51
|
Needs HI, Protasoni M, Henley JM, Prudent J, Collinson I, Pereira GC. Interplay between Mitochondrial Protein Import and Respiratory Complexes Assembly in Neuronal Health and Degeneration. Life (Basel) 2021; 11:432. [PMID: 34064758 PMCID: PMC8151517 DOI: 10.3390/life11050432] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/27/2021] [Accepted: 05/02/2021] [Indexed: 12/14/2022] Open
Abstract
The fact that >99% of mitochondrial proteins are encoded by the nuclear genome and synthesised in the cytosol renders the process of mitochondrial protein import fundamental for normal organelle physiology. In addition to this, the nuclear genome comprises most of the proteins required for respiratory complex assembly and function. This means that without fully functional protein import, mitochondrial respiration will be defective, and the major cellular ATP source depleted. When mitochondrial protein import is impaired, a number of stress response pathways are activated in order to overcome the dysfunction and restore mitochondrial and cellular proteostasis. However, prolonged impaired mitochondrial protein import and subsequent defective respiratory chain function contributes to a number of diseases including primary mitochondrial diseases and neurodegeneration. This review focuses on how the processes of mitochondrial protein translocation and respiratory complex assembly and function are interlinked, how they are regulated, and their importance in health and disease.
Collapse
Affiliation(s)
- Hope I. Needs
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (H.I.N.); (J.M.H.)
| | - Margherita Protasoni
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; (M.P.); (J.P.)
| | - Jeremy M. Henley
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (H.I.N.); (J.M.H.)
- Centre for Neuroscience and Regenerative Medicine, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Julien Prudent
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; (M.P.); (J.P.)
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (H.I.N.); (J.M.H.)
| | - Gonçalo C. Pereira
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; (M.P.); (J.P.)
| |
Collapse
|
52
|
Guan Z, Yan L, Wang Q, Qi L, Hong S, Gong Z, Yan C, Yin P. Structural insights into assembly of human mitochondrial translocase TOM complex. Cell Discov 2021; 7:22. [PMID: 33846286 PMCID: PMC8041818 DOI: 10.1038/s41421-021-00252-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/16/2021] [Indexed: 11/10/2022] Open
Affiliation(s)
- Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Ling Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qiang Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Liangbo Qi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Sixing Hong
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhou Gong
- Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| |
Collapse
|
53
|
Amphipathic environments for determining the structure of membrane proteins by single-particle electron cryo-microscopy. Q Rev Biophys 2021; 54:e6. [PMID: 33785082 DOI: 10.1017/s0033583521000044] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, the structural biology of membrane proteins (MPs) has taken a new turn thanks to epoch-making technical progress in single-particle electron cryo-microscopy (cryo-EM) as well as to improvements in sample preparation. The present analysis provides an overview of the extent and modes of usage of the various types of surfactants for cryo-EM studies. Digitonin, dodecylmaltoside, protein-based nanodiscs, lauryl maltoside-neopentyl glycol, glyco-diosgenin, and amphipols (APols) are the most popular surfactants at the vitrification step. Surfactant exchange is frequently used between MP purification and grid preparation, requiring extensive optimization each time the study of a new MP is undertaken. The variety of both the surfactants and experimental approaches used over the past few years bears witness to the need to continue developing innovative surfactants and optimizing conditions for sample preparation. The possibilities offered by novel APols for EM applications are discussed.
Collapse
|
54
|
Abstract
Significance: The molecular processes that determine Huntington's disease (HD) pathogenesis are not yet fully understood, and until now no effective neuroprotective therapeutic strategies have been developed. Mitochondria are one of most important organelles required for neuronal homeostasis, by providing metabolic pathways relevant for energy production, regulating calcium homeostasis, or controlling free radical generation and cell death. Because augmented reactive oxygen species (ROS) accompanied by mitochondrial dysfunction are relevant early HD mechanisms, targeting these cellular mechanisms may constitute relevant therapeutic approaches. Recent Advances: Previous findings point toward a close relationship between mitochondrial dysfunction and redox changes in HD. Mutant huntingtin (mHTT) can directly interact with mitochondrial proteins, as translocase of the inner membrane 23 (TIM23), disrupting mitochondrial proteostasis and favoring ROS production and HD progression. Furthermore, abnormal brain and muscle redox signaling contributes to altered proteostasis and motor impairment in HD, which can be improved with the mitochondria-targeted antioxidant mitoquinone or resveratrol, an SIRT1 activator that ameliorates mitochondrial biogenesis and function. Critical Issues: Various antioxidants and metabolic enhancers have been studied in HD; however, the real outcome of these molecules is still debatable. New compounds have proven to ameliorate mitochondrial and redox-based signaling pathways in early stages of HD, potentially precluding selective neurodegeneration. Future Directions: Unraveling the molecular etiology of deregulated mitochondrial function and dynamics, and oxidative stress opens new prospects for HD therapeutics. In this review, we explore the role of redox unbalance and mitochondrial dysfunction in HD progression, and further describe advances on clinical trials in HD based on mitochondrial and redox-based therapeutic strategies.
Collapse
Affiliation(s)
- Lígia Fão
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,CIBB-Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Ana Cristina Rego
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,CIBB-Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| |
Collapse
|
55
|
Diederichs KA, Buchanan SK, Botos I. Building Better Barrels - β-barrel Biogenesis and Insertion in Bacteria and Mitochondria. J Mol Biol 2021; 433:166894. [PMID: 33639212 PMCID: PMC8292188 DOI: 10.1016/j.jmb.2021.166894] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 01/20/2023]
Abstract
β-barrel proteins are folded and inserted into outer membranes by multi-subunit protein complexes that are conserved across different types of outer membranes. In Gram-negative bacteria this complex is the barrel-assembly machinery (BAM), in mitochondria it is the sorting and assembly machinery (SAM) complex, and in chloroplasts it is the outer envelope protein Oep80. Mitochondrial β-barrel precursor proteins are translocated from the cytoplasm to the intermembrane space by the translocase of the outer membrane (TOM) complex, and stabilized by molecular chaperones before interaction with the assembly machinery. Outer membrane bacterial BamA interacts with four periplasmic accessory proteins, whereas mitochondrial Sam50 interacts with two cytoplasmic accessory proteins. Despite these major architectural differences between BAM and SAM complexes, their core proteins, BamA and Sam50, seem to function the same way. Based on the new SAM complex structures, we propose that the mitochondrial β-barrel folding mechanism follows the budding model with barrel-switching aiding in the release of new barrels. We also built a new molecular model for Tom22 interacting with Sam37 to identify regions that could mediate TOM-SAM supercomplex formation.
Collapse
Affiliation(s)
- Kathryn A Diederichs
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Istvan Botos
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| |
Collapse
|
56
|
Zhang Z, Huang B, Zhang XC, Lin J. Cysteine-based crosslinking approach for characterization of oligomeric pore-forming proteins in the mitochondrial membranes. Methods Enzymol 2021; 649:371-396. [PMID: 33712193 DOI: 10.1016/bs.mie.2021.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Mitochondria are important not only to healthy but also dying cells. In particular, apoptotic cell death initiates when the mitochondrial outer membrane is permeabilized by Bax, a protein of the Bcl-2 family. Bax shares a structural fold with some α-helical bacterial pore-forming toxins before these proteins actively engage membranes. Despite decades of intensive research, the structures of the pores formed by these proteins are mostly unknown, mainly because the pores are assembled by different numbers of the proteins whose conformation and interaction are highly dynamic. Site-specific crosslinking of the pore-forming proteins in cellular membranes where the pores are assembled is a powerful approach to assess the biological pore structure, dynamics and function. In this chapter, we describe a cysteine-based site-specific crosslinking protocol for the Bax protein in the mitochondrial membrane. We discuss the expected results and the resulting structural-functional models for the pore-forming Bax oligomer, in comparison with other crosslinking approaches that have been used to study other mitochondrial protein complexes. At the end, we highlight the advantages of the crosslinking approaches as well as the limitations and alternative approaches.
