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Xu Y, Tummala SR, Chen X, Vardi N. VDAC in Retinal Health and Disease. Biomolecules 2024; 14:654. [PMID: 38927058 PMCID: PMC11201675 DOI: 10.3390/biom14060654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/22/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
The retina, a tissue of the central nervous system, is vital for vision as its photoreceptors capture light and transform it into electrical signals, which are further processed before they are sent to the brain to be interpreted as images. The retina is unique in that it is continuously exposed to light and has the highest metabolic rate and demand for energy amongst all the tissues in the body. Consequently, the retina is very susceptible to oxidative stress. VDAC, a pore in the outer membrane of mitochondria, shuttles metabolites between mitochondria and the cytosol and normally protects cells from oxidative damage, but when a cell's integrity is greatly compromised it initiates cell death. There are three isoforms of VDAC, and existing evidence indicates that all three are expressed in the retina. However, their precise localization and function in each cell type is unknown. It appears that most retinal cells express substantial amounts of VDAC2 and VDAC3, presumably to protect them from oxidative stress. Photoreceptors express VDAC2, HK2, and PKM2-key proteins in the Warburg pathway that also protect these cells. Consistent with its role in initiating cell death, VDAC is overexpressed in the retinal degenerative diseases retinitis pigmentosa, age related macular degeneration (AMD), and glaucoma. Treatment with antioxidants or inhibiting VDAC oligomerization reduced its expression and improved cell survival. Thus, VDAC may be a promising therapeutic candidate for the treatment of these diseases.
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Affiliation(s)
- Ying Xu
- Guangdong Key Laboratory of Non-Human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China; (Y.X.); (X.C.)
| | - Shanti R. Tummala
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Xiongmin Chen
- Guangdong Key Laboratory of Non-Human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China; (Y.X.); (X.C.)
| | - Noga Vardi
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA
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2
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Guna A, Stevens TA, Inglis AJ, Replogle JM, Esantsi TK, Muthukumar G, Shaffer KCL, Wang ML, Pogson AN, Jones JJ, Lomenick B, Chou TF, Weissman JS, Voorhees RM. MTCH2 is a mitochondrial outer membrane protein insertase. Science 2022; 378:317-322. [PMID: 36264797 PMCID: PMC9674023 DOI: 10.1126/science.add1856] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the mitochondrial outer membrane, α-helical transmembrane proteins play critical roles in cytoplasmic-mitochondrial communication. Using genome-wide CRISPR screens, we identified MTCH2, and its paralog MTCH1, and showed that it is required for insertion of biophysically diverse tail-anchored (TA), signal-anchored, and multipass proteins, but not outer membrane β-barrel proteins. Purified MTCH2 was sufficient to mediate insertion into reconstituted proteoliposomes. Functional and mutational studies suggested that MTCH2 has evolved from a solute carrier transporter. MTCH2 uses membrane-embedded hydrophilic residues to function as a gatekeeper for the outer membrane, controlling mislocalization of TAs into the endoplasmic reticulum and modulating the sensitivity of leukemia cells to apoptosis. Our identification of MTCH2 as an insertase provided a mechanistic explanation for the diverse phenotypes and disease states associated with MTCH2 dysfunction. We showed that MTCH2 was both necessary and sufficient for insertion of diverse α-helical proteins into the mitochondrial outer membrane, and was the defining member of a family of insertases that have co-opted the SLC25 transporter fold.
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Affiliation(s)
- Alina Guna
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Taylor A Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alison J Inglis
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA.,Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Gayathri Muthukumar
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kelly C L Shaffer
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Maxine L Wang
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Angela N Pogson
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jeff J Jones
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Brett Lomenick
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
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3
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Modeling Adsorption, Conformation, and Orientation of the Fis1 Tail Anchor at the Mitochondrial Outer Membrane. MEMBRANES 2022; 12:membranes12080752. [PMID: 36005667 PMCID: PMC9413518 DOI: 10.3390/membranes12080752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 12/04/2022]
Abstract
Proteins can be targeted to organellar membranes by using a tail anchor (TA), a stretch of hydrophobic amino acids found at the polypeptide carboxyl-terminus. The Fis1 protein (Fis1p), which promotes mitochondrial and peroxisomal division in the yeast Saccharomyces cerevisiae, is targeted to those organelles by its TA. Substantial evidence suggests that Fis1p insertion into the mitochondrial outer membrane can occur without the need for a translocation machinery. However, recent findings raise the possibility that Fis1p insertion into mitochondria might be promoted by a proteinaceous complex. Here, we have performed atomistic and coarse-grained molecular dynamics simulations to analyze the adsorption, conformation, and orientation of the Fis1(TA). Our results support stable insertion at the mitochondrial outer membrane in a monotopic, rather than a bitopic (transmembrane), configuration. Once inserted in the monotopic orientation, unassisted transition to the bitopic orientation is expected to be blocked by the highly charged nature of the TA carboxyl-terminus and by the Fis1p cytosolic domain. Our results are consistent with a model in which Fis1p does not require a translocation machinery for insertion at mitochondria.
