipzig University Medical SchoolLeipzigGermany
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10
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Wang Q, Zhuang J, Huang R, Guan Z, Yan L, Hong S, Zhang L, Huang C, Liu Z, Yin P. The architecture of substrate-engaged TOM-TIM23 supercomplex reveals preprotein proximity sites for mitochondrial protein translocation. Cell Discov 2024; 10:19. [PMID: 38360717 PMCID: PMC10869343 DOI: 10.1038/s41421-023-00643-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/24/2023] [Indexed: 02/17/2024] Open
Affiliation(s)
- Qiang Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinjin Zhuang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Rui Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ling Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Sixing Hong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Liying Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Can Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.
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11
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Gao L, Peng L, Wang J, Zhang JH, Xia Y. Mitochondrial stress: a key role of neuroinflammation in stroke. J Neuroinflammation 2024; 21:44. [PMID: 38321473 PMCID: PMC10845693 DOI: 10.1186/s12974-024-03033-7] [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: 11/03/2023] [Accepted: 01/27/2024] [Indexed: 02/08/2024] Open
Abstract
Stroke is a clinical syndrome characterized by an acute, focal neurological deficit, primarily caused by the occlusion or rupture of cerebral blood vessels. In stroke, neuroinflammation emerges as a pivotal event contributing to neuronal cell death. The occurrence and progression of neuroinflammation entail intricate processes, prominently featuring mitochondrial dysfunction and adaptive responses. Mitochondria, a double membrane-bound organelle are recognized as the "energy workshop" of the body. Brain is particularly vulnerable to mitochondrial disturbances due to its high energy demands from mitochondria-related energy production. The interplay between mitochondria and neuroinflammation plays a significant role in the pathogenesis of stroke. The biological and pathological consequences resulting from mitochondrial stress have substantial implications for cerebral function. Mitochondrial stress serves as an adaptive mechanism aimed at mitigating the stress induced by the import of misfolded proteins, which occurs in response to stroke. This adaptive response involves a reduction in misfolded protein accumulation and overall protein synthesis. The influence of mitochondrial stress on the pathological state of stroke is underscored by its capacity to interact with neuroinflammation. The impact of mitochondrial stress on neuroinflammation varies according to its severity. Moderate mitochondrial stress can bolster cellular adaptive defenses, enabling cells to better withstand detrimental stressors. In contrast, sustained and excessive mitochondrial stress detrimentally affects cellular and tissue integrity. The relationship between neuroinflammation and mitochondrial stress depends on the degree of mitochondrial stress present. Understanding its role in stroke pathogenesis is instrumental in excavating the novel treatment of stroke. This review aims to provide the evaluation of the cross-talk between mitochondrial stress and neuroinflammation within the context of stroke. We aim to reveal how mitochondrial stress affects neuroinflammation environment in stroke.
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Affiliation(s)
- Ling Gao
- Department of Neurosurgery, Xiangya School of Medicine, Affiliated Haikou Hospital, Central South University, Haikou, 570208, China
- Department of Physiology and Pharmacology, School of Medicine, Loma Linda University, Loma Linda, CA, 92354, USA
| | - Li Peng
- Department of Ophthalmology, Xiangya School of Medicine, Affiliated Haikou Hospital, Central South University, Haikou, 570208, China
| | - Jian Wang
- Department of Neurosurgery, Xiangya School of Medicine, Affiliated Haikou Hospital, Central South University, Haikou, 570208, China
| | - John H Zhang
- Department of Physiology and Pharmacology, School of Medicine, Loma Linda University, Loma Linda, CA, 92354, USA.
- Department of Neurosurgery and Anesthesiology, Loma Linda University Medical Center, Loma Linda, CA, 92354, USA.
| | - Ying Xia
- Department of Neurosurgery, Xiangya School of Medicine, Affiliated Haikou Hospital, Central South University, Haikou, 570208, China.
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12
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den Brave F, Pfanner N, Becker T. Mitochondrial entry gate as regulatory hub. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119529. [PMID: 37951505 DOI: 10.1016/j.bbamcr.2023.119529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 11/14/2023]
Abstract
Mitochondria import 1000-1300 different precursor proteins from the cytosol. The main mitochondrial entry gate is formed by the translocase of the outer membrane (TOM complex). Molecular coupling and modification of TOM subunits control and modulate protein import in response to cellular signaling. The TOM complex functions as regulatory hub to integrate mitochondrial protein biogenesis and quality control into the cellular proteostasis network.
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Affiliation(s)
- Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany.
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13
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Ronayne CT, Latorre-Muro P. Navigating the landscape of mitochondrial-ER communication in health and disease. Front Mol Biosci 2024; 11:1356500. [PMID: 38323074 PMCID: PMC10844478 DOI: 10.3389/fmolb.2024.1356500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024] Open
Abstract
Intracellular organelle communication enables the maintenance of tissue homeostasis and health through synchronized adaptive processes triggered by environmental cues. Mitochondrial-Endoplasmic Reticulum (ER) communication sustains cellular fitness by adjusting protein synthesis and degradation, and metabolite and protein trafficking through organelle membranes. Mitochondrial-ER communication is bidirectional and requires that the ER-components of the Integrated Stress Response signal to mitochondria upon activation and, likewise, mitochondria signal to the ER under conditions of metabolite and protein overload to maintain proper functionality and ensure cellular survival. Declines in the mitochondrial-ER communication occur upon ageing and correlate with the onset of a myriad of heterogeneous age-related diseases such as obesity, type 2 diabetes, cancer, or neurodegenerative pathologies. Thus, the exploration of the molecular mechanisms of mitochondrial-ER signaling and regulation will provide insights into the most fundamental cellular adaptive processes with important therapeutical opportunities. In this review, we will discuss the pathways and mechanisms of mitochondrial-ER communication at the mitochondrial-ER interface and their implications in health and disease.
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Affiliation(s)
- Conor T. Ronayne
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Pedro Latorre-Muro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
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14
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Moitra A, Tiku V, Rapaport D. Yeast mitochondria can process de novo designed β-barrel proteins. FEBS J 2024; 291:292-307. [PMID: 37723586 DOI: 10.1111/febs.16950] [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: 12/29/2022] [Revised: 08/18/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023]
Abstract
Mitochondrial outer membrane β-barrel proteins are encoded in the nucleus, translated in the cytosol and then targeted to and imported into the respective organelles. Detailed studies have uncovered the mechanisms involved in the import of these proteins and identified the targeting signals and the cytosolic factors that govern their proper biogenesis. Recently, de novo designed eight-stranded β-barrel proteins (Tmb2.3 and Tmb2.17) were shown to fold and assemble into lipid membranes. To better understand the general aspects of the biogenesis of β-barrel proteins, we investigated the fate of these artificial proteins upon their expression in yeast cells. We demonstrate that although these proteins are de novo designed and are not related to bona fide mitochondrial β-barrel proteins, they were targeted to mitochondria and integrated into the organelle outer membrane. We further studied whether this integration requires components of the yeast mitochondrial import machinery like Tom20, Tom70, Tob55/Sam50 and Mas37/Sam37. Whereas it seems that none of the import receptors was required for the biogenesis of the artificial β-barrel proteins, we observed a strong dependency on the TOB/SAM complex. Collectively, our findings demonstrate that the mitochondrial outer membrane is the preferential location in yeast cells for any membrane-embedded β-barrel protein.