Collapse
Affiliation(s)
- Zhi Zhang
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Bo Huang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xuejun C Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jialing Lin
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.
| |
Collapse
|
57
|
Palmer CS, Anderson AJ, Stojanovski D. Mitochondrial protein import dysfunction: mitochondrial disease, neurodegenerative disease and cancer. FEBS Lett 2021; 595:1107-1131. [PMID: 33314127 DOI: 10.1002/1873-3468.14022] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/12/2020] [Accepted: 10/17/2020] [Indexed: 12/13/2022]
Abstract
The majority of proteins localised to mitochondria are encoded by the nuclear genome, with approximately 1500 proteins imported into mammalian mitochondria. Dysfunction in this fundamental cellular process is linked to a variety of pathologies including neuropathies, cardiovascular disorders, myopathies, neurodegenerative diseases and cancer, demonstrating the importance of mitochondrial protein import machinery for cellular function. Correct import of proteins into mitochondria requires the co-ordinated activity of multimeric protein translocation and sorting machineries located in both the outer and inner mitochondrial membranes, directing the imported proteins to the destined mitochondrial compartment. This dynamic process maintains cellular homeostasis, and its dysregulation significantly affects cellular signalling pathways and metabolism. This review summarises current knowledge of the mammalian mitochondrial import machinery and the pathological consequences of mutation of its components. In addition, we will discuss the role of mitochondrial import in cancer, and our current understanding of the role of mitochondrial import in neurodegenerative diseases including Alzheimer's disease, Huntington's disease and Parkinson's disease.
Collapse
Affiliation(s)
- Catherine S Palmer
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Alexander J Anderson
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| |
Collapse
|
58
|
Kotov V, Mlynek G, Vesper O, Pletzer M, Wald J, Teixeira‐Duarte CM, Celia H, Garcia‐Alai M, Nussberger S, Buchanan SK, Morais‐Cabral JH, Loew C, Djinovic‐Carugo K, Marlovits TC. In-depth interrogation of protein thermal unfolding data with MoltenProt. Protein Sci 2021; 30:201-217. [PMID: 33140490 PMCID: PMC7737771 DOI: 10.1002/pro.3986] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 01/06/2023]
Abstract
Protein stability is a key factor in successful structural and biochemical research. However, the approaches for systematic comparison of protein stability are limited by sample consumption or compatibility with sample buffer components. Here we describe how miniaturized measurement of intrinsic tryptophan fluorescence (NanoDSF assay) in combination with a simplified description of protein unfolding can be used to interrogate the stability of a protein sample. We demonstrate that improved protein stability measures, such as apparent Gibbs free energy of unfolding, rather than melting temperature Tm , should be used to rank the results of thermostability screens. The assay is compatible with protein samples of any composition, including protein complexes and membrane proteins. Our data analysis software, MoltenProt, provides an easy and robust way to perform characterization of multiple samples. Potential applications of MoltenProt and NanoDSF include buffer and construct optimization for X-ray crystallography and cryo-electron microscopy, screening for small-molecule binding partners and comparison of effects of point mutations.
Collapse
Affiliation(s)
- Vadim Kotov
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- Institute for Structural and Systems BiologyUniversity Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- German Electron Synchrotron Centre (DESY)HamburgGermany
| | - Georg Mlynek
- Department of Structural and Computational Biology, Max Perutz Labs ViennaUniversity of ViennaViennaAustria
| | - Oliver Vesper
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- Institute for Structural and Systems BiologyUniversity Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- German Electron Synchrotron Centre (DESY)HamburgGermany
| | - Marina Pletzer
- Department of Structural and Computational Biology, Max Perutz Labs ViennaUniversity of ViennaViennaAustria
| | - Jiri Wald
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- Institute for Structural and Systems BiologyUniversity Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- German Electron Synchrotron Centre (DESY)HamburgGermany
| | - Celso M. Teixeira‐Duarte
- Instituto de Investigação e Inovação em Saúde (i3S) and Instituto de Biologia Molecular e Celular (IBMC)Universidade do PortoPortoPortugal
| | - Herve Celia
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Maria Garcia‐Alai
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- European Molecular Biology Laboratory (EMBL)Hamburg UnitHamburgGermany
| | - Stephan Nussberger
- Department of Biophysics, Institute of Biomaterials and Biomolecular SystemsUniversity of StuttgartStuttgartGermany
| | - Susan K. Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - João H. Morais‐Cabral
- Instituto de Investigação e Inovação em Saúde (i3S) and Instituto de Biologia Molecular e Celular (IBMC)Universidade do PortoPortoPortugal
| | - Christian Loew
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- European Molecular Biology Laboratory (EMBL)Hamburg UnitHamburgGermany
| | - Kristina Djinovic‐Carugo
- Department of Structural and Computational Biology, Max Perutz Labs ViennaUniversity of ViennaViennaAustria
- Department of Biochemistry, Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaLjubljanaSlovenia
| | - Thomas C. Marlovits
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- Institute for Structural and Systems BiologyUniversity Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- German Electron Synchrotron Centre (DESY)HamburgGermany
| |
Collapse
|
59
|
Araiso Y, Imai K, Endo T. Structural snapshot of the mitochondrial protein import gate. FEBS J 2020; 288:5300-5310. [PMID: 33305524 DOI: 10.1111/febs.15661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/28/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022]
Abstract
The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate for most mitochondrial proteins. The TOM complex is a multisubunit membrane protein complex consisting of a β-barrel protein Tom40 and six α-helical transmembrane (TM) proteins, receptor subunits Tom20, Tom22, and Tom70, and regulatory subunits Tom5, Tom6, and Tom7. Although nearly 30 years have passed since the main components of the TOM complex were identified and characterized, the structural details of the TOM complex remained poorly understood until recently. Thanks to the rapid development of the cryoelectron microscopy (EM) technology, high-resolution structures of the yeast TOM complex have become available. The identified structures showed a symmetric dimer containing five different subunits including Tom22. Biochemical and mutational analyses based on the TOM complex structure revealed the presence of different translocation paths within the Tom40 import channel for different classes of translocating precursor proteins. Previous studies including our cross-linking analyses indicated that the TOM complex in intact mitochondria is present as a mixture of the trimeric complex containing Tom22. Furthermore, the dimeric complex lacking Tom22, and the trimer and dimer may handle different sets of mitochondrial precursor proteins for translocation across the outer membrane. In this Structural Snapshot, we will discuss possible rearrangement of the subunit interactions upon dynamic conversion of the TOM complex between the different subunit assembly states, the Tom22-containing core dimer and trimer.
Collapse
Affiliation(s)
- Yuhei Araiso
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 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, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| |
Collapse
|
60
|
Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics. Int J Mol Sci 2020; 22:ijms22010050. [PMID: 33374526 PMCID: PMC7793082 DOI: 10.3390/ijms22010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
Collapse
|
61
|
Tsuboi T, Leff J, Zid BM. Post-transcriptional control of mitochondrial protein composition in changing environmental conditions. Biochem Soc Trans 2020; 48:2565-2578. [PMID: 33245320 PMCID: PMC8108647 DOI: 10.1042/bst20200250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/26/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023]
Abstract
In fluctuating environmental conditions, organisms must modulate their bioenergetic production in order to maintain cellular homeostasis for optimal fitness. Mitochondria are hubs for metabolite and energy generation. Mitochondria are also highly dynamic in their function: modulating their composition, size, density, and the network-like architecture in relation to the metabolic demands of the cell. Here, we review the recent research on the post-transcriptional regulation of mitochondrial composition focusing on mRNA localization, mRNA translation, protein import, and the role that dynamic mitochondrial structure may have on these gene expression processes. As mitochondrial structure and function has been shown to be very important for age-related processes, including cancer, metabolic disorders, and neurodegeneration, understanding how mitochondrial composition can be affected in fluctuating conditions can lead to new therapeutic directions to pursue.
Collapse
Affiliation(s)
- Tatsuhisa Tsuboi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92023-0358, USA
| | - Jordan Leff
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92023-0358, USA
| | - Brian M. Zid
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92023-0358, USA
| |
Collapse
|
62
|
Krämer L, Groh C, Herrmann JM. The proteasome: friend and foe of mitochondrial biogenesis. FEBS Lett 2020; 595:1223-1238. [PMID: 33249599 DOI: 10.1002/1873-3468.14010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/26/2020] [Accepted: 11/01/2020] [Indexed: 01/06/2023]
Abstract
Most mitochondrial proteins are synthesized in the cytosol and subsequently translocated as unfolded polypeptides into mitochondria. Cytosolic chaperones maintain precursor proteins in an import-competent state. This post-translational import reaction is under surveillance of the cytosolic ubiquitin-proteasome system, which carries out several distinguishable activities. On the one hand, the proteasome degrades nonproductive protein precursors from the cytosol and nucleus, import intermediates that are stuck in mitochondrial translocases, and misfolded or damaged proteins from the outer membrane and the intermembrane space. These surveillance activities of the proteasome are essential for mitochondrial functionality, as well as cellular fitness and survival. On the other hand, the proteasome competes with mitochondria for nonimported cytosolic precursor proteins, which can compromise mitochondrial biogenesis. In order to balance the positive and negative effects of the cytosolic protein quality control system on mitochondria, mitochondrial import efficiency directly regulates the capacity of the proteasome via transcription factor Rpn4 in yeast and nuclear respiratory factor (Nrf) 1 and 2 in animal cells. In this review, we provide a thorough overview of how the proteasome regulates mitochondrial biogenesis.