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4
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Eaglesfield R, Tokatlidis K. Targeting and Insertion of Membrane Proteins in Mitochondria. Front Cell Dev Biol 2022; 9:803205. [PMID: 35004695 PMCID: PMC8740019 DOI: 10.3389/fcell.2021.803205] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/09/2021] [Indexed: 01/26/2023] Open
Abstract
Mitochondrial membrane proteins play an essential role in all major mitochondrial functions. The respiratory complexes of the inner membrane are key for the generation of energy. The carrier proteins for the influx/efflux of essential metabolites to/from the matrix. Many other inner membrane proteins play critical roles in the import and processing of nuclear encoded proteins (∼99% of all mitochondrial proteins). The outer membrane provides another lipidic barrier to nuclear-encoded protein translocation and is home to many proteins involved in the import process, maintenance of ionic balance, as well as the assembly of outer membrane components. While many aspects of the import and assembly pathways of mitochondrial membrane proteins have been elucidated, many open questions remain, especially surrounding the assembly of the respiratory complexes where certain highly hydrophobic subunits are encoded by the mitochondrial DNA and synthesised and inserted into the membrane from the matrix side. This review will examine the various assembly pathways for inner and outer mitochondrial membrane proteins while discussing the most recent structural and biochemical data examining the biogenesis process.
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Affiliation(s)
- Ross Eaglesfield
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, University Avenue, Scotland, United Kingdom
| | - Kostas Tokatlidis
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, University Avenue, Scotland, United Kingdom
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5
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VDAC2 and the BCL-2 family of proteins. Biochem Soc Trans 2021; 49:2787-2795. [PMID: 34913469 PMCID: PMC8786305 DOI: 10.1042/bst20210753] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/21/2021] [Accepted: 11/26/2021] [Indexed: 12/26/2022]
Abstract
The BCL-2 protein family govern whether a cell dies or survives by controlling mitochondrial apoptosis. As dysregulation of mitochondrial apoptosis is a common feature of cancer cells, targeting protein–protein interactions within the BCL-2 protein family is a key strategy to seize control of apoptosis and provide favourable outcomes for cancer patients. Non-BCL-2 family proteins are emerging as novel regulators of apoptosis and are potential drug targets. Voltage dependent anion channel 2 (VDAC2) can regulate apoptosis. However, it is unclear how this occurs at the molecular level, with conflicting evidence in the literature for its role in regulating the BCL-2 effector proteins, BAK and BAX. Notably, VDAC2 is required for efficient BAX-mediated apoptosis, but conversely inhibits BAK-mediated apoptosis. This review focuses on the role of VDAC2 in apoptosis, discussing the current knowledge of the interaction between VDAC2 and BCL-2 family proteins and the recent development of an apoptosis inhibitor that targets the VDAC2–BAK interaction.
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6
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Morgenstern M, Peikert CD, Lübbert P, Suppanz I, Klemm C, Alka O, Steiert C, Naumenko N, Schendzielorz A, Melchionda L, Mühlhäuser WWD, Knapp B, Busch JD, Stiller SB, Dannenmaier S, Lindau C, Licheva M, Eickhorst C, Galbusera R, Zerbes RM, Ryan MT, Kraft C, Kozjak-Pavlovic V, Drepper F, Dennerlein S, Oeljeklaus S, Pfanner N, Wiedemann N, Warscheid B. Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. Cell Metab 2021; 33:2464-2483.e18. [PMID: 34800366 PMCID: PMC8664129 DOI: 10.1016/j.cmet.2021.11.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/01/2021] [Accepted: 11/01/2021] [Indexed: 12/18/2022]
Abstract
Mitochondria are key organelles for cellular energetics, metabolism, signaling, and quality control and have been linked to various diseases. Different views exist on the composition of the human mitochondrial proteome. We classified >8,000 proteins in mitochondrial preparations of human cells and defined a mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP). We identified interactors of translocases, respiratory chain, and ATP synthase assembly factors. The abundance of MitoCoP proteins covers six orders of magnitude and amounts to 7% of the cellular proteome with the chaperones HSP60-HSP10 being the most abundant mitochondrial proteins. MitoCoP dynamics spans three orders of magnitudes, with half-lives from hours to months, and suggests a rapid regulation of biosynthesis and assembly processes. 460 MitoCoP genes are linked to human diseases with a strong prevalence for the central nervous system and metabolism. MitoCoP will provide a high-confidence resource for placing dynamics, functions, and dysfunctions of mitochondria into the cellular context.