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Affiliation(s)
- Anasuya Moitra
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Vitasta Tiku
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
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15
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Topitsch A, Schwede T, Pereira J. Outer membrane β-barrel structure prediction through the lens of AlphaFold2. Proteins 2024; 92:3-14. [PMID: 37465978 DOI: 10.1002/prot.26552] [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: 02/18/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/20/2023]
Abstract
Most proteins found in the outer membrane of gram-negative bacteria share a common domain: the transmembrane β-barrel. These outer membrane β-barrels (OMBBs) occur in multiple sizes and different families with a wide range of functions evolved independently by amplification from a pool of homologous ancestral ββ-hairpins. This is part of the reason why predicting their three-dimensional (3D) structure, especially by homology modeling, is a major challenge. Recently, DeepMind's AlphaFold v2 (AF2) became the first structure prediction method to reach close-to-experimental atomic accuracy in CASP even for difficult targets. However, membrane proteins, especially OMBBs, were not abundant during their training, raising the question of how accurate the predictions are for these families. In this study, we assessed the performance of AF2 in the prediction of OMBBs and OMBB-like folds of various topologies using an in-house-developed tool for the analysis of OMBB 3D structures, and barrOs. In agreement with previous studies on other membrane protein classes, our results indicate that AF2 predicts transmembrane β-barrel structures at high accuracy independently of the use of templates, even for novel topologies absent from the training set. These results provide confidence on the models generated by AF2 and open the door to the structural elucidation of novel transmembrane β-barrel topologies identified in high-throughput OMBB annotation studies or designed de novo.
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Affiliation(s)
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Joana Pereira
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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16
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Mukhtar M, Thakkur K, Chacinska A, Bragoszewski P. Mechanisms of stress management in mitochondrial protein import. Biochem Soc Trans 2023; 51:2117-2126. [PMID: 37987513 DOI: 10.1042/bst20230377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Mitochondria are vital to the functions of eukaryotic cells. Most mitochondrial proteins are transported into the organelle following their synthesis by cytoplasmic ribosomes. However, precise protein targeting is complex because the two diverse lipid membranes encase mitochondria. Efficient protein translocation across membranes and accurate sorting to specific sub-compartments require the cooperation of multiple factors. Any failure in mitochondrial protein import can disrupt organelle fitness. Proteins intended for mitochondria make up a significant portion of all proteins produced in the cytosol. Therefore, import defects causing their mislocalization can significantly stress cellular protein homeostasis. Recognition of this phenomenon has increased interest in molecular mechanisms that respond to import-related stress and restore proteostasis, which is the focus of this review. Significantly, disruptions in protein homeostasis link strongly to the pathology of several degenerative disorders highly relevant in ageing societies. A comprehensive understanding of protein import quality control will allow harnessing this machinery in therapeutic approaches.
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Affiliation(s)
- Maryam Mukhtar
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Krutika Thakkur
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | - Piotr Bragoszewski
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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17
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Jahn H, Bartoš L, Dearden GI, Dittman JS, Holthuis JCM, Vácha R, Menon AK. Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase. Nat Commun 2023; 14:8115. [PMID: 38065946 PMCID: PMC10709637 DOI: 10.1038/s41467-023-43570-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Mitochondria are double-membrane-bounded organelles that depend critically on phospholipids supplied by the endoplasmic reticulum. These lipids must cross the outer membrane to support mitochondrial function, but how they do this is unclear. We identify the Voltage Dependent Anion Channel (VDAC), an abundant outer membrane protein, as a scramblase-type lipid transporter that catalyzes lipid entry. On reconstitution into membrane vesicles, dimers of human VDAC1 and VDAC2 catalyze rapid transbilayer translocation of phospholipids by a mechanism that is unrelated to their channel activity. Coarse-grained molecular dynamics simulations of VDAC1 reveal that lipid scrambling occurs at a specific dimer interface where polar residues induce large water defects and bilayer thinning. The rate of phospholipid import into yeast mitochondria is an order of magnitude lower in the absence of VDAC homologs, indicating that VDACs provide the main pathway for lipid entry. Thus, VDAC isoforms, members of a superfamily of beta barrel proteins, moonlight as a class of phospholipid scramblases - distinct from alpha-helical scramblase proteins - that act to import lipids into mitochondria.
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Affiliation(s)
- Helene Jahn
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Ladislav Bartoš
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Grace I Dearden
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jeremy S Dittman
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Joost C M Holthuis
- Department of Molecular Cell Biology, University of Osnabrück, Osnabrück, 49076, Germany
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA.
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18
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Genge MG, Roy Chowdhury S, Dohnálek V, Yunoki K, Hirashima T, Endo T, Doležal P, Mokranjac D. Two domains of Tim50 coordinate translocation of proteins across the two mitochondrial membranes. Life Sci Alliance 2023; 6:e202302122. [PMID: 37748811 PMCID: PMC10520260 DOI: 10.26508/lsa.202302122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023] Open
Abstract
Hundreds of mitochondrial proteins with N-terminal presequences are translocated across the outer and inner mitochondrial membranes via the TOM and TIM23 complexes, respectively. How translocation of proteins across two mitochondrial membranes is coordinated is largely unknown. Here, we show that the two domains of Tim50 in the intermembrane space, named core and PBD, both have essential roles in this process. Building upon the surprising observation that the two domains of Tim50 can complement each other in trans, we establish that the core domain contains the main presequence-binding site and serves as the main recruitment point to the TIM23 complex. On the other hand, the PBD plays, directly or indirectly, a critical role in cooperation of the TOM and TIM23 complexes and supports the receptor function of Tim50. Thus, the two domains of Tim50 both have essential but distinct roles and together coordinate translocation of proteins across two mitochondrial membranes.
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Affiliation(s)
- Marcel G Genge
- Biocenter-Department of Cell Biology, LMU Munich, Munich, Germany
| | | | - Vít Dohnálek
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Kaori Yunoki
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Takashi Hirashima
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Toshiya Endo
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Dejana Mokranjac
- Biocenter-Department of Cell Biology, LMU Munich, Munich, Germany
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19
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Zhou X, Yang Y, Wang G, Wang S, Sun D, Ou X, Lian Y, Li L. Molecular pathway of mitochondrial preprotein import through the TOM-TIM23 supercomplex. Nat Struct Mol Biol 2023; 30:1996-2008. [PMID: 37696957 DOI: 10.1038/s41594-023-01103-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/18/2023] [Indexed: 09/13/2023]
Abstract
Over half of mitochondrial proteins are imported from the cytosol via the pre-sequence pathway, controlled by the TOM complex in the outer membrane and the TIM23 complex in the inner membrane. The mechanisms through which proteins are translocated via the TOM and TIM23 complexes remain unclear. Here we report the assembly of the active TOM-TIM23 supercomplex of Saccharomyces cerevisiae with translocating polypeptide substrates. Electron cryo-microscopy analyses reveal that the polypeptide substrates pass the TOM complex through the center of a Tom40 subunit, interacting with a glutamine-rich region. Structural and biochemical analyses show that the TIM23 complex contains a heterotrimer of the subunits Tim23, Tim17 and Mgr2. The polypeptide substrates are shielded from lipids by Mgr2 and Tim17, which creates a translocation pathway characterized by a negatively charged entrance and a central hydrophobic region. These findings reveal an unexpected pre-sequence pathway through the TOM-TIM23 supercomplex spanning the double membranes of mitochondria.
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Affiliation(s)
- Xueyin Zhou
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yuqi Yang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Guopeng Wang
- School of Life Sciences, Peking University, Beijing, China
| | - Shanshan Wang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Dongjie Sun
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Xiaomin Ou
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Yuke Lian
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Long Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.