Collapse
Affiliation(s)
- Lena Krämer
- Cell Biology, University of Kaiserslautern, Germany
| | - Carina Groh
- Cell Biology, University of Kaiserslautern, Germany
| | | |
Collapse
|
63
|
Kreimendahl S, Schwichtenberg J, Günnewig K, Brandherm L, Rassow J. The selectivity filter of the mitochondrial protein import machinery. BMC Biol 2020; 18:156. [PMID: 33121519 PMCID: PMC7596997 DOI: 10.1186/s12915-020-00888-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 10/02/2020] [Indexed: 12/22/2022] Open
Abstract
Background The uptake of newly synthesized nuclear-encoded mitochondrial proteins from the cytosol is mediated by a complex of mitochondrial outer membrane proteins comprising a central pore-forming component and associated receptor proteins. Distinct fractions of proteins initially bind to the receptor proteins and are subsequently transferred to the pore-forming component for import. The aim of this study was the identification of the decisive elements of this machinery that determine the specific selection of the proteins that should be imported. Results We identified the essential internal targeting signal of the members of the mitochondrial metabolite carrier proteins, the largest protein family of the mitochondria, and we investigated the specific recognition of this signal by the protein import machinery at the mitochondrial outer surface. We found that the outer membrane import receptors facilitated the uptake of these proteins, and we identified the corresponding binding site, marked by cysteine C141 in the receptor protein Tom70. However, in tests both in vivo and in vitro, the import receptors were neither necessary nor sufficient for specific recognition of the targeting signals. Although these signals are unrelated to the amino-terminal presequences that mediate the targeting of other mitochondrial preproteins, they were found to resemble presequences in their strict dependence on a content of positively charged residues as a prerequisite of interactions with the import pore. Conclusions The general import pore of the mitochondrial outer membrane appears to represent not only the central channel of protein translocation but also to form the decisive general selectivity filter in the uptake of the newly synthesized mitochondrial proteins.
Collapse
Affiliation(s)
- Sebastian Kreimendahl
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Jan Schwichtenberg
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Kathrin Günnewig
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Lukas Brandherm
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Joachim Rassow
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany.
| |
Collapse
|
64
|
Sekine S. PINK1 import regulation at a crossroad of mitochondrial fate: the molecular mechanisms of PINK1 import. J Biochem 2020; 167:217-224. [PMID: 31504668 DOI: 10.1093/jb/mvz069] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/17/2019] [Indexed: 12/17/2022] Open
Abstract
PTEN-induced kinase 1 (PINK1) is a mitochondrial kinase whose activity is tightly regulated by the mitochondrial health status. In response to mitochondrial damage, activated PINK1 can promote mitophagy, an autophagic elimination of damaged mitochondria, by cooperating with Parkin ubiquitin ligase. Loss-of-function of PINK1/Parkin-mediated mitophagy results in the accumulation of dysfunctional mitochondria, which could be one aetiology of Parkinson's disease (PD). Within step-by-step signalling cascades of PINK1/Parkin-mediated mitophagy, mitochondrial damage-dependent PINK1 kinase activation is a critical step to trigger the mitophagy signal. Recent investigation of this process reveals that this stress-dependent PINK1 kinase activation is achieved by its regulated import into different mitochondrial compartments. Thus, PINK1 import regulation stands at an important crossroad to determine the mitochondrial fate-'keep' or 'remove'? In this review, we will summarize how the PINK1 import is regulated in a mitochondrial health status-dependent manner and how this process could be pharmacologically modulated to activate the PINK1/Parkin pathway.
Collapse
Affiliation(s)
- Shiori Sekine
- Aging Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| |
Collapse
|
65
|
Zöller E, Laborenz J, Krämer L, Boos F, Räschle M, Alexander RT, Herrmann JM. The intermembrane space protein Mix23 is a novel stress-induced mitochondrial import factor. J Biol Chem 2020; 295:14686-14697. [PMID: 32826315 PMCID: PMC7586232 DOI: 10.1074/jbc.ra120.014247] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/19/2020] [Indexed: 12/20/2022] Open
Abstract
The biogenesis of mitochondria requires the import of hundreds of precursor proteins. These proteins are transported post-translationally with the help of chaperones, meaning that the overproduction of mitochondrial proteins or the limited availability of chaperones can lead to the accumulation of cytosolic precursor proteins. This imposes a severe challenge to cytosolic proteostasis and triggers a specific transcription program called the mitoprotein-induced stress response, which activates the proteasome system. This coincides with the repression of mitochondrial proteins, including many proteins of the intermembrane space. In contrast, herein we report that the so-far-uncharacterized intermembrane space protein Mix23 is considerably up-regulated when mitochondrial import is perturbed. Mix23 is evolutionarily conserved and a homolog of the human protein CCDC58. We found that, like the subunits of the proteasome, Mix23 is under control of the transcription factor Rpn4. It is imported into mitochondria by the mitochondrial disulfide relay. Mix23 is critical for the efficient import of proteins into the mitochondrial matrix, particularly if the function of the translocase of the inner membrane 23 is compromised such as in temperature-sensitive mutants of Tim17. Our observations identify Mix23 as a novel regulator or stabilizer of the mitochondrial protein import machinery that is specifically up-regulated upon mitoprotein-induced stress conditions.
Collapse
Affiliation(s)
- Eva Zöller
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Janina Laborenz
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Lena Krämer
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Felix Boos
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Markus Räschle
- Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - R Todd Alexander
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Johannes M Herrmann
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany.
| |
Collapse
|
66
|
Abstract
Mitochondria contain about 1,000-1,500 proteins that fulfil multiple functions. Mitochondrial proteins originate from two genomes: mitochondrial and nuclear. Hence, proper mitochondrial function requires synchronization of gene expression in the nucleus and in mitochondria and necessitates efficient import of mitochondrial proteins into the organelle from the cytosol. Furthermore, the mitochondrial proteome displays high plasticity to allow the adaptation of mitochondrial function to cellular requirements. Maintenance of this complex and adaptable mitochondrial proteome is challenging, but is of crucial importance to cell function. Defects in mitochondrial proteostasis lead to proteotoxic insults and eventually cell death. Different quality control systems monitor the mitochondrial proteome. The cytosolic ubiquitin-proteasome system controls protein transport across the mitochondrial outer membrane and removes damaged or mislocalized proteins. Concomitantly, a number of mitochondrial chaperones and proteases govern protein folding and degrade damaged proteins inside mitochondria. The quality control factors also regulate processing and turnover of native proteins to control protein import, mitochondrial metabolism, signalling cascades, mitochondrial dynamics and lipid biogenesis, further ensuring proper function of mitochondria. Thus, mitochondrial protein quality control mechanisms are of pivotal importance to integrate mitochondria into the cellular environment.
Collapse
|
67
|
Wang N, Zhu P, Huang R, Wang C, Sun L, Lan B, He Y, Zhao H, Gao Y. PINK1: The guard of mitochondria. Life Sci 2020; 259:118247. [PMID: 32805222 DOI: 10.1016/j.lfs.2020.118247] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/26/2020] [Accepted: 08/06/2020] [Indexed: 12/22/2022]
Abstract
PTEN-induced putative kinase 1 (PINK1) performs many important functions in cells and has been highlighted for its role in early-onset Parkinson's disease. In recent years, an increasing number of studies have revealed the involvement of PINK1 in regulation of a variety of cell physiological and pathophysiological processes, of which regulation of mitochondrial function remains the most prominent. As the "energy factory" of cells, mitochondria provide energy support for various cellular activities. Changes in mitochondrial function often have a fundamental and global impact on cellular activities. Moreover, mitochondrial dysfunction has been implicated in many diseases, especially those related to aging. Thus, a comprehensive study of PINK1 will help us better understand the various cell physiological and pathophysiological processes in which PINK1 is involved, including a variety of mitochondria-related diseases such as Parkinson's disease. This article will review the structural characteristics and expression regulation of PINK1, as well as its unique role in mitochondrial quality control (MQC) systems.