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Affiliation(s)
- Marcel Morgenstern
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Christian D Peikert
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Philipp Lübbert
- 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
| | - Ida Suppanz
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Cinzia Klemm
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Oliver Alka
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Conny Steiert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Nataliia Naumenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Alexander Schendzielorz
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Laura Melchionda
- 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
| | - Wignand W D Mühlhäuser
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Bettina Knapp
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jakob D Busch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Sebastian B Stiller
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Stefan Dannenmaier
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Caroline Lindau
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Mariya Licheva
- 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
| | - Christopher Eickhorst
- 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; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Riccardo Galbusera
- Neurologic Clinic and Policlinic, Departments of Medicine, Clinical Research and Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Ralf M Zerbes
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800 Melbourne, VIC, Australia
| | - Claudine Kraft
- 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
| | - Vera Kozjak-Pavlovic
- Department of Microbiology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Friedel Drepper
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Silke Oeljeklaus
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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7
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Mehlhorn DG, Asseck LY, Grefen C. Looking for a safe haven: tail-anchored proteins and their membrane insertion pathways. PLANT PHYSIOLOGY 2021; 187:1916-1928. [PMID: 35235667 PMCID: PMC8644595 DOI: 10.1093/plphys/kiab298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/05/2021] [Indexed: 06/14/2023]
Abstract
Insertion of membrane proteins into the lipid bilayer is a crucial step during their biosynthesis. Eukaryotic cells face many challenges in directing these proteins to their predestined target membrane. The hydrophobic signal peptide or transmembrane domain (TMD) of the nascent protein must be shielded from the aqueous cytosol and its target membrane identified followed by transport and insertion. Components that evolved to deal with each of these challenging steps range from chaperones to receptors, insertases, and sophisticated translocation complexes. One prominent translocation pathway for most proteins is the signal recognition particle (SRP)-dependent pathway which mediates co-translational translocation of proteins across or into the endoplasmic reticulum (ER) membrane. This textbook example of protein insertion is stretched to its limits when faced with secretory or membrane proteins that lack an amino-terminal signal sequence or TMD. Particularly, a large group of so-called tail-anchored (TA) proteins that harbor a single carboxy-terminal TMD require an alternative, post-translational insertion route into the ER membrane. In this review, we summarize the current research in TA protein insertion with a special focus on plants, address challenges, and highlight future research avenues.
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Affiliation(s)
- Dietmar G Mehlhorn
- Faculty of Biology and Biotechnology, Molecular and Cellular Botany, University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Lisa Y Asseck
- Faculty of Biology and Biotechnology, Molecular and Cellular Botany, University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Christopher Grefen
- Faculty of Biology and Biotechnology, Molecular and Cellular Botany, University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
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8
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Labeling and measuring stressed mitochondria using a PINK1-based ratiometric fluorescent sensor. J Biol Chem 2021; 297:101279. [PMID: 34624312 PMCID: PMC8560995 DOI: 10.1016/j.jbc.2021.101279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/23/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are essential organelles that carry out a number of pivotal metabolic processes and maintain cellular homeostasis. Mitochondrial dysfunction caused by various stresses is associated with many diseases such as type 2 diabetes, obesity, cancer, heart failure, neurodegenerative disorders, and aging. Therefore, it is important to understand the stimuli that induce mitochondrial stress. However, broad analysis of mitochondrial stress has not been carried out to date. Here, we present a set of fluorescent tools, called mito-Pain (mitochondrial PINK1 accumulation index), which enable the labeling of stressed mitochondria. Mito-Pain uses PTEN-induced putative kinase 1 (PINK1) stabilization on mitochondria and quantifies mitochondrial stress levels by comparison with PINK1-GFP, which is stabilized under mitochondrial stress, and RFP-Omp25, which is constitutively localized on mitochondria. To identify compounds that induce mitochondrial stress, we screened a library of 3374 compounds using mito-Pain and identified 57 compounds as mitochondrial stress inducers. Furthermore, we classified each compound into several categories based on mitochondrial response: depolarization, mitochondrial morphology, or Parkin recruitment. Parkin recruitment to mitochondria was often associated with mitochondrial depolarization and aggregation, suggesting that Parkin is recruited to heavily damaged mitochondria. In addition, many of the compounds led to various mitochondrial morphological changes, including fragmentation, aggregation, elongation, and swelling, with or without Parkin recruitment or mitochondrial depolarization. We also found that several compounds induced an ectopic response of Parkin, leading to the formation of cytosolic puncta dependent on PINK1. Thus, mito-Pain enables the detection of stressed mitochondria under a wide variety of conditions and provides insights into mitochondrial quality control systems.