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20
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Reed AL, Mitchell W, Alexandrescu AT, Alder NN. Interactions of amyloidogenic proteins with mitochondrial protein import machinery in aging-related neurodegenerative diseases. Front Physiol 2023; 14:1263420. [PMID: 38028797 PMCID: PMC10652799 DOI: 10.3389/fphys.2023.1263420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Most mitochondrial proteins are targeted to the organelle by N-terminal mitochondrial targeting sequences (MTSs, or "presequences") that are recognized by the import machinery and subsequently cleaved to yield the mature protein. MTSs do not have conserved amino acid compositions, but share common physicochemical properties, including the ability to form amphipathic α-helical structures enriched with basic and hydrophobic residues on alternating faces. The lack of strict sequence conservation implies that some polypeptides can be mistargeted to mitochondria, especially under cellular stress. The pathogenic accumulation of proteins within mitochondria is implicated in many aging-related neurodegenerative diseases, including Alzheimer's, Parkinson's, and Huntington's diseases. Mechanistically, these diseases may originate in part from mitochondrial interactions with amyloid-β precursor protein (APP) or its cleavage product amyloid-β (Aβ), α-synuclein (α-syn), and mutant forms of huntingtin (mHtt), respectively, that are mediated in part through their associations with the mitochondrial protein import machinery. Emerging evidence suggests that these amyloidogenic proteins may present cryptic targeting signals that act as MTS mimetics and can be recognized by mitochondrial import receptors and transported into different mitochondrial compartments. Accumulation of these mistargeted proteins could overwhelm the import machinery and its associated quality control mechanisms, thereby contributing to neurological disease progression. Alternatively, the uptake of amyloidogenic proteins into mitochondria may be part of a protein quality control mechanism for clearance of cytotoxic proteins. Here we review the pathomechanisms of these diseases as they relate to mitochondrial protein import and effects on mitochondrial function, what features of APP/Aβ, α-syn and mHtt make them suitable substrates for the import machinery, and how this information can be leveraged for the development of therapeutic interventions.
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Affiliation(s)
- Ashley L. Reed
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Wayne Mitchell
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Andrei T. Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Nathan N. Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
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21
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den Brave F, Schulte U, Fakler B, Pfanner N, Becker T. Mitochondrial complexome and import network. Trends Cell Biol 2023:S0962-8924(23)00208-8. [PMID: 37914576 DOI: 10.1016/j.tcb.2023.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023]
Abstract
Mitochondria perform crucial functions in cellular metabolism, protein and lipid biogenesis, quality control, and signaling. The systematic analysis of protein complexes and interaction networks provided exciting insights into the structural and functional organization of mitochondria. Most mitochondrial proteins do not act as independent units, but are interconnected by stable or dynamic protein-protein interactions. Protein translocases are responsible for importing precursor proteins into mitochondria and form central elements of several protein interaction networks. These networks include molecular chaperones and quality control factors, metabolite channels and respiratory chain complexes, and membrane and organellar contact sites. Protein translocases link the distinct networks into an overarching network, the mitochondrial import network (MitimNet), to coordinate biogenesis, membrane organization and function of mitochondria.
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Affiliation(s)
- Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany.
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22
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Sim SI, Chen Y, Lynch DL, Gumbart JC, Park E. Structural basis of mitochondrial protein import by the TIM23 complex. Nature 2023; 621:620-626. [PMID: 37344598 DOI: 10.1038/s41586-023-06239-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 05/19/2023] [Indexed: 06/23/2023]
Abstract
Mitochondria import nearly all of their approximately 1,000-2,000 constituent proteins from the cytosol across their double-membrane envelope1-5. Genetic and biochemical studies have shown that the conserved protein translocase, termed the TIM23 complex, mediates import of presequence-containing proteins (preproteins) into the mitochondrial matrix and inner membrane. Among about ten different subunits of the TIM23 complex, the essential multipass membrane protein Tim23, together with the evolutionarily related protein Tim17, has long been postulated to form a protein-conducting channel6-11. However, the mechanism by which these subunits form a translocation path in the membrane and enable the import process remains unclear due to a lack of structural information. Here we determined the cryo-electron microscopy structure of the core TIM23 complex (heterotrimeric Tim17-Tim23-Tim44) from Saccharomyces cerevisiae. Contrary to the prevailing model, Tim23 and Tim17 themselves do not form a water-filled channel, but instead have separate, lipid-exposed concave cavities that face in opposite directions. Our structural and biochemical analyses show that the cavity of Tim17, but not Tim23, forms the protein translocation path, whereas Tim23 probably has a structural role. The results further suggest that, during translocation of substrate polypeptides, the nonessential subunit Mgr2 seals the lateral opening of the Tim17 cavity to facilitate the translocation process. We propose a new model for the TIM23-mediated protein import and sorting mechanism, a central pathway in mitochondrial biogenesis.
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Affiliation(s)
- Sue Im Sim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Yuanyuan Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eunyong Park
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
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23
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Li D, Rocha-Roa C, Schilling MA, Reinisch KM, Vanni S. Lipid scrambling is a general feature of protein insertases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555937. [PMID: 37693532 PMCID: PMC10491306 DOI: 10.1101/2023.09.01.555937] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Glycerophospholipids are synthesized primarily in the cytosolic leaflet of the endoplasmic reticulum (ER) membrane and must be equilibrated between bilayer leaflets to allow the ER and membranes derived from it to grow. Lipid equilibration is facilitated by integral membrane proteins called "scramblases". These proteins feature a hydrophilic groove allowing the polar heads of lipids to traverse the hydrophobic membrane interior, similar to a credit-card moving through a reader. Nevertheless, despite their fundamental role in membrane expansion and dynamics, the identity of most scramblases has remained elusive. Here, combining biochemical reconstitution and molecular dynamics simulations, we show that lipid scrambling is a general feature of protein insertases, integral membrane proteins which insert polypeptide chains into membranes of the ER and organelles disconnected from vesicle trafficking. Our data indicate that lipid scrambling occurs in the same hydrophilic channel through which protein insertion takes place, and that scrambling is abolished in the presence of nascent polypeptide chains. We propose that protein insertases could have a so-far overlooked role in membrane dynamics as scramblases.
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Affiliation(s)
- Dazhi Li
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Matthew A Schilling
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Karin M Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Switzerland
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24
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Ornelas P, Bausewein T, Martin J, Morgner N, Nussberger S, Kühlbrandt W. Two conformations of the Tom20 preprotein receptor in the TOM holo complex. Proc Natl Acad Sci U S A 2023; 120:e2301447120. [PMID: 37579144 PMCID: PMC10450662 DOI: 10.1073/pnas.2301447120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
The TOM complex is the main entry point for precursor proteins (preproteins) into mitochondria. Preproteins containing targeting sequences are recognized by the TOM complex and imported into mitochondria. We have determined the structure of the TOM core complex from Neurospora crassa by single-particle electron cryomicroscopy at 3.3 Å resolution, showing its interaction with a bound preprotein at 4 Å resolution, and of the TOM holo complex including the Tom20 receptor at 6 to 7 Å resolution. TOM is a transmembrane complex consisting of two β-barrels, three receptor subunits, and three short transmembrane subunits. Tom20 has a transmembrane helix and a receptor domain on the cytoplasmic side. We propose that Tom20 acts as a dynamic gatekeeper, guiding preproteins into the pores of the TOM complex. We analyze the interactions of Tom20 with other TOM subunits, present insights into the structure of the TOM holo complex, and suggest a translocation mechanism.