Collapse
Affiliation(s)
- Nan Wang
- China-Japan Union Hospital, Jilin University, China
| | - Peining Zhu
- China-Japan Union Hospital, Jilin University, China
| | | | - Chong Wang
- China-Japan Union Hospital, Jilin University, China
| | - Liankun Sun
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, China
| | - Beiwu Lan
- China-Japan Union Hospital, Jilin University, China
| | - Yichun He
- China-Japan Union Hospital, Jilin University, China
| | | | - Yufei Gao
- China-Japan Union Hospital, Jilin University, China.
| |
Collapse
|
68
|
Garin S, Levi O, Cohen B, Golani-Armon A, Arava YS. Localization and RNA Binding of Mitochondrial Aminoacyl tRNA Synthetases. Genes (Basel) 2020; 11:genes11101185. [PMID: 33053729 PMCID: PMC7600831 DOI: 10.3390/genes11101185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondria contain a complete translation machinery that is used to translate its internally transcribed mRNAs. This machinery uses a distinct set of tRNAs that are charged with cognate amino acids inside the organelle. Interestingly, charging is executed by aminoacyl tRNA synthetases (aaRS) that are encoded by the nuclear genome, translated in the cytosol, and need to be imported into the mitochondria. Here, we review import mechanisms of these enzymes with emphasis on those that are localized to both mitochondria and cytosol. Furthermore, we describe RNA recognition features of these enzymes and their interaction with tRNA and non-tRNA molecules. The dual localization of mitochondria-destined aaRSs and their association with various RNA types impose diverse impacts on cellular physiology. Yet, the breadth and significance of these functions are not fully resolved. We highlight here possibilities for future explorations.
Collapse
|
69
|
Gupta A, Becker T. Mechanisms and pathways of mitochondrial outer membrane protein biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148323. [PMID: 33035511 DOI: 10.1016/j.bbabio.2020.148323] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 11/29/2022]
Abstract
Outer membrane proteins integrate mitochondria into the cellular environment. They warrant exchange of small molecules like metabolites and ions, transport proteins into mitochondria, form contact sites to other cellular organelles for lipid exchange, constitute a signaling platform for apoptosis and inflammation and mediate organelle fusion and fission. The outer membrane contains two types of integral membrane proteins. Proteins with a transmembrane β-barrel structure and proteins with a single or multiple α-helical membrane spans. All outer membrane proteins are produced on cytosolic ribosomes and imported into the target organelle. Precursors of β-barrel and α-helical proteins are transported into the outer membrane via distinct import routes. The translocase of the outer membrane (TOM complex) transports β-barrel precursors across the outer membrane and the sorting and assembly machinery (SAM complex) inserts them into the target membrane. The mitochondrial import (MIM) complex constitutes the major integration site for α-helical embedded proteins. The import of some MIM-substrates involves TOM receptors, while others are imported in a TOM-independent manner. Remarkably, TOM, SAM and MIM complexes dynamically interact to import a large set of different proteins and to coordinate their assembly into protein complexes. Thus, protein import into the mitochondrial outer membrane involves a dynamic platform of protein translocases.
Collapse
Affiliation(s)
- Arushi Gupta
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, Medizinische Fakultät, Universität Bonn, Nussallee 11, 53115 Bonn, Germany.
| |
Collapse
|
70
|
Wang L, Walter P. Msp1/ATAD1 in Protein Quality Control and Regulation of Synaptic Activities. Annu Rev Cell Dev Biol 2020; 36:141-164. [DOI: 10.1146/annurev-cellbio-031220-015840] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mitochondrial function depends on the efficient import of proteins synthesized in the cytosol. When cells experience stress, the efficiency and faithfulness of the mitochondrial protein import machinery are compromised, leading to homeostatic imbalances and damage to the organelle. Yeast Msp1 (mitochondrial sorting of proteins 1) and mammalian ATAD1 (ATPase family AAA domain–containing 1) are orthologous AAA proteins that, fueled by ATP hydrolysis, recognize and extract mislocalized membrane proteins from the outer mitochondrial membrane. Msp1 also extracts proteins that have become stuck in the import channel. The extracted proteins are targeted for proteasome-dependent degradation or, in the case of mistargeted tail-anchored proteins, are given another chance to be routed correctly. In addition, ATAD1 is implicated in the regulation of synaptic plasticity, mediating the release of neurotransmitter receptors from postsynaptic scaffolds to allow their trafficking. Here we discuss how structural and functional specialization imparts the unique properties that allow Msp1/ATAD1 ATPases to fulfill these diverse functions and also highlight outstanding questions in the field.
Collapse
Affiliation(s)
- Lan Wang
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143, USA;,
| | - Peter Walter
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143, USA;,
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94122, USA
| |
Collapse
|
71
|
Kreimendahl S, Rassow J. The Mitochondrial Outer Membrane Protein Tom70-Mediator in Protein Traffic, Membrane Contact Sites and Innate Immunity. Int J Mol Sci 2020; 21:E7262. [PMID: 33019591 PMCID: PMC7583919 DOI: 10.3390/ijms21197262] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/08/2023] Open
Abstract
Tom70 is a versatile adaptor protein of 70 kDa anchored in the outer membrane of mitochondria in metazoa, fungi and amoeba. The tertiary structure was resolved for the Tom70 of yeast, showing 26 α-helices, most of them participating in the formation of 11 tetratricopeptide repeat (TPR) motifs. Tom70 serves as a docking site for cytosolic chaperone proteins and co-chaperones and is thereby involved in the uptake of newly synthesized chaperone-bound proteins in mitochondrial biogenesis. In yeast, Tom70 additionally mediates ER-mitochondria contacts via binding to sterol transporter Lam6/Ltc1. In mammalian cells, TOM70 promotes endoplasmic reticulum (ER) to mitochondria Ca2+ transfer by association with the inositol-1,4,5-triphosphate receptor type 3 (IP3R3). TOM70 is specifically targeted by the Bcl-2-related protein MCL-1 that acts as an anti-apoptotic protein in macrophages infected by intracellular pathogens, but also in many cancer cells. By participating in the recruitment of PINK1 and the E3 ubiquitin ligase Parkin, TOM70 can be implicated in the development of Parkinson's disease. TOM70 acts as receptor of the mitochondrial antiviral-signaling protein (MAVS) and thereby participates in the corresponding system of innate immunity against viral infections. The protein encoded by Orf9b in the genome of SARS-CoV-2 binds to TOM70, probably compromising the synthesis of type I interferons.
Collapse
Affiliation(s)
| | - Joachim Rassow
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44801 Bochum, Germany;
| |
Collapse
|
72
|
Wang W, Chen X, Zhang L, Yi J, Ma Q, Yin J, Zhuo W, Gu J, Yang M. Atomic structure of human TOM core complex. Cell Discov 2020; 6:67. [PMID: 33083003 PMCID: PMC7522991 DOI: 10.1038/s41421-020-00198-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/20/2020] [Indexed: 12/22/2022] Open
Abstract
The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate for mitochondrial precursor proteins synthesized on cytosolic ribosomes. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the dimeric human TOM core complex (TOM-CC). Two Tom40 β-barrel proteins, connected by two Tom22 receptor subunits and one phospholipid, form the protein-conducting channels. The small Tom proteins Tom5, Tom6, and Tom7 surround the channel and have notable configurations. The distinct electrostatic features of the complex, including the pronounced negative interior and the positive regions at the periphery and center of the dimer on the intermembrane space (IMS) side, provide insight into the preprotein translocation mechanism. Further, two dimeric TOM complexes may associate to form tetramer in the shape of a parallelogram, offering a potential explanation into the unusual structural features of Tom subunits and a new perspective of viewing the import of mitochondrial proteins.