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9
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Coukos R, Yao D, Sanchez MI, Strand ET, Olive ME, Udeshi ND, Weissman JS, Carr SA, Bassik MC, Ting AY. An engineered transcriptional reporter of protein localization identifies regulators of mitochondrial and ER membrane protein trafficking in high-throughput CRISPRi screens. eLife 2021; 10:69142. [PMID: 34414886 PMCID: PMC8423448 DOI: 10.7554/elife.69142] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022] Open
Abstract
The trafficking of specific protein cohorts to correct subcellular locations at correct times is essential for every signaling and regulatory process in biology. Gene perturbation screens could provide a powerful approach to probe the molecular mechanisms of protein trafficking, but only if protein localization or mislocalization can be tied to a simple and robust phenotype for cell selection, such as cell proliferation or fluorescence-activated cell sorting (FACS). To empower the study of protein trafficking processes with gene perturbation, we developed a genetically encoded molecular tool named HiLITR (High-throughput Localization Indicator with Transcriptional Readout). HiLITR converts protein colocalization into proteolytic release of a membrane-anchored transcription factor, which drives the expression of a chosen reporter gene. Using HiLITR in combination with FACS-based CRISPRi screening in human cell lines, we identified genes that influence the trafficking of mitochondrial and ER tail-anchored proteins. We show that loss of the SUMO E1 component SAE1 results in mislocalization and destabilization of many mitochondrial tail-anchored proteins. We also demonstrate a distinct regulatory role for EMC10 in the ER membrane complex, opposing the transmembrane-domain insertion activity of the complex. Through transcriptional integration of complex cellular functions, HiLITR expands the scope of biological processes that can be studied by genetic perturbation screening technologies.
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Affiliation(s)
- Robert Coukos
- Department of Genetics, Stanford University, Stanford, United States
| | - David Yao
- Department of Genetics, Stanford University, Stanford, United States
| | - Mateo I Sanchez
- Department of Genetics, Stanford University, Stanford, United States.,Chan Zuckerberg Biohub, Stanford, United States
| | - Eric T Strand
- Department of Genetics, Stanford University, Stanford, United States
| | - Meagan E Olive
- Broad Institute of MIT and Harvard, Cambridge, United States
| | | | - Jonathan S Weissman
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, United States
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, United States.,Chan Zuckerberg Biohub, Stanford, United States.,Department of Biology, Stanford University, Stanford, United States
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10
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Drwesh L, Rapaport D. Biogenesis pathways of α-helical mitochondrial outer membrane proteins. Biol Chem 2021; 401:677-686. [PMID: 32017702 DOI: 10.1515/hsz-2019-0440] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/21/2020] [Indexed: 01/23/2023]
Abstract
Mitochondria harbor in their outer membrane (OM) proteins of different topologies. These proteins are encoded by the nuclear DNA, translated on cytosolic ribosomes and inserted into their target organelle by sophisticated protein import machineries. Recently, considerable insights have been accumulated on the insertion pathways of proteins into the mitochondrial OM. In contrast, little is known regarding the early cytosolic stages of their biogenesis. It is generally presumed that chaperones associate with these proteins following their synthesis in the cytosol, thereby keeping them in an import-competent conformation and preventing their aggregation and/or mis-folding and degradation. In this review, we outline the current knowledge about the biogenesis of different mitochondrial OM proteins with various topologies, and highlight the recent findings regarding their import pathways starting from early cytosolic events until their recognition on the mitochondrial surface that lead to their final insertion into the mitochondrial OM.