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Affiliation(s)
- Pamela Ornelas
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt60438, Germany
| | - Thomas Bausewein
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt60438, Germany
| | - Janosch Martin
- Department of Structural Biology, Institute of Physical and Theoretical Chemistry, Goethe University of Frankfurt, Frankfurt60439, Germany
| | - Nina Morgner
- Department of Structural Biology, Institute of Physical and Theoretical Chemistry, Goethe University of Frankfurt, Frankfurt60439, Germany
| | - Stephan Nussberger
- Department of Biophysics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart70569, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt60438, Germany
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25
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Needs HI, Wilkinson KA, Henley JM, Collinson I. Aggregation-prone Tau impairs mitochondrial import, which affects organelle morphology and neuronal complexity. J Cell Sci 2023; 136:jcs260993. [PMID: 37303235 PMCID: PMC10357015 DOI: 10.1242/jcs.260993] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023] Open
Abstract
Mitochondrial protein import is essential for organellar biogenesis, and thereby for the sufficient supply of cytosolic ATP - which is particularly important for cells with high energy demands like neurons. This study explores the prospect of import machinery perturbation as a cause of neurodegeneration instigated by the accumulation of aggregating proteins linked to disease. We found that the aggregation-prone Tau variant (TauP301L) reduces the levels of components of the import machinery of the outer (TOM20, encoded by TOMM20) and inner membrane (TIM23, encoded by TIMM23) while associating with TOM40 (TOMM40). Intriguingly, this interaction affects mitochondrial morphology, but not protein import or respiratory function; raising the prospect of an intrinsic rescue mechanism. Indeed, TauP301L induced the formation of tunnelling nanotubes (TNTs), potentially for the recruitment of healthy mitochondria from neighbouring cells and/or the disposal of mitochondria incapacitated by aggregated Tau. Consistent with this, inhibition of TNT formation (and rescue) reveals Tau-induced import impairment. In primary neuronal cultures, TauP301L induced morphological changes characteristic of neurodegeneration. Interestingly, these effects were mirrored in cells where the import sites were blocked artificially. Our results reveal a link between aggregation-prone Tau and defective mitochondrial import relevant to disease.
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Affiliation(s)
- Hope I. Needs
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - Jeremy M. Henley
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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26
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Meurant S, Mauclet L, Dieu M, Arnould T, Eyckerman S, Renard P. Endogenous TOM20 Proximity Labeling: A Swiss-Knife for the Study of Mitochondrial Proteins in Human Cells. Int J Mol Sci 2023; 24:ijms24119604. [PMID: 37298552 DOI: 10.3390/ijms24119604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Biotin-based proximity labeling approaches, such as BioID, have demonstrated their use for the study of mitochondria proteomes in living cells. The use of genetically engineered BioID cell lines enables the detailed characterization of poorly characterized processes such as mitochondrial co-translational import. In this process, translation is coupled to the translocation of the mitochondrial proteins, alleviating the energy cost typically associated with the post-translational import relying on chaperone systems. However, the mechanisms are still unclear with only few actors identified but none that have been described in mammals yet. We thus profiled the TOM20 proxisome using BioID, assuming that some of the identified proteins could be molecular actors of the co-translational import in human cells. The obtained results showed a high enrichment of RNA binding proteins close to the TOM complex. However, for the few selected candidates, we could not demonstrate a role in the mitochondrial co-translational import process. Nonetheless, we were able to demonstrate additional uses of our BioID cell line. Indeed, the experimental approach used in this study is thus proposed for the identification of mitochondrial co-translational import effectors and for the monitoring of protein entry inside mitochondria with a potential application in the prediction of mitochondrial protein half-life.
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Affiliation(s)
- Sébastien Meurant
- URBC, Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
| | - Lorris Mauclet
- URBC, Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
| | - Marc Dieu
- Mass Spectrometry Platform (MaSUN), Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
| | - Thierry Arnould
- URBC, Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Patricia Renard
- URBC, Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
- Mass Spectrometry Platform (MaSUN), Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
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27
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Srinivasan K, Erramilli SK, Chakravarthy S, Gonzalez A, Kossiakoff A, Noinaj N. Characterization of synthetic antigen binding fragments targeting Toc75 for the isolation of TOC in A. thaliana and P. sativum. Structure 2023; 31:595-606.e5. [PMID: 36977410 PMCID: PMC10164082 DOI: 10.1016/j.str.2023.03.002] [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: 07/15/2022] [Revised: 12/21/2022] [Accepted: 03/02/2023] [Indexed: 03/29/2023]
Abstract
Roughly 95% of the proteins that make up the chloroplast must be imported from the cytoplasm. The machinery responsible for the translocation of these cargo proteins is called the translocon at the outer membrane of chloroplast (TOC). The TOC core consists of three proteins, Toc34, Toc75, and Toc159; no high-resolution structure has been solved of fully assembled TOC from plants. Efforts toward determining the structure of the TOC have been hindered almost entirely by difficulties in producing sufficient yields for structural studies. In this study, we introduce an innovative method that utilizes synthetic antigen binding fragments (sABs) to isolate TOC directly from wild-type plant biomass including A. thaliana and P. sativum. Binding between the sABs and the POTRA domains was characterized by size-exclusion chromatography coupled with small-angle X-ray scattering (SEC-SAXS), X-ray crystallography, and isothermal titration calorimetry. We also demonstrate the isolation of the TOC from P. sativum, laying the framework for large-scale isolation and purification of TOC for functional and structural studies.
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Affiliation(s)
- Karthik Srinivasan
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Adrian Gonzalez
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Anthony Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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28
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Busch JD, Fielden LF, Pfanner N, Wiedemann N. Mitochondrial protein transport: Versatility of translocases and mechanisms. Mol Cell 2023; 83:890-910. [PMID: 36931257 DOI: 10.1016/j.molcel.2023.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023]
Abstract
Biogenesis of mitochondria requires the import of approximately 1,000 different precursor proteins into and across the mitochondrial membranes. Mitochondria exhibit a wide variety of mechanisms and machineries for the translocation and sorting of precursor proteins. Five major import pathways that transport proteins to their functional intramitochondrial destination have been elucidated; these pathways range from the classical amino-terminal presequence-directed pathway to pathways using internal or even carboxy-terminal targeting signals in the precursors. Recent studies have provided important insights into the structural organization of membrane-embedded preprotein translocases of mitochondria. A comparison of the different translocases reveals the existence of at least three fundamentally different mechanisms: two-pore-translocase, β-barrel switching, and transport cavities open to the lipid bilayer. In addition, translocases are physically engaged in dynamic interactions with respiratory chain complexes, metabolite transporters, quality control factors, and machineries controlling membrane morphology. Thus, mitochondrial preprotein translocases are integrated into multi-functional networks of mitochondrial and cellular machineries.