Collapse
Affiliation(s)
- Wenhe Wang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Xudong Chen
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Laixing Zhang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jingbo Yi
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Qingxi Ma
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jian Yin
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Wei Zhuo
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China
| |
Collapse
|
73
|
Bonnet C, Guillet P, Mahler F, Igonet S, Keller S, Jawhari A, Durand G. Detergent‐Like Polymerizable Monomers: Synthesis, Physicochemical, and Biochemical Characterization. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Christophe Bonnet
- Chimie Bioorganique et Systèmes amphiphiles Institut des Biomolécules Max Mousseron (UMR 5247 UM‐CNRS‐ENSCM) & Avignon University 301 rue Baruch de Spinoza – 84916 AVIGNON cedex 9 France
- CHEM2STAB 301 rue Baruch de Spinoza – 84916 AVIGNON cedex 9 France
| | - Pierre Guillet
- Chimie Bioorganique et Systèmes amphiphiles Institut des Biomolécules Max Mousseron (UMR 5247 UM‐CNRS‐ENSCM) & Avignon University 301 rue Baruch de Spinoza – 84916 AVIGNON cedex 9 France
- CHEM2STAB 301 rue Baruch de Spinoza – 84916 AVIGNON cedex 9 France
| | - Florian Mahler
- Molecular Biophysics Technische Universität Kaiserslautern (TUK) Erwin‐Schrödinger‐Str. 13 67663 Kaiserslautern Germany
| | - Sébastien Igonet
- CHEM2STAB 301 rue Baruch de Spinoza – 84916 AVIGNON cedex 9 France
- CALIXAR 60A Avenue Rockefeller – 69008 Lyon France
| | - Sandro Keller
- Molecular Biophysics Technische Universität Kaiserslautern (TUK) Erwin‐Schrödinger‐Str. 13 67663 Kaiserslautern Germany
| | - Anass Jawhari
- CHEM2STAB 301 rue Baruch de Spinoza – 84916 AVIGNON cedex 9 France
- CALIXAR 60A Avenue Rockefeller – 69008 Lyon France
| | - Grégory Durand
- Chimie Bioorganique et Systèmes amphiphiles Institut des Biomolécules Max Mousseron (UMR 5247 UM‐CNRS‐ENSCM) & Avignon University 301 rue Baruch de Spinoza – 84916 AVIGNON cedex 9 France
- CHEM2STAB 301 rue Baruch de Spinoza – 84916 AVIGNON cedex 9 France
| |
Collapse
|
74
|
Grevel A, Pfanner N, Becker T. Coupling of import and assembly pathways in mitochondrial protein biogenesis. Biol Chem 2020; 401:117-129. [PMID: 31513529 DOI: 10.1515/hsz-2019-0310] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 08/13/2019] [Indexed: 12/14/2022]
Abstract
Biogenesis and function of mitochondria depend on the import of about 1000 precursor proteins that are produced on cytosolic ribosomes. The translocase of the outer membrane (TOM) forms the entry gate for most proteins. After passage through the TOM channel, dedicated preprotein translocases sort the precursor proteins into the mitochondrial subcompartments. Many proteins have to be assembled into oligomeric membrane-integrated complexes in order to perform their functions. In this review, we discuss a dual role of mitochondrial preprotein translocases in protein translocation and oligomeric assembly, focusing on the biogenesis of the TOM complex and the respiratory chain. The sorting and assembly machinery (SAM) of the outer mitochondrial membrane forms a dynamic platform for coupling transport and assembly of TOM subunits. The biogenesis of the cytochrome c oxidase of the inner membrane involves a molecular circuit to adjust translation of mitochondrial-encoded core subunits to the availability of nuclear-encoded partner proteins. Thus, mitochondrial protein translocases not only import precursor proteins but can also support their assembly into functional complexes.
Collapse
Affiliation(s)
- Alexander Grevel
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| |
Collapse
|
75
|
Srivastava SR, Mahalakshmi R. Evolutionary selection of a 19-stranded mitochondrial β-barrel scaffold bears structural and functional significance. J Biol Chem 2020; 295:14653-14665. [PMID: 32817169 PMCID: PMC7586230 DOI: 10.1074/jbc.ra120.014366] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/15/2020] [Indexed: 12/12/2022] Open
Abstract
Transmembrane β-barrels of eukaryotic outer mitochondrial membranes (OMMs) are major channels of communication between the cytosol and mitochondria and are indispensable for cellular homeostasis. A structurally intriguing exception to all known transmembrane β-barrels is the unique odd-stranded, i.e. 19-stranded, structures found solely in the OMM. The molecular origins of this 19-stranded structure and its associated functional significance are unclear. In humans, the most abundant OMM transporter is the voltage-dependent anion channel. Here, using the human voltage-dependent anion channel as our template scaffold, we designed and engineered odd- and even-stranded structures of smaller (V216, V217, V218) and larger (V220, V221) barrel diameters. Determination of the structure, dynamics, and energetics of these engineered structures in bilayer membranes reveals that the 19-stranded barrel surprisingly holds modest to low stability in a lipid-dependent manner. However, we demonstrate that this structurally metastable protein possesses superior voltage-gated channel regulation, efficient mitochondrial targeting, and in vivo cell survival, with lipid-modulated stability, all of which supersede the occurrence of a metastable 19-stranded scaffold. We propose that the unique structural adaptation of these transmembrane transporters exclusively in mitochondria bears strong evolutionary basis and is functionally significant for homeostasis.
Collapse
Affiliation(s)
- Shashank Ranjan Srivastava
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India.
| |
Collapse
|
76
|
Cytosolic Events in the Biogenesis of Mitochondrial Proteins. Trends Biochem Sci 2020; 45:650-667. [DOI: 10.1016/j.tibs.2020.04.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 03/18/2020] [Accepted: 04/02/2020] [Indexed: 01/08/2023]
|
77
|
Horten P, Colina-Tenorio L, Rampelt H. Biogenesis of Mitochondrial Metabolite Carriers. Biomolecules 2020; 10:E1008. [PMID: 32645990 PMCID: PMC7408425 DOI: 10.3390/biom10071008] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 12/28/2022] Open
Abstract
: Metabolite carriers of the mitochondrial inner membrane are crucial for cellular physiology since mitochondria contribute essential metabolic reactions and synthesize the majority of the cellular ATP. Like almost all mitochondrial proteins, carriers have to be imported into mitochondria from the cytosol. Carrier precursors utilize a specialized translocation pathway dedicated to the biogenesis of carriers and related proteins, the carrier translocase of the inner membrane (TIM22) pathway. After recognition and import through the mitochondrial outer membrane via the translocase of the outer membrane (TOM) complex, carrier precursors are ushered through the intermembrane space by hexameric TIM chaperones and ultimately integrated into the inner membrane by the TIM22 carrier translocase. Recent advances have shed light on the mechanisms of TOM translocase and TIM chaperone function, uncovered an unexpected versatility of the machineries, and revealed novel components and functional crosstalk of the human TIM22 translocase.
Collapse
Affiliation(s)
- Patrick Horten
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (P.H.); (L.C.-T.)
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Lilia Colina-Tenorio
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (P.H.); (L.C.-T.)
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Heike Rampelt
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (P.H.); (L.C.-T.)
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
78
|
Kornmann B. The endoplasmic reticulum-mitochondria encounter structure: coordinating lipid metabolism across membranes. Biol Chem 2020; 401:811-820. [DOI: 10.1515/hsz-2020-0102] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 02/05/2020] [Indexed: 02/06/2023]
Abstract
AbstractEndosymbiosis, the beginning of a collaboration between an archaeon and a bacterium and a founding step in the evolution of eukaryotes, owes its success to the establishment of communication routes between the host and the symbiont to allow the exchange of metabolites. As far as lipids are concerned, it is the host that has learnt the symbiont’s language, as eukaryote lipids appear to have been borrowed from the bacterial symbiont. Mitochondria exchange lipids with the rest of the cell at membrane contact sites. In fungi, the endoplasmic reticulum-mitochondria encounter structure (ERMES) is one of the best understood membrane tethering complexes. Its discovery has yielded crucial insight into the mechanisms of intracellular lipid trafficking. Despite a wealth of data, our understanding of ERMES formation and its exact role(s) remains incomplete. Here, I endeavour to summarise our knowledge on the ERMES complex and to identify lingering gaps.