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Affiliation(s)
- Layla Drwesh
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
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11
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Doan KN, Grevel A, Mårtensson CU, Ellenrieder L, Thornton N, Wenz LS, Opaliński Ł, Guiard B, Pfanner N, Becker T. The Mitochondrial Import Complex MIM Functions as Main Translocase for α-Helical Outer Membrane Proteins. Cell Rep 2021; 31:107567. [PMID: 32348752 DOI: 10.1016/j.celrep.2020.107567] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/19/2020] [Accepted: 04/02/2020] [Indexed: 01/08/2023] Open
Abstract
The mitochondrial outer membrane contains integral proteins with α-helical membrane anchors or a transmembrane β-barrel. The translocase of the outer membrane (TOM) cooperates with the sorting and assembly machinery (SAM) in the import of β-barrel proteins, whereas the mitochondrial import (MIM) complex inserts precursors of multi-spanning α-helical proteins. Single-spanning proteins constitute more than half of the integral outer membrane proteins; however, their biogenesis is poorly understood. We report that the yeast MIM complex promotes the insertion of proteins with N-terminal (signal-anchored) or C-terminal (tail-anchored) membrane anchors. The MIM complex exists in three dynamic populations. MIM interacts with TOM to accept precursor proteins from the receptor Tom70. Free MIM complexes insert single-spanning proteins that are imported in a Tom70-independent manner. Finally, coupling of MIM and SAM promotes early assembly steps of TOM subunits. We conclude that the MIM complex is a major and versatile protein translocase of the mitochondrial outer membrane.
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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
| | - Alexander Grevel
- 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
| | - Christoph U Mårtensson
- 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
| | - Nicolas Thornton
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Lena-Sophie Wenz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Łukasz Opaliński
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Bernard Guiard
- Centre de Génétique Moléculaire, CNRS, 91190 Gif-sur-Yvette, France
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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12
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Maity S, Chakrabarti O. Mitochondrial protein import as a quality control sensor. Biol Cell 2021; 113:375-400. [PMID: 33870508 DOI: 10.1111/boc.202100002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/04/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Mitochondria are organelles involved in various functions related to cellular metabolism and homoeostasis. Though mitochondria contain own genome, their nuclear counterparts encode most of the different mitochondrial proteins. These are synthesised as precursors in the cytosol and have to be delivered into the mitochondria. These organelles hence have elaborate machineries for the import of precursor proteins from cytosol. The protein import machineries present in both mitochondrial membrane and aqueous compartments show great variability in pre-protein recognition, translocation and sorting across or into it. Mitochondrial protein import machineries also interact transiently with other protein complexes of the respiratory chain or those involved in the maintenance of membrane architecture. Hence mitochondrial protein translocation is an indispensable part of the regulatory network that maintains protein biogenesis, bioenergetics, membrane dynamics and quality control of the organelle. Various stress conditions and diseases that are associated with mitochondrial import defects lead to changes in cellular transcriptomic and proteomic profiles. Dysfunction in mitochondrial protein import also causes over-accumulation of precursor proteins and their aggregation in the cytosol. Multiple pathways may be activated for buffering these harmful consequences. Here, we present a comprehensive picture of import machinery and its role in cellular quality control in response to defective mitochondrial import. We also discuss the pathological consequences of dysfunctional mitochondrial protein import in neurodegeneration and cancer.
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Affiliation(s)
- Sebabrata Maity
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, 700064, India.,Homi Bhabha National Institute, India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, 700064, India.,Homi Bhabha National Institute, India
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13
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Pogmore JP, Uehling D, Andrews DW. Pharmacological Targeting of Executioner Proteins: Controlling Life and Death. J Med Chem 2021; 64:5276-5290. [PMID: 33939407 DOI: 10.1021/acs.jmedchem.0c02200] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Small-molecule mediated modulation of protein interactions of Bcl-2 (B-cell lymphoma-2) family proteins was clinically validated in 2015 when Venetoclax, a selective inhibitor of the antiapoptotic protein BCL-2, achieved breakthrough status designation by the FDA for treatment of lymphoid malignancies. Since then, substantial progress has been made in identifying inhibitors of other interactions of antiapoptosis proteins. However, targeting their pro-apoptotic counterparts, the "executioners" BAX, BAK, and BOK that both initiate and commit the cell to dying, has lagged behind. However, recent publications demonstrate that these proteins can be positively or negatively regulated using small molecule tool compounds. The results obtained with these molecules suggest that pharmaceutical regulation of apoptosis will have broad implications that extend beyond activating cell death in cancer. We review recent advances in identifying compounds and their utility in the exogenous control of life and death by regulating executioner proteins, with emphasis on the prototype BAX.