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Affiliation(s)
- Jakob D Busch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Laura F Fielden
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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29
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Sohrabi T, Mirzaei-Behbahani B, Zadali R, Pirhaghi M, Morozova-Roche LA, Meratan AA. Common Mechanisms Underlying α-Synuclein-Induced Mitochondrial Dysfunction in Parkinson's Disease. J Mol Biol 2023:167992. [PMID: 36736886 DOI: 10.1016/j.jmb.2023.167992] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
Parkinson's disease (PD) is the most common neurological movement disorder characterized by the selective and irreversible loss of dopaminergic neurons in substantia nigra pars compacta resulting in dopamine deficiency in the striatum. While most cases are sporadic or environmental, about 10% of patients have a positive family history with a genetic cause. The misfolding and aggregation of α-synuclein (α-syn) as a casual factor in the pathogenesis of PD has been supported by a great deal of literature. Extensive studies of mechanisms underpinning degeneration of the dopaminergic neurons induced by α-syn dysfunction suggest a complex process that involves multiple pathways, including mitochondrial dysfunction and increased oxidative stress, impaired calcium homeostasis through membrane permeabilization, synaptic dysfunction, impairment of quality control systems, disruption of microtubule dynamics and axonal transport, endoplasmic reticulum/Golgi dysfunction, nucleus malfunction, and microglia activation leading to neuroinflammation. Among them mitochondrial dysfunction has been considered as the most primary target of α-syn-induced toxicity, leading to neuronal cell death in both sporadic and familial forms of PD. Despite reviewing many aspects of PD pathogenesis related to mitochondrial dysfunction, a systemic study on how α-syn malfunction/aggregation damages mitochondrial functionality and leads to neurodegeneration is missing in the literature. In this review, we give a detailed molecular overview of the proposed mechanisms by which α-syn, directly or indirectly, contributes to mitochondrial dysfunction. This may provide valuable insights for development of new therapeutic approaches in relation to PD. Antioxidant-based therapy as a potential strategy to protect mitochondria against oxidative damage, its challenges, and recent developments in the field are discussed.
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Affiliation(s)
- Tahereh Sohrabi
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Behnaz Mirzaei-Behbahani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Ramin Zadali
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Mitra Pirhaghi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Akbar Meratan
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
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30
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Kim DB, Na C, Hwang I, Lee DW. Understanding protein translocation across chloroplast membranes: Translocons and motor proteins. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:408-416. [PMID: 36223071 DOI: 10.1111/jipb.13385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Subcellular organelles in eukaryotes are surrounded by lipid membranes. In an endomembrane system, vesicle trafficking is the primary mechanism for the delivery of organellar proteins to specific organelles. However, organellar proteins for chloroplasts, mitochondria, the nucleus, and peroxisomes that are translated in the cytosol are directly imported into their target organelles. Chloroplasts are a plant-specific organelle with outer and inner envelope membranes, a dual-membrane structure that is similar to mitochondria. Interior chloroplast proteins translated by cytosolic ribosomes are thus translocated through TOC and TIC complexes (translocons in the outer and inner envelope of chloroplasts, respectively), with stromal ATPase motor proteins playing a critical role in pulling pre-proteins through these import channels. Over the last three decades, the identity and function of TOC/TIC components and stromal motor proteins have been actively investigated, which has shed light on the action mechanisms at a molecular level. However, there remains some disagreement over the exact composition of TIC complexes and genuine stromal motor proteins. In this review, we discuss recent findings on the mechanisms by which proteins are translocated through TOC/TIC complexes and discuss future prospects for this field of research.
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Affiliation(s)
- Da Been Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Korea
| | - Changhee Na
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Korea
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Dong Wook Lee
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Korea
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, 61186, Korea
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31
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Li J, Yang D, Li Z, Zhao M, Wang D, Sun Z, Wen P, Dai Y, Gou F, Ji Y, Zhao D, Yang L. PINK1/Parkin-mediated mitophagy in neurodegenerative diseases. Ageing Res Rev 2023; 84:101817. [PMID: 36503124 DOI: 10.1016/j.arr.2022.101817] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/21/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Mitochondria play key roles in bioenergetics, metabolism, and signaling; therefore, stable mitochondrial function is essential for cell survival, particularly in energy-intensive neuronal cells. In neurodegenerative diseases, damaged mitochondria accumulate in neurons causing associated bioenergetics deficiency, impaired cell signaling, defective cytoplasmic calcium buffering, and other pathological changes. Mitochondrial quality control is an important mechanism to ensure the maintenance of mitochondrial health, homeostasis, and mitophagy, the latter of which is a pathway that delivers defective mitochondria to the lysosome for degradation. Defective mitophagy is thought to be responsible for the accumulation of damaged mitochondria, which leads to cellular dysfunction and/or death in neurodegenerative diseases. PINK1/Parkin mainly regulates ubiquitin-dependent mitophagy, which is crucial for many aspects of mitochondrial physiology, particularly the initiation of autophagic mechanisms. Therefore, in the present review, we summarize the current knowledge of the conventional mitophagy pathway, focusing on the molecular mechanisms underlying mitophagy dysregulation in prion disease and other age-related neurodegenerative diseases, especially in relation to the PINK1/Parkin pathway. Moreover, we list the inducers of mitophagy that possess neuroprotective effects, in addition to their mechanisms related to the PINK1/Parkin pathway. These mechanisms may provide potential interventions centered on the regulation of mitophagy and offer therapeutic strategies for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Jie Li
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Dongming Yang
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Zhiping Li
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Mengyang Zhao
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Dongdong Wang
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Zhixin Sun
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Pei Wen
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Yuexin Dai
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Fengting Gou
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Yilan Ji
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Deming Zhao
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Lifeng Yang
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China.
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32
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Takeda H, Busto JV, Lindau C, Tsutsumi A, Tomii K, Imai K, Yamamori Y, Hirokawa T, Motono C, Ganesan I, Wenz LS, Becker T, Kikkawa M, Pfanner N, Wiedemann N, Endo T. A multipoint guidance mechanism for β-barrel folding on the SAM complex. Nat Struct Mol Biol 2023; 30:176-187. [PMID: 36604501 DOI: 10.1038/s41594-022-00897-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 11/11/2022] [Indexed: 01/07/2023]
Abstract
Mitochondrial β-barrel proteins are essential for the transport of metabolites, ions and proteins. The sorting and assembly machinery (SAM) mediates their folding and membrane insertion. We report the cryo-electron microscopy structure of the yeast SAM complex carrying an early eukaryotic β-barrel folding intermediate. The lateral gate of Sam50 is wide open and pairs with the last β-strand (β-signal) of the substrate-the 19-β-stranded Tom40 precursor-to form a hybrid barrel in the membrane plane. The Tom40 barrel grows and curves, guided by an extended bridge with Sam50. Tom40's first β-segment (β1) penetrates into the nascent barrel, interacting with its inner wall. The Tom40 amino-terminal segment then displaces β1 to promote its pairing with Tom40's last β-strand to complete barrel formation with the assistance of Sam37's dynamic α-protrusion. Our study thus reveals a multipoint guidance mechanism for mitochondrial β-barrel folding.
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Affiliation(s)
- Hironori Takeda
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Nara Institute of Science and Technology, Ikoma, Japan
| | - Jon V Busto
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Caroline Lindau
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan
| | - Yu Yamamori
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Takatsugu Hirokawa
- Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
| | - Chie Motono
- Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo, Japan.,Computational Bio Big-Data Open Innovation Laboratory, AIST, Waseda University, Tokyo, Japan
| | - Iniyan Ganesan
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lena-Sophie Wenz
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan. .,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.
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33
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Shan SO. Role of Hsp70 in Post-Translational Protein Targeting: Tail-Anchored Membrane Proteins and Beyond. Int J Mol Sci 2023; 24:1170. [PMID: 36674686 PMCID: PMC9866221 DOI: 10.3390/ijms24021170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The Hsp70 family of molecular chaperones acts as a central 'hub' in the cell that interacts with numerous newly synthesized proteins to assist in their biogenesis. Apart from its central and well-established role in facilitating protein folding, Hsp70s also act as key decision points in the cellular chaperone network that direct client proteins to distinct biogenesis and quality control pathways. In this paper, we review accumulating data that illustrate a new branch in the Hsp70 network: the post-translational targeting of nascent membrane and organellar proteins to diverse cellular organelles. Work in multiple pathways suggests that Hsp70, via its ability to interact with components of protein targeting and translocation machineries, can initiate elaborate substrate relays in a sophisticated cascade of chaperones, cochaperones, and receptor proteins, and thus provide a mechanism to safeguard and deliver nascent membrane proteins to the correct cellular membrane. We discuss the mechanistic principles gleaned from better-studied Hsp70-dependent targeting pathways and outline the observations and outstanding questions in less well-studied systems.