Collapse
Affiliation(s)
- Benoît Kornmann
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
| |
Collapse
|
79
|
Schneider A. Evolution of mitochondrial protein import – lessons from trypanosomes. Biol Chem 2020; 401:663-676. [DOI: 10.1515/hsz-2019-0444] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/02/2020] [Indexed: 01/02/2023]
Abstract
AbstractThe evolution of mitochondrial protein import and the systems that mediate it marks the boundary between the endosymbiotic ancestor of mitochondria and a true organelle that is under the control of the nucleus. Protein import has been studied in great detail inSaccharomyces cerevisiae. More recently, it has also been extensively investigated in the parasitic protozoanTrypanosoma brucei, making it arguably the second best studied system. A comparative analysis of the protein import complexes of yeast and trypanosomes is provided. Together with data from other systems, this allows to reconstruct the ancestral features of import complexes that were present in the last eukaryotic common ancestor (LECA) and to identify which subunits were added later in evolution. How these data can be translated into plausible scenarios is discussed, providing insights into the evolution of (i) outer membrane protein import receptors, (ii) proteins involved in biogenesis of α-helically anchored outer membrane proteins, and (iii) of the intermembrane space import and assembly system. Finally, it is shown that the unusual presequence-associated import motor of trypanosomes suggests a scenario of how the two ancestral inner membrane protein translocases present in LECA evolved into the single bifunctional one found in extant trypanosomes.
Collapse
Affiliation(s)
- André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| |
Collapse
|
80
|
Avendaño-Monsalve MC, Ponce-Rojas JC, Funes S. From cytosol to mitochondria: the beginning of a protein journey. Biol Chem 2020; 401:645-661. [DOI: 10.1515/hsz-2020-0110] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/24/2020] [Indexed: 01/18/2023]
Abstract
AbstractMitochondrial protein import is one of the key processes during mitochondrial biogenesis that involves a series of events necessary for recognition and delivery of nucleus-encoded/cytosol-synthesized mitochondrial proteins into the organelle. The past research efforts have mainly unraveled how membrane translocases ensure the correct protein sorting within the different mitochondrial subcompartments. However, early steps of recognition and delivery remain relatively uncharacterized. In this review, we discuss our current understanding about the signals on mitochondrial proteins, as well as in the mRNAs encoding them, which with the help of cytosolic chaperones and membrane receptors support protein targeting to the organelle in order to avoid improper localization. In addition, we discuss recent findings that illustrate how mistargeting of mitochondrial proteins triggers stress responses, aiming to restore cellular homeostasis.
Collapse
Affiliation(s)
- Maria Clara Avendaño-Monsalve
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n Ciudad Universitaria Coyoacán, México, Cd.Mx. 04510, Mexico
| | - José Carlos Ponce-Rojas
- Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Soledad Funes
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n Ciudad Universitaria Coyoacán, México, Cd.Mx. 04510, Mexico
| |
Collapse
|
81
|
Rosen CB, Bayley H, Rodriguez-Larrea D. Free-energy landscapes of membrane co-translocational protein unfolding. Commun Biol 2020; 3:160. [PMID: 32246057 PMCID: PMC7125183 DOI: 10.1038/s42003-020-0841-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/20/2020] [Indexed: 11/09/2022] Open
Abstract
Protein post-translational translocation is found at the plasma membrane of prokaryotes and protein import into organellae. Translocon structures are becoming available, however the dynamics of proteins during membrane translocation remain largely obscure. Here we study, at the single-molecule level, the folding landscape of a model protein while forced to translocate a transmembrane pore. We use a DNA tag to drive the protein into the α-hemolysin pore under a quantifiable force produced by an applied electric potential. Using a voltage-quench approach we find that the protein fluctuates between the native state and an intermediate in the translocation process at estimated forces as low as 1.9 pN. The fluctuation kinetics provide the free energy landscape as a function of force. We show that our stable, ≈15 kBT, substrate can be unfolded and translocated with physiological membrane potentials and that selective divalent cation binding may have a profound effect on the translocation kinetics.
Collapse
Affiliation(s)
- Christian Bech Rosen
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Novozymes A/S, Biologiens Vej 2, 2800, Kgs. Lyngby, Denmark
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - David Rodriguez-Larrea
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology (UPV/EHU) Barrio Sarriena s/n, Leioa, 48940, Spain.
| |
Collapse
|
82
|
Pfanner N, Warscheid B, Wiedemann N. Mitochondrial proteins: from biogenesis to functional networks. Nat Rev Mol Cell Biol 2020; 20:267-284. [PMID: 30626975 DOI: 10.1038/s41580-018-0092-0] [Citation(s) in RCA: 555] [Impact Index Per Article: 138.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mitochondria are essential for the viability of eukaryotic cells as they perform crucial functions in bioenergetics, metabolism and signalling and have been associated with numerous diseases. Recent functional and proteomic studies have revealed the remarkable complexity of mitochondrial protein organization. Protein machineries with diverse functions such as protein translocation, respiration, metabolite transport, protein quality control and the control of membrane architecture interact with each other in dynamic networks. In this Review, we discuss the emerging role of the mitochondrial protein import machinery as a key organizer of these mitochondrial protein networks. The preprotein translocases that reside on the mitochondrial membranes not only function during organelle biogenesis to deliver newly synthesized proteins to their final mitochondrial destination but also cooperate with numerous other mitochondrial protein complexes that perform a wide range of functions. Moreover, these protein networks form membrane contact sites, for example, with the endoplasmic reticulum, that are key for integration of mitochondria with cellular function, and defects in protein import can lead to diseases.
Collapse
Affiliation(s)
- Nikolaus Pfanner
- 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.
| | - Bettina Warscheid
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,Institute of Biology II, Biochemistry - Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, 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.
| |
Collapse
|
83
|
Phu L, Rose CM, Tea JS, Wall CE, Verschueren E, Cheung TK, Kirkpatrick DS, Bingol B. Dynamic Regulation of Mitochondrial Import by the Ubiquitin System. Mol Cell 2020; 77:1107-1123.e10. [DOI: 10.1016/j.molcel.2020.02.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/30/2019] [Accepted: 02/12/2020] [Indexed: 01/05/2023]
|
84
|
Multifaceted roles of porin in mitochondrial protein and lipid transport. Biochem Soc Trans 2020; 47:1269-1277. [PMID: 31670371 DOI: 10.1042/bst20190153] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 11/17/2022]
Abstract
Mitochondria are essential eukaryotic organelles responsible for primary cellular energy production. Biogenesis, maintenance, and functions of mitochondria require correct assembly of resident proteins and lipids, which require their transport into and within mitochondria. Mitochondrial normal functions also require an exchange of small metabolites between the cytosol and mitochondria, which is primarily mediated by a metabolite channel of the outer membrane (OM) called porin or voltage-dependent anion channel. Here, we describe recently revealed novel roles of porin in the mitochondrial protein and lipid transport. First, porin regulates the formation of the mitochondrial protein import gate in the OM, the translocase of the outer membrane (TOM) complex, and its dynamic exchange between the major form of a trimer and the minor form of a dimer. The TOM complex dimer lacks a core subunit Tom22 and mediates the import of a subset of mitochondrial proteins while the TOM complex trimer facilitates the import of most other mitochondrial proteins. Second, porin interacts with both a translocating inner membrane (IM) protein like a carrier protein accumulated at the small TIM chaperones in the intermembrane space and the TIM22 complex, a downstream translocator in the IM for the carrier protein import. Porin thereby facilitates the efficient transfer of carrier proteins to the IM during their import. Third, porin facilitates the transfer of lipids between the OM and IM and promotes a back-up pathway for the cardiolipin synthesis in mitochondria. Thus, porin has roles more than the metabolite transport in the protein and lipid transport into and within mitochondria, which is likely conserved from yeast to human.