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Affiliation(s)
- Justin P Pogmore
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1J7, Canada.,Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, Ontario M4N 3M5, Canada
| | - David Uehling
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 1M1, Canada
| | - David W Andrews
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1J7, Canada.,Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, Ontario M4N 3M5, Canada
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14
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Intrinsically Connected: Therapeutically Targeting the Cathepsin Proteases and the Bcl-2 Family of Protein Substrates as Co-regulators of Apoptosis. Int J Mol Sci 2021; 22:ijms22094669. [PMID: 33925117 PMCID: PMC8124540 DOI: 10.3390/ijms22094669] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/14/2022] Open
Abstract
Taken with the growing importance of cathepsin-mediated substrate proteolysis in tumor biology and progression, the focus and emphasis placed on therapeutic design and development is coming into fruition. Underpinning this approach is the invariable progression from the direction of fully characterizing cathepsin protease members and their substrate targets, towards targeting such an interaction with tangible therapeutics. The two groups of such substrates that have gained much attention over the years are the pro- and anti- apoptotic protein intermediates from the extrinsic and intrinsic signaling arms of the apoptosis pathway. As proteins that are central to determining cellular fate, some of them present themselves as very favorable candidates for therapeutic targeting. However, considering that both anti- and pro- apoptotic signaling intermediates have been reported to be downstream substrates for certain activated cathepsin proteases, therapeutic targeting approaches based on greater selectivity do need to be given greater consideration. Herein, we review the relationships shared by the cathepsin proteases and the Bcl-2 homology domain proteins, in the context of how the topical approach of adopting 'BH3-mimetics' can be explored further in modulating the relationship between the anti- and pro- apoptotic signaling intermediates from the intrinsic apoptosis pathway and their upstream cathepsin protease regulators. Based on this, we highlight important future considerations for improved therapeutic design.
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15
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Jiang H. Quality control pathways of tail-anchored proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118922. [PMID: 33285177 DOI: 10.1016/j.bbamcr.2020.118922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/14/2020] [Accepted: 12/01/2020] [Indexed: 12/20/2022]
Abstract
Tail-anchored (TA) proteins have an N-terminal domain in the cytosol and a C-terminal transmembrane domain anchored to a variety of organelle membranes. TA proteins are recognized by targeting factors at the transmembrane domain and C-terminal sequence and are guided to distinct membranes. The promiscuity of targeting sequences and the dysfunction of targeting pathways cause mistargeting of TA proteins. TA proteins are under surveillance by quality control pathways. For resident TA proteins at mitochondrial and ER membranes, intrinsic instability or stimuli induced degrons of the cytosolic and transmembrane domains are sensed by quality control factors to initiate degradation of TA proteins. These pathways are summarized as TA protein degradation-Cytosol (TAD-C) and TAD-Membrane (TAD-M) pathways. For mistargeted and a subset of solitary TA proteins at mitochondrial and peroxisomal membranes, a unique pathway has been revealed in recent years. Msp1/ATAD1 is an AAA-ATPase dually-localized to mitochondrial and peroxisomal membranes. It directly recognizes mistargeted and solitary TA proteins and dislocates them out of membrane. Dislocated substrates are subsequently ubiquitinated by the ER-resident Doa10 ubiquitin E3 ligase complex for degradation. We summarize and discuss the substrate recognition, dislocation and degradation mechanisms of the Msp1 pathway.
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Affiliation(s)
- Hui Jiang
- National Institute of Biological Sciences, Beijing 102206, China; Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100871, China.
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16
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Pedley R, King LE, Mallikarjun V, Wang P, Swift J, Brennan K, Gilmore AP. BioID-based proteomic analysis of the Bid interactome identifies novel proteins involved in cell-cycle-dependent apoptotic priming. Cell Death Dis 2020; 11:872. [PMID: 33067418 PMCID: PMC7567853 DOI: 10.1038/s41419-020-03091-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/12/2022]
Abstract
Apoptotic priming controls the commitment of cells to apoptosis by determining how close they lie to mitochondrial permeabilisation. Variations in priming are important for how both healthy and cancer cells respond to chemotherapeutic agents, but how it is dynamically coordinated by Bcl-2 proteins remains unclear. The Bcl-2 family protein Bid is phosphorylated when cells enter mitosis, increasing apoptotic priming and sensitivity to antimitotic drugs. Here, we report an unbiased proximity biotinylation (BioID) screen to identify regulators of apoptotic priming in mitosis, using Bid as bait. The screen primarily identified proteins outside of the canonical Bid interactome. Specifically, we found that voltage-dependent anion-selective channel protein 2 (VDAC2) was required for Bid phosphorylation-dependent changes in apoptotic priming during mitosis. These results highlight the importance of the wider Bcl-2 family interactome in regulating the temporal control of apoptotic priming.