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Affiliation(s)
- Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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34
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Schulte U, den Brave F, Haupt A, Gupta A, Song J, Müller CS, Engelke J, Mishra S, Mårtensson C, Ellenrieder L, Priesnitz C, Straub SP, Doan KN, Kulawiak B, Bildl W, Rampelt H, Wiedemann N, Pfanner N, Fakler B, Becker T. Mitochondrial complexome reveals quality-control pathways of protein import. Nature 2023; 614:153-159. [PMID: 36697829 PMCID: PMC9892010 DOI: 10.1038/s41586-022-05641-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 12/09/2022] [Indexed: 01/26/2023]
Abstract
Mitochondria have crucial roles in cellular energetics, metabolism, signalling and quality control1-4. They contain around 1,000 different proteins that often assemble into complexes and supercomplexes such as respiratory complexes and preprotein translocases1,3-7. The composition of the mitochondrial proteome has been characterized1,3,5,6; however, the organization of mitochondrial proteins into stable and dynamic assemblies is poorly understood for major parts of the proteome1,4,7. Here we report quantitative mapping of mitochondrial protein assemblies using high-resolution complexome profiling of more than 90% of the yeast mitochondrial proteome, termed MitCOM. An analysis of the MitCOM dataset resolves >5,200 protein peaks with an average of six peaks per protein and demonstrates a notable complexity of mitochondrial protein assemblies with distinct appearance for respiration, metabolism, biogenesis, dynamics, regulation and redox processes. We detect interactors of the mitochondrial receptor for cytosolic ribosomes, of prohibitin scaffolds and of respiratory complexes. The identification of quality-control factors operating at the mitochondrial protein entry gate reveals pathways for preprotein ubiquitylation, deubiquitylation and degradation. Interactions between the peptidyl-tRNA hydrolase Pth2 and the entry gate led to the elucidation of a constitutive pathway for the removal of preproteins. The MitCOM dataset-which is accessible through an interactive profile viewer-is a comprehensive resource for the identification, organization and interaction of mitochondrial machineries and pathways.
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Affiliation(s)
- Uwe Schulte
- grid.5963.9Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.5963.9CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Fabian den Brave
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Alexander Haupt
- grid.5963.9Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Arushi Gupta
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany ,grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jiyao Song
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany ,grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Catrin S. Müller
- grid.5963.9Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jeannine Engelke
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Swadha Mishra
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Christoph Mårtensson
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,Present Address: MTIP, Basel, Switzerland
| | - Lars Ellenrieder
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.419481.10000 0001 1515 9979Present Address: Novartis, Basel, Switzerland
| | - Chantal Priesnitz
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian P. Straub
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.5963.9Faculty of Biology, University of Freiburg, Freiburg, Germany ,grid.482402.8Present Address: Sanofi-Aventis (Suisse), Vernier, Switzerland
| | - Kim Nguyen Doan
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bogusz Kulawiak
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.413454.30000 0001 1958 0162Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Wolfgang Bildl
- grid.5963.9Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heike Rampelt
- grid.5963.9CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany ,grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nils Wiedemann
- grid.5963.9CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany ,grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.5963.9BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Nikolaus Pfanner
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,Center for Basics in NeuroModulation, Freiburg, Germany.
| | - Thomas Becker
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
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35
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Down the membrane hole: Ion channels in protozoan parasites. PLoS Pathog 2022; 18:e1011004. [PMID: 36580479 PMCID: PMC9799330 DOI: 10.1371/journal.ppat.1011004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Parasitic diseases caused by protozoans are highly prevalent around the world, disproportionally affecting developing countries, where coinfection with other microorganisms is common. Control and treatment of parasitic infections are constrained by the lack of specific and effective drugs, plus the rapid emergence of resistance. Ion channels are main drug targets for numerous diseases, but their potential against protozoan parasites is still untapped. Ion channels are membrane proteins expressed in all types of cells, allowing for the flow of ions between compartments, and regulating cellular functions such as membrane potential, excitability, volume, signaling, and death. Channels and transporters reside at the interface between parasites and their hosts, controlling nutrient uptake, viability, replication, and infectivity. To understand how ion channels control protozoan parasites fate and to evaluate their suitability for therapeutics, we must deepen our knowledge of their structure, function, and modulation. However, methodological approaches commonly used in mammalian cells have proven difficult to apply in protozoans. This review focuses on ion channels described in protozoan parasites of clinical relevance, mainly apicomplexans and trypanosomatids, highlighting proteins for which molecular and functional evidence has been correlated with their physiological functions.
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36
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Bennett CF, Latorre-Muro P, Puigserver P. Mechanisms of mitochondrial respiratory adaptation. Nat Rev Mol Cell Biol 2022; 23:817-835. [PMID: 35804199 PMCID: PMC9926497 DOI: 10.1038/s41580-022-00506-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2022] [Indexed: 02/07/2023]
Abstract
Mitochondrial energetic adaptations encompass a plethora of conserved processes that maintain cell and organismal fitness and survival in the changing environment by adjusting the respiratory capacity of mitochondria. These mitochondrial responses are governed by general principles of regulatory biology exemplified by changes in gene expression, protein translation, protein complex formation, transmembrane transport, enzymatic activities and metabolite levels. These changes can promote mitochondrial biogenesis and membrane dynamics that in turn support mitochondrial respiration. The main regulatory components of mitochondrial energetic adaptation include: the transcription coactivator peroxisome proliferator-activated receptor-γ (PPARγ) coactivator 1α (PGC1α) and associated transcription factors; mTOR and endoplasmic reticulum stress signalling; TOM70-dependent mitochondrial protein import; the cristae remodelling factors, including mitochondrial contact site and cristae organizing system (MICOS) and OPA1; lipid remodelling; and the assembly and metabolite-dependent regulation of respiratory complexes. These adaptive molecular and structural mechanisms increase respiration to maintain basic processes specific to cell types and tissues. Failure to execute these regulatory responses causes cell damage and inflammation or senescence, compromising cell survival and the ability to adapt to energetically demanding conditions. Thus, mitochondrial adaptive cellular processes are important for physiological responses, including to nutrient availability, temperature and physical activity, and their failure leads to diseases associated with mitochondrial dysfunction such as metabolic and age-associated diseases and cancer.
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Affiliation(s)
- Christopher F Bennett
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pedro Latorre-Muro
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pere Puigserver
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
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37
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Rödl S, den Brave F, Räschle M, Kizmaz B, Lenhard S, Groh C, Becker H, Zimmermann J, Morgan B, Richling E, Becker T, Herrmann JM. The metabolite-controlled ubiquitin conjugase Ubc8 promotes mitochondrial protein import. Life Sci Alliance 2022; 6:6/1/e202201526. [PMID: 36253107 PMCID: PMC9579816 DOI: 10.26508/lsa.202201526] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 11/26/2022] Open
Abstract
Mitochondria play a key role in cellular energy metabolism. Transitions between glycolytic and respiratory conditions induce considerable adaptations of the cellular proteome. These metabolism-dependent changes are particularly pronounced for the protein composition of mitochondria. Here, we show that the yeast cytosolic ubiquitin conjugase Ubc8 plays a crucial role in the remodeling process when cells transition from respiratory to fermentative conditions. Ubc8 is a conserved and well-studied component of the catabolite control system that is known to regulate the stability of gluconeogenic enzymes. Unexpectedly, we found that Ubc8 also promotes the assembly of the translocase of the outer membrane of mitochondria (TOM) and increases the levels of its cytosol-exposed receptor subunit Tom22. Ubc8 deficiency results in compromised protein import into mitochondria and reduced steady-state levels of mitochondrial proteins. Our observations show that Ubc8, which is controlled by the prevailing metabolic conditions, promotes the switch from glucose synthesis to glucose usage in the cytosol and induces the biogenesis of the mitochondrial TOM machinery to improve mitochondrial protein import during phases of metabolic transition.