Collapse
|
85
|
|
86
|
Basch M, Wagner M, Rolland S, Carbonell A, Zeng R, Khosravi S, Schmidt A, Aftab W, Imhof A, Wagener J, Conradt B, Wagener N. Msp1 cooperates with the proteasome for extraction of arrested mitochondrial import intermediates. Mol Biol Cell 2020; 31:753-767. [PMID: 32049577 PMCID: PMC7185958 DOI: 10.1091/mbc.e19-06-0329] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The mitochondrial AAA ATPase Msp1 is well known for extraction of mislocalized tail-anchored ER proteins from the mitochondrial outer membrane. Here, we analyzed the extraction of precursors blocking the import pore in the outer membrane. We demonstrate strong genetic interactions of Msp1 and the proteasome with components of the TOM complex, the main translocase in the outer membrane. Msp1 and the proteasome both contribute to the removal of arrested precursor proteins that specifically accumulate in these mutants. The proteasome activity is essential for the removal as proteasome inhibitors block extraction. Furthermore, the proteasomal subunit Rpn10 copurified with Msp1. The human Msp1 homologue has been implicated in neurodegenerative diseases, and we show that the lack of the Caenorhabditis elegans Msp1 homologue triggers an import stress response in the worm, which indicates a conserved role in metazoa. In summary, our results suggest a role of Msp1 as an adaptor for the proteasome that drives the extraction of arrested and mislocalized proteins at the mitochondrial outer membrane.
Collapse
Affiliation(s)
- Marion Basch
- Zell- und Entwicklungsbiologie, Department Biologie II, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Mirjam Wagner
- Zell- und Entwicklungsbiologie, Department Biologie II, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Stéphane Rolland
- Zell- und Entwicklungsbiologie, Department Biologie II, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Andres Carbonell
- Zell- und Entwicklungsbiologie, Department Biologie II, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Rachel Zeng
- Max-Planck-Institut für Biochemie, Martinsried 82152, Germany
| | - Siavash Khosravi
- Zellbiologie-Anatomie III, Biomedizinisches Centrum, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Andreas Schmidt
- Protein Analysis Unit ZfP, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Wasim Aftab
- Protein Analysis Unit ZfP, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Axel Imhof
- Protein Analysis Unit ZfP, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Johannes Wagener
- Institut für Hygiene und Mikrobiologie, Julius-Maximilians-Universität Würzburg, Würzburg 97080, Germany
| | - Barbara Conradt
- Zell- und Entwicklungsbiologie, Department Biologie II, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Nikola Wagener
- Zell- und Entwicklungsbiologie, Department Biologie II, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany.,Max-Planck-Institut für Biochemie, Martinsried 82152, Germany
| |
Collapse
|
87
|
Roumia AF, Theodoropoulou MC, Tsirigos KD, Nielsen H, Bagos PG. Landscape of Eukaryotic Transmembrane Beta Barrel Proteins. J Proteome Res 2020; 19:1209-1221. [PMID: 32008325 DOI: 10.1021/acs.jproteome.9b00740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Even though in the last few years several families of eukaryotic β-barrel outer membrane proteins have been discovered, their computational characterization and their annotation in public databases are far from complete. The PFAM database includes only very few characteristic profiles for these families, and in most cases, the profile hidden Markov models (pHMMs) have been trained using prokaryotic and eukaryotic proteins together. Here, we present for the first time a comprehensive computational analysis of eukaryotic transmembrane β-barrels. Twelve characteristic pHMMs were built, based on an extensive literature search, which can discriminate eukaryotic β-barrels from other classes of proteins (globular and bacterial β-barrel ones), as well as between mitochondrial and chloroplastic ones. We built eight novel profiles for the chloroplastic β-barrel families that are not present in the PFAM database and also updated the profile for the MDM10 family (PF12519) in the PFAM database and divide the porin family (PF01459) into two separate families, namely, VDAC and TOM40.
Collapse
Affiliation(s)
- Ahmed F Roumia
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35100 Lamia, Greece
| | | | - Konstantinos D Tsirigos
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Henrik Nielsen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35100 Lamia, Greece
| |
Collapse
|
88
|
Abstract
Mitochondria are essential organelles of eukaryotic cells. They consist of hundreds of different proteins that exhibit crucial activities in respiration, catabolic metabolism and the synthesis of amino acids, lipids, heme and iron-sulfur clusters. With the exception of a handful of hydrophobic mitochondrially encoded membrane proteins, all these proteins are synthesized on cytosolic ribosomes, targeted to receptors on the mitochondrial surface, and transported across or inserted into the outer and inner mitochondrial membrane before they are folded and assembled into their final native structure. This review article provides a comprehensive overview of the mechanisms and components of the mitochondrial protein import systems with a particular focus on recent developments in the field.
Collapse
Affiliation(s)
- Katja G Hansen
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany
| | - Johannes M Herrmann
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany.
| |
Collapse
|
89
|
|
90
|
Kumar A, Matta SK, D'Silva P. Role of conserved regions of Tim22 in the structural organization of the carrier translocase. J Cell Sci 2020; 133:jcs.244632. [DOI: 10.1242/jcs.244632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/15/2020] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial biogenesis requires efficient sorting of various proteins into different mitochondrial sub-compartments mediated by dedicated protein machinery present in the outer and inner membrane. Among them, the TIM22 complex enables the integration of complex membrane proteins with internal targeting signals into the inner membrane. Although the Tim22 forms the core of the complex, the dynamic recruitment of subunits to the channel is still enigmatic. The present study first-time highlights that IMS and TM4 regions of Tim22 are critically required for the interaction of the membrane-embedded subunits including, Tim54, Tim18, and Sdh3, thereby maintain the functional architecture of TIM22 translocase. On the other hand, TM1 and TM2 regions of Tim22 are important for the Tim18 association, while TM3 is exclusively required for the Sdh3 interaction. Moreover, the impairment in TIM22 complex assembly influences its translocase activity, mitochondrial network, and the viability of cells lacking mitochondrial DNA. Overall our findings provide compelling evidence to highlight the significance of conserved regions of Tim22 that are important for the maintenance of the TIM22 complex and mitochondrial integrity.
Collapse
Affiliation(s)
- Abhishek Kumar
- Department of Biochemistry, New Biological Sciences Building, Indian Institute of Science, C V Raman Avenue, Bangalore-560012, India
| | - Srujan Kumar Matta
- Department of Biochemistry, New Biological Sciences Building, Indian Institute of Science, C V Raman Avenue, Bangalore-560012, India
| | - Patrick D'Silva
- Department of Biochemistry, New Biological Sciences Building, Indian Institute of Science, C V Raman Avenue, Bangalore-560012, India
| |
Collapse
|
91
|
Tucker K, Park E. Cryo-EM structure of the mitochondrial protein-import channel TOM complex at near-atomic resolution. Nat Struct Mol Biol 2019; 26:1158-1166. [PMID: 31740857 DOI: 10.1038/s41594-019-0339-2] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/23/2019] [Indexed: 11/09/2022]
Abstract
Nearly all mitochondrial proteins are encoded by the nuclear genome and imported into mitochondria after synthesis on cytosolic ribosomes. These precursor proteins are translocated into mitochondria by the TOM complex, a protein-conducting channel in the mitochondrial outer membrane. We have determined high-resolution cryo-EM structures of the core TOM complex from Saccharomyces cerevisiae in dimeric and tetrameric forms. Dimeric TOM consists of two copies each of five proteins arranged in two-fold symmetry: pore-forming β-barrel protein Tom40 and four auxiliary α-helical transmembrane proteins. The pore of each Tom40 has an overall negatively charged inner surface attributed to multiple functionally important acidic patches. The tetrameric complex is essentially a dimer of dimeric TOM, which may be capable of forming higher-order oligomers. Our study reveals the detailed molecular organization of the TOM complex and provides new insights about the mechanism of protein translocation into mitochondria.
Collapse
Affiliation(s)
- Kyle Tucker
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Eunyong Park
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
| |
Collapse
|
92
|
Synthetic protein-conductive membrane nanopores built with DNA. Nat Commun 2019; 10:5018. [PMID: 31685824 PMCID: PMC6828756 DOI: 10.1038/s41467-019-12639-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 09/23/2019] [Indexed: 11/08/2022] Open
Abstract
AbstractNanopores are key in portable sequencing and research given their ability to transport elongated DNA or small bioactive molecules through narrow transmembrane channels. Transport of folded proteins could lead to similar scientific and technological benefits. Yet this has not been realised due to the shortage of wide and structurally defined natural pores. Here we report that a synthetic nanopore designed via DNA nanotechnology can accommodate folded proteins. Transport of fluorescent proteins through single pores is kinetically analysed using massively parallel optical readout with transparent silicon-on-insulator cavity chips vs. electrical recordings to reveal an at least 20-fold higher speed for the electrically driven movement. Pores nevertheless allow a high diffusive flux of more than 66 molecules per second that can also be directed beyond equillibria. The pores may be exploited to sense diagnostically relevant proteins with portable analysis technology, to create molecular gates for drug delivery, or to build synthetic cells.