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Affiliation(s)
- Robert Pedley
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Louise E King
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Venkatesh Mallikarjun
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Pengbo Wang
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Cancer Research UK Manchester Institute, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Joe Swift
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Keith Brennan
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Andrew P Gilmore
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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17
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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.
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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.
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18
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Ferdigg A, Dimmer KS, Rapaport D, Vitali DG. Hydrogenosomal tail-anchored proteins are targeted to both mitochondria and ER upon their expression in yeast cells. PLoS One 2020; 15:e0237982. [PMID: 32817700 PMCID: PMC7446849 DOI: 10.1371/journal.pone.0237982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/06/2020] [Indexed: 11/18/2022] Open
Abstract
Some organisms, like Trichomonas vaginalis, contain mitochondria-related hydrogen-producing organelles, called hydrogenosomes. The protein targeting into these organelles is proposed to be similar to the well-studied mitochondria import. Indeed, S. cerevisiae mitochondria and T. vaginalis hydrogenosomes share some components of protein import complexes. However, it is still unknown whether targeting signals directing substrate proteins to hydrogenosomes can support in other eukaryotes specific mitochondrial localization. To address this issue, we investigated the intracellular localization of three hydrogenosomal tail-anchored proteins expressed in yeast cells. We observed that these proteins were targeted to both mitochondria and ER with a variable dependency on the mitochondrial MIM complex. Our results suggest that the targeting signal of TA proteins are only partially conserved between hydrogenosomes and yeast mitochondria.
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Affiliation(s)
- Andrè Ferdigg
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Kai S. Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
- * E-mail: (DR); (DGV)
| | - Daniela G. Vitali
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
- * E-mail: (DR); (DGV)
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19
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Dudko HV, Urban VA, Davidovskii AI, Veresov VG. Structure-based modeling of turnover of Bcl-2 family proteins bound to voltage-dependent anion channel 2 (VDAC2): Implications for the mechanisms of proapoptotic activation of Bak and Bax in vivo. Comput Biol Chem 2020; 85:107203. [DOI: 10.1016/j.compbiolchem.2020.107203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/31/2019] [Accepted: 01/13/2020] [Indexed: 12/15/2022]
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20
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Abstract
Due to their topology tail-anchored (TA) proteins must target to the membrane independently of the co-translational route defined by the signal sequence recognition particle (SRP), its receptor and the translocon Sec61. More than a decade of work has extensively characterized a highly conserved pathway, the yeast GET or mammalian TRC40 pathway, which is capable of countering the biogenetic challenge posed by the C-terminal TA anchor. In this review we briefly summarize current models of this targeting route and focus on emerging aspects such as the intricate interplay with the proteostatic network of cells and with other targeting pathways. Importantly, we consider the lessons provided by the in vivo analysis of the pathway in different model organisms and by the consideration of its full client spectrum in more recent studies. This analysis of the state of the field highlights directions in which the current models may be experimentally probed and conceptually extended.
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Affiliation(s)
- Nica Borgese
- Institute of Neuroscience and BIOMETRA Department, Consiglio Nazionale delle Ricerche and Università degli Studi di Milano, via Vanvitelli 32, 20129, Milan, Italy.
| | - Javier Coy-Vergara
- Department of Molecular Biology, University of Göttingen Medical Centre, Humboldtallee 23, 37073, Göttingen, Germany
| | - Sara Francesca Colombo
- Institute of Neuroscience and BIOMETRA Department, Consiglio Nazionale delle Ricerche and Università degli Studi di Milano, via Vanvitelli 32, 20129, Milan, Italy
| | - Blanche Schwappach
- Department of Molecular Biology, University of Göttingen Medical Centre, Humboldtallee 23, 37073, Göttingen, Germany.
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21
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Vitali DG, Drwesh L, Cichocki BA, Kolb A, Rapaport D. The Biogenesis of Mitochondrial Outer Membrane Proteins Show Variable Dependence on Import Factors. iScience 2019; 23:100779. [PMID: 31945731 PMCID: PMC6965732 DOI: 10.1016/j.isci.2019.100779] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/12/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022] Open
Abstract
Biogenesis of mitochondrial outer membrane proteins involves their integration into the lipid bilayer. Among these proteins are those that form a single-span topology, but our understanding of their biogenesis is scarce. In this study, we found that the MIM complex is required for the membrane insertion of some single-span proteins. However, other such proteins integrate into the membrane in a MIM-independent manner. Moreover, the biogenesis of the studied proteins was dependent to a variable degree on the TOM receptors Tom20 and Tom70. We found that Atg32 C-terminal domain mediates dependency on Tom20, whereas the cytosolic domains of Atg32 and Gem1 facilitate MIM involvement. Collectively, our findings (1) enlarge the repertoire of MIM substrates to include also tail-anchored proteins, (2) provide new mechanistic insights to the functions of the MIM complex and TOM import receptors, and (3) demonstrate that the biogenesis of MOM single-span proteins shows variable dependence on import factors.