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Affiliation(s)
- Saskia Rödl
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Büsra Kizmaz
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Svenja Lenhard
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Carina Groh
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Hanna Becker
- Food Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jannik Zimmermann
- Biochemistry, Center for Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Bruce Morgan
- Biochemistry, Center for Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Elke Richling
- Food Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
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38
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Rozov SM, Deineko EV. Increasing the Efficiency of the Accumulation of Recombinant Proteins in Plant Cells: The Role of Transport Signal Peptides. PLANTS (BASEL, SWITZERLAND) 2022; 11:2561. [PMID: 36235427 PMCID: PMC9572730 DOI: 10.3390/plants11192561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The problem with increasing the yield of recombinant proteins is resolvable using different approaches, including the transport of a target protein to cell compartments with a low protease activity. In the cell, protein targeting involves short-signal peptide sequences recognized by intracellular protein transport systems. The main systems of the protein transport across membranes of the endoplasmic reticulum and endosymbiotic organelles are reviewed here, as are the major types and structure of the signal sequences targeting proteins to the endoplasmic reticulum and its derivatives, to plastids, and to mitochondria. The role of protein targeting to certain cell organelles depending on specific features of recombinant proteins and the effect of this targeting on the protein yield are discussed, in addition to the main directions of the search for signal sequences based on their primary structure. This knowledge makes it possible not only to predict a protein localization in the cell but also to reveal the most efficient sequences with potential biotechnological utility.
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39
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Caudal A, Tang X, Chavez JD, Keller A, Mohr JP, Bakhtina AA, Villet O, Chen H, Zhou B, Walker MA, Tian R, Bruce JE. Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart. NATURE CARDIOVASCULAR RESEARCH 2022; 1:855-866. [PMID: 36405497 PMCID: PMC9667921 DOI: 10.1038/s44161-022-00127-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/02/2022] [Indexed: 11/09/2022]
Abstract
Advancements in cross-linking mass spectrometry (XL-MS) bridge the gap between purified systems and native tissue environments, allowing the detection of protein structural interactions in their native state. Here we use isobaric quantitative protein interaction reporter technology (iqPIR) to compare the mitochondria protein interactomes in healthy and hypertrophic murine hearts, 4 weeks post-transaortic constriction. The failing heart interactome includes 588 statistically significant cross-linked peptide pairs altered in the disease condition. We observed an increase in the assembly of ketone oxidation oligomers corresponding to an increase in ketone metabolic utilization; remodeling of NDUA4 interaction in Complex IV, likely contributing to impaired mitochondria respiration; and conformational enrichment of ADP/ATP carrier ADT1, which is non-functional for ADP/ATP translocation but likely possesses non-selective conductivity. Our application of quantitative cross-linking technology in cardiac tissue provides molecular-level insights into the complex mitochondria remodeling in heart failure while bringing forth new hypotheses for pathological mechanisms.
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Affiliation(s)
- Arianne Caudal
- Department of Biochemistry, Department of Anesthesiology & Pain Medicine, University of Washington
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington
- These authors contributed equally
| | - Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
- These authors contributed equally
| | - Juan D. Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Jared P. Mohr
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Anna A. Bakhtina
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Outi Villet
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington
| | - Hongye Chen
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington
| | - Bo Zhou
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington
| | - Matthew A. Walker
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington
| | - Rong Tian
- Department of Biochemistry, Department of Anesthesiology & Pain Medicine, University of Washington
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington
- These authors jointly supervised this work
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
- These authors jointly supervised this work
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40
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Li S. Detergents and alternatives in cryo-EM studies of membrane proteins. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1049-1056. [PMID: 35866608 PMCID: PMC9828306 DOI: 10.3724/abbs.2022088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/28/2022] [Indexed: 11/25/2022] Open
Abstract
Structure determination of membrane proteins has been a long-standing challenge to understand the molecular basis of life processes. Detergents are widely used to study the structure and function of membrane proteins by various experimental methods, and the application of membrane mimetics is also a prevalent trend in the field of cryo-EM analysis. This review focuses on the widely-used detergents and corresponding properties and structures, and also discusses the growing interests in membrane mimetic systems used in cryo-EM studies, providing insights into the role of detergent alternatives in structure determination.
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Affiliation(s)
- Shuo Li
- />Department of Life ScienceNational Natural Science Foundation of ChinaBeijing100085China
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41
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Structural basis of Tom20 and Tom22 cytosolic domains as the human TOM complex receptors. Proc Natl Acad Sci U S A 2022; 119:e2200158119. [PMID: 35733257 PMCID: PMC9245660 DOI: 10.1073/pnas.2200158119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial preproteins synthesized in cytosol are imported into mitochondria by a multisubunit translocase of the outer membrane (TOM) complex. Functioned as the receptor, the TOM complex components, Tom 20, Tom22, and Tom70, recognize the presequence and further guide the protein translocation. Their deficiency has been linked with neurodegenerative diseases and cardiac pathology. Although several structures of the TOM complex have been reported by cryoelectron microscopy (cryo-EM), how Tom22 and Tom20 function as TOM receptors remains elusive. Here we determined the structure of TOM core complex at 2.53 Å and captured the structure of the TOM complex containing Tom22 and Tom20 cytosolic domains at 3.74 Å. Structural analysis indicates that Tom20 and Tom22 share a similar three-helix bundle structural feature in the cytosolic domain. Further structure-guided biochemical analysis reveals that the Tom22 cytosolic domain is responsible for binding to the presequence, and the helix H1 is critical for this binding. Altogether, our results provide insights into the functional mechanism of the TOM complex recognizing and transferring preproteins across the mitochondrial membrane.
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42
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Ford HC, Allen WJ, Pereira GC, Liu X, Dillingham MS, Collinson I. Towards a molecular mechanism underlying mitochondrial protein import through the TOM and TIM23 complexes. eLife 2022; 11:75426. [PMID: 35674314 PMCID: PMC9255969 DOI: 10.7554/elife.75426] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/07/2022] [Indexed: 12/27/2022] Open
Abstract
Nearly all mitochondrial proteins need to be targeted for import from the cytosol. For the majority, the first port of call is the translocase of the outer membrane (TOM complex), followed by a procession of alternative molecular machines, conducting transport to their final destination. The pre-sequence translocase of the inner membrane (TIM23-complex) imports proteins with cleavable pre-sequences. Progress in understanding these transport mechanisms has been hampered by the poor sensitivity and time resolution of import assays. However, with the development of an assay based on split NanoLuc luciferase, we can now explore this process in greater detail. Here, we apply this new methodology to understand how ∆ψ and ATP hydrolysis, the two main driving forces for import into the matrix, contribute to the transport of pre-sequence-containing precursors (PCPs) with varying properties. Notably, we found that two major rate-limiting steps define PCP import time: passage of PCP across the outer membrane and initiation of inner membrane transport by the pre-sequence - the rates of which are influenced by PCP size and net charge. The apparent distinction between transport through the two membranes (passage through TOM is substantially complete before PCP-TIM engagement) is in contrast with the current view that import occurs through TOM and TIM in a single continuous step. Our results also indicate that PCPs spend very little time in the TIM23 channel - presumably rapid success or failure of import is critical for maintenance of mitochondrial fitness.