Collapse
|
93
|
Structure of the mitochondrial import gate reveals distinct preprotein paths. Nature 2019; 575:395-401. [PMID: 31600774 DOI: 10.1038/s41586-019-1680-7] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 09/30/2019] [Indexed: 11/08/2022]
Abstract
The translocase of the outer mitochondrial membrane (TOM) is the main entry gate for proteins1-4. Here we use cryo-electron microscopy to report the structure of the yeast TOM core complex5-9 at 3.8-Å resolution. The structure reveals the high-resolution architecture of the translocator consisting of two Tom40 β-barrel channels and α-helical transmembrane subunits, providing insight into critical features that are conserved in all eukaryotes1-3. Each Tom40 β-barrel is surrounded by small TOM subunits, and tethered by two Tom22 subunits and one phospholipid. The N-terminal extension of Tom40 forms a helix inside the channel; mutational analysis reveals its dual role in early and late steps in the biogenesis of intermembrane-space proteins in cooperation with Tom5. Each Tom40 channel possesses two precursor exit sites. Tom22, Tom40 and Tom7 guide presequence-containing preproteins to the exit in the middle of the dimer, whereas Tom5 and the Tom40 N extension guide preproteins lacking a presequence to the exit at the periphery of the dimer.
Collapse
|
94
|
Becker T, Song J, Pfanner N. Versatility of Preprotein Transfer from the Cytosol to Mitochondria. Trends Cell Biol 2019; 29:534-548. [PMID: 31030976 DOI: 10.1016/j.tcb.2019.03.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 11/16/2022]
Abstract
Mitochondrial biogenesis requires the import of a large number of precursor proteins from the cytosol. Although specific membrane-bound preprotein translocases have been characterized in detail, it was assumed that protein transfer from the cytosol to mitochondria mainly involved unselective binding to molecular chaperones. Recent findings suggest an unexpected versatility of protein transfer to mitochondria. Cytosolic factors have been identified that bind to selected subsets of preproteins and guide them to mitochondrial receptors in a post-translational manner. Cotranslational import processes are emerging. Mechanisms for crosstalk between protein targeting to mitochondria and other cell organelles, in particular the endoplasmic reticulum (ER) and peroxisomes, have been uncovered. We discuss how a network of cytosolic machineries and targeting pathways promote and regulate preprotein transfer into mitochondria.
Collapse
Affiliation(s)
- Thomas Becker
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany.
| | - Jiyao Song
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany.
| |
Collapse
|
95
|
Edwards R, Tokatlidis K. The Yeast Voltage-Dependent Anion Channel Porin: More IMPORTant than Just Metabolite Transport. Mol Cell 2019; 73:861-862. [PMID: 30849391 DOI: 10.1016/j.molcel.2019.02.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Porin is crucial for metabolite flux in mitochondria. In this issue of Molecular Cell, Sakaue et al. (2019) and Ellenrieder et al. (2019) describe an unexpected role for Porin in mitochondrial protein import by regulating the oligomeric state of the major protein import gate, the TOM complex, and the inner membrane insertion of metabolite carriers.
Collapse
Affiliation(s)
- Ruairidh Edwards
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Kostas Tokatlidis
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
96
|
Mitochondrial protein translocation-associated degradation. Nature 2019; 569:679-683. [PMID: 31118508 DOI: 10.1038/s41586-019-1227-y] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/25/2019] [Indexed: 01/12/2023]
Abstract
Mitochondrial biogenesis and functions depend on the import of precursor proteins via the 'translocase of the outer membrane' (TOM complex). Defects in protein import lead to an accumulation of mitochondrial precursor proteins that induces a range of cellular stress responses. However, constitutive quality-control mechanisms that clear trapped precursor proteins from the TOM channel under non-stress conditions have remained unknown. Here we report that in Saccharomyces cerevisiae Ubx2, which functions in endoplasmic reticulum-associated degradation, is crucial for this quality-control process. A pool of Ubx2 binds to the TOM complex to recruit the AAA ATPase Cdc48 for removal of arrested precursor proteins from the TOM channel. This mitochondrial protein translocation-associated degradation (mitoTAD) pathway continuously monitors the TOM complex under non-stress conditions to prevent clogging of the TOM channel with precursor proteins. The mitoTAD pathway ensures that mitochondria maintain their full protein-import capacity, and protects cells against proteotoxic stress induced by impaired transport of proteins into mitochondria.
Collapse
|
97
|
Impaired Mitochondrial Fusion and Oxidative Phosphorylation Triggered by High Glucose Is Mediated by Tom22 in Endothelial Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:4508762. [PMID: 31236191 PMCID: PMC6545771 DOI: 10.1155/2019/4508762] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/22/2019] [Accepted: 03/18/2019] [Indexed: 11/18/2022]
Abstract
Much evidence demonstrates that mitochondrial dysfunction plays a crucial role in the pathogenesis of vascular complications of diabetes. However, the signaling pathways through which hyperglycemia leads to mitochondrial dysfunction of endothelial cells are not fully understood. Here, we treated human umbilical vein endothelial cells (HUVECs) with high glucose and examined the role of translocase of mitochondrial outer membrane (Tom) 22 on mitochondrial dynamics and cellular function. Impaired Tom22 expression and protein expression of oxidative phosphorylation (OXPHOS) as well as decreased mitochondrial fusion were observed in HUVECs treated with high glucose. The deletion of Tom22 resulted in reduced mitochondrial fusion and ATP production and increased apoptosis in HUVECs. The overexpression of Tom22 restored the balance of mitochondrial dynamics and OXPHOS disrupted by high glucose. Importantly, we found that Tom22 modulates mitochondrial dynamics and OXPHOS by interacting with mitofusin (Mfn) 1. Taken together, our findings demonstrate for the first time that Tom22 is a novel regulator of both mitochondrial dynamics and bioenergetic function and contributes to cell survival following high-glucose exposure.
Collapse
|
98
|
Doan KN, Ellenrieder L, Becker T. Mitochondrial porin links protein biogenesis to metabolism. Curr Genet 2019; 65:899-903. [PMID: 30944955 DOI: 10.1007/s00294-019-00965-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 12/18/2022]
Abstract
In this report, we summarize recent findings about a role of the outer membrane metabolite channel VDAC/porin in protein import into mitochondria. Mitochondria fulfill key functions for cellular energy metabolism. Their biogenesis involves the import of about 1000 different proteins that are produced as precursors on cytosolic ribosomes. The translocase of the outer membrane (TOM complex) forms the entry gate for mitochondrial precursor proteins. Dedicated protein translocases sort the preproteins into the different mitochondrial subcompartments. While protein transport pathways are analyzed to some detail, only little is known about regulatory mechanisms that fine-tune protein import upon metabolic signaling. Recently, a dual role of the voltage-dependent anion channel (VDAC), also termed porin, in mitochondrial protein biogenesis was reported. First, VDAC/porin promotes as a coupling factor import of carrier proteins into the inner membrane. Second, VDAC/porin regulates the formation of the TOM complex. Thus, the major metabolite channel in the outer membrane VDAC/porin connects protein import to mitochondrial metabolism.
Collapse
Affiliation(s)
- Kim Nguyen Doan
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Lars Ellenrieder
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany.,Kelly Services AG Providing Services To Novartis Pharma AG, 4058, Basel, Switzerland
| | - Thomas Becker
- 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.
| |
Collapse
|
99
|
Sakaue H, Shiota T, Ishizaka N, Kawano S, Tamura Y, Tan KS, Imai K, Motono C, Hirokawa T, Taki K, Miyata N, Kuge O, Lithgow T, Endo T. Porin Associates with Tom22 to Regulate the Mitochondrial Protein Gate Assembly. Mol Cell 2019; 73:1044-1055.e8. [DOI: 10.1016/j.molcel.2019.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 11/06/2018] [Accepted: 01/02/2019] [Indexed: 10/27/2022]
|
100
|
Sekine S, Wang C, Sideris DP, Bunker E, Zhang Z, Youle RJ. Reciprocal Roles of Tom7 and OMA1 during Mitochondrial Import and Activation of PINK1. Mol Cell 2019; 73:1028-1043.e5. [DOI: 10.1016/j.molcel.2019.01.002] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/05/2018] [Accepted: 12/28/2018] [Indexed: 12/26/2022]
|