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Affiliation(s)
- Holly C Ford
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - William J Allen
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Gonçalo C Pereira
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Xia Liu
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | | | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
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43
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Diederichs KA, Pitt AS, Varughese JT, Hackel TN, Buchanan SK, Shaw PL. Mechanistic insights into fungal mitochondrial outer membrane protein biogenesis. Curr Opin Struct Biol 2022; 74:102383. [DOI: 10.1016/j.sbi.2022.102383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/11/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
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44
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Spatiotemporal stop-and-go dynamics of the mitochondrial TOM core complex correlates with channel activity. Commun Biol 2022; 5:471. [PMID: 35581327 PMCID: PMC9114391 DOI: 10.1038/s42003-022-03419-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/26/2022] [Indexed: 11/08/2022] Open
Abstract
Single-molecule studies can reveal phenomena that remain hidden in ensemble measurements. Here we show the correlation between lateral protein diffusion and channel activity of the general protein import pore of mitochondria (TOM-CC) in membranes resting on ultrathin hydrogel films. Using electrode-free optical recordings of ion flux, we find that TOM-CC switches reversibly between three states of ion permeability associated with protein diffusion. While freely diffusing TOM-CC molecules are predominantly in a high permeability state, non-mobile molecules are mostly in an intermediate or low permeability state. We explain this behavior by the mechanical binding of the two protruding Tom22 subunits to the hydrogel and a concomitant combinatorial opening and closing of the two β-barrel pores of TOM-CC. TOM-CC could thus represent a β-barrel membrane protein complex to exhibit membrane state-dependent mechanosensitive properties, mediated by its two Tom22 subunits.
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45
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Hoffmann JJ, Becker T. Crosstalk between Mitochondrial Protein Import and Lipids. Int J Mol Sci 2022; 23:ijms23095274. [PMID: 35563660 PMCID: PMC9101885 DOI: 10.3390/ijms23095274] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 12/10/2022] Open
Abstract
Mitochondria import about 1000 precursor proteins from the cytosol. The translocase of the outer membrane (TOM complex) forms the major entry site for precursor proteins. Subsequently, membrane-bound protein translocases sort the precursor proteins into the outer and inner membrane, the intermembrane space, and the matrix. The phospholipid composition of mitochondrial membranes is critical for protein import. Structural and biochemical data revealed that phospholipids affect the stability and activity of mitochondrial protein translocases. Integration of proteins into the target membrane involves rearrangement of phospholipids and distortion of the lipid bilayer. Phospholipids are present in the interface between subunits of protein translocases and affect the dynamic coupling of partner proteins. Phospholipids are required for full activity of the respiratory chain to generate membrane potential, which in turn drives protein import across and into the inner membrane. Finally, outer membrane protein translocases are closely linked to organellar contact sites that mediate lipid trafficking. Altogether, intensive crosstalk between mitochondrial protein import and lipid biogenesis controls mitochondrial biogenesis.
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Sayyed UMH, Mahalakshmi R. Mitochondrial protein translocation machinery: From TOM structural biogenesis to functional regulation. J Biol Chem 2022; 298:101870. [PMID: 35346689 PMCID: PMC9052162 DOI: 10.1016/j.jbc.2022.101870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 01/15/2023] Open
Abstract
The human mitochondrial outer membrane is biophysically unique as it is the only membrane possessing transmembrane β-barrel proteins (mitochondrial outer membrane proteins, mOMPs) in the cell. The most vital of the three mOMPs is the core protein of the translocase of the outer mitochondrial membrane (TOM) complex. Identified first as MOM38 in Neurospora in 1990, the structure of Tom40, the core 19-stranded β-barrel translocation channel, was solved in 2017, after nearly three decades. Remarkably, the past four years have witnessed an exponential increase in structural and functional studies of yeast and human TOM complexes. In addition to being conserved across all eukaryotes, the TOM complex is the sole ATP-independent import machinery for nearly all of the ∼1000 to 1500 known mitochondrial proteins. Recent cryo-EM structures have provided detailed insight into both possible assembly mechanisms of the TOM core complex and organizational dynamics of the import machinery and now reveal novel regulatory interplay with other mOMPs. Functional characterization of the TOM complex using biochemical and structural approaches has also revealed mechanisms for substrate recognition and at least five defined import pathways for precursor proteins. In this review, we discuss the discovery, recently solved structures, molecular function, and regulation of the TOM complex and its constituents, along with the implications these advances have for alleviating human diseases.
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Affiliation(s)
- Ulfat Mohd Hanif Sayyed
- Molecular Biophysics Laboratory, Indian Institute of Science Education and Research, Bhopal, India
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Song J, Becker T. Fidelity of organellar protein targeting. Curr Opin Cell Biol 2022; 75:102071. [DOI: 10.1016/j.ceb.2022.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 11/26/2022]
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Moesin: A novel receptor on NK lymphocytes binds to TOMM40 on K562 leukemia cells initiating cytolysis. Hum Immunol 2022; 83:418-427. [DOI: 10.1016/j.humimm.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 11/04/2022]
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Kühlbrandt W. Forty years in cryoEM of membrane proteins. Microscopy (Oxf) 2022; 71:i30-i50. [PMID: 35275191 PMCID: PMC8855526 DOI: 10.1093/jmicro/dfab041] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/05/2021] [Accepted: 11/10/2021] [Indexed: 12/13/2022] Open
Abstract
In a surprisingly short time, electron cryo-microscopy (cryoEM) has developed from a niche technique in structural biology to a mainstream method practiced in a rapidly growing number of laboratories around the world. From its beginnings about 40 years ago, cryoEM has had a major impact on the study of membrane proteins, in particular the energy-converting systems from bacterial, mitochondrial and chloroplast membranes. Early work on two-dimensional crystals attained resolutions ∼3.5 Å, but at present, single-particle cryoEM delivers much more detailed structures without crystals. Electron cryo-tomography of membranes and membrane-associated proteins adds valuable context, usually at lower resolution. The review ends with a brief outlook on future prospects.
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Affiliation(s)
- Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, Frankfurt am Main 60438, Germany
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Araiso Y, Imai K, Endo T. Role of the TOM Complex in Protein Import into Mitochondria: Structural Views. Annu Rev Biochem 2022; 91:679-703. [PMID: 35287471 DOI: 10.1146/annurev-biochem-032620-104527] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mitochondria are central to energy production, metabolism and signaling, and apoptosis. To make new mitochondria from preexisting mitochondria, the cell needs to import mitochondrial proteins from the cytosol into the mitochondria with the aid of translocators in the mitochondrial membranes. The translocase of the outer membrane (TOM) complex, an outer membrane translocator, functions as an entry gate for most mitochondrial proteins. Although high-resolution structures of the receptor subunits of the TOM complex were deposited in the early 2000s, those of entire TOM complexes became available only in 2019. The structural details of these TOM complexes, consisting of the dimer of the β-barrel import channel Tom40 and four α-helical membrane proteins, revealed the presence of several distinct paths and exits for the translocation of over 1,000 different mitochondrial precursor proteins. High-resolution structures of TOM complexes now open up a new era of studies on the structures, functions, and dynamics of the mitochondrial import system. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Yuhei Araiso
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan; .,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
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