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Affiliation(s)
- Daniela G Vitali
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Layla Drwesh
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Bogdan A Cichocki
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Antonia Kolb
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany.
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22
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Molecular pathways of mitochondrial outer membrane protein degradation. Biochem Soc Trans 2019; 47:1437-1447. [DOI: 10.1042/bst20190275] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 01/23/2023]
Abstract
Abstract
Mitochondrial outer membrane (MOM) encloses inner compartments of mitochondria and integrates cytoplasmic signals to regulate essential mitochondrial processes, such as protein import, dynamics, metabolism, cell death, etc. A substantial understanding of MOM associated proteostatic stresses and quality control pathways has been obtained in recent years. Six MOM associated protein degradation (MAD) pathways center on three AAA ATPases: Cdc48 in the cytoplasm, Msp1 integral to MOM, and Yme1 integral to the inner membrane. These pathways survey MOM proteome from the cytoplasmic and the inter-membrane space (IMS) sides. They detect and degrade MOM proteins with misfolded cytoplasmic and IMS domains, remove mistargeted tail-anchored proteins, and clear mitochondrial precursor proteins clogged in the TOM import complex. These MOM associated protein quality control pathways collaboratively maintain mitochondrial proteostasis and cell viability.
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23
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Li L, Zheng J, Wu X, Jiang H. Mitochondrial AAA-ATPase Msp1 detects mislocalized tail-anchored proteins through a dual-recognition mechanism. EMBO Rep 2019; 20:embr.201846989. [PMID: 30858337 DOI: 10.15252/embr.201846989] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/28/2019] [Accepted: 02/11/2019] [Indexed: 01/09/2023] Open
Abstract
The conserved AAA-ATPase Msp1 is embedded in the outer mitochondrial membrane and removes mislocalized tail-anchored (TA) proteins upon dysfunction of the guided entry of tail-anchored (GET) pathway. It remains unclear how Msp1 recognizes its substrates. Here, we extensively characterize Msp1 and its substrates, including the mitochondrially targeted Pex15Δ30, and full-length Pex15, which mislocalizes to mitochondria upon dysfunction of Pex19 but not the GET pathway. Moreover, we identify two new substrates, Frt1 and Ysy6. Our results suggest that mislocalized TA proteins expose hydrophobic surfaces in the cytoplasm and are recognized by Msp1 through conserved hydrophobic residues. Introducing a hydrophobic patch into mitochondrial TA proteins transforms them into Msp1 substrates. In addition, Pex15Δ30 and Frt1 contain basic inter-membrane space (IMS) residues critical for their mitochondrial mistargeting. Remarkably, Msp1 recognizes this feature through the acidic D12 residue in its IMS domain. This dual-recognition mechanism involving interactions at the cytoplasmic and IMS domains of Msp1 and substrates greatly facilitates substrate recognition and is required by Msp1 to safeguard mitochondrial functions.
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Affiliation(s)
- Lanlan Li
- College of Life Sciences, Beijing Normal University, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing, China
| | - Jing Zheng
- National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xi Wu
- National Institute of Biological Sciences, Beijing, China
| | - Hui Jiang
- National Institute of Biological Sciences, Beijing, China .,Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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24
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Topology of active, membrane-embedded Bax in the context of a toroidal pore. Cell Death Differ 2018; 25:1717-1731. [PMID: 30185826 DOI: 10.1038/s41418-018-0184-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/20/2018] [Accepted: 05/21/2018] [Indexed: 01/18/2023] Open
Abstract
Bax is a Bcl-2 protein critical for apoptosis induction. In healthy cells, Bax is mostly a monomeric, cytosolic protein, while upon apoptosis initiation it inserts into the outer mitochondrial membrane, oligomerizes, and forms pores that release proapoptotic factors like Cytochrome c into the cytosol. The structures of active Bax and its homolog Bak are only partially understood and the topology of the proteins with respect to the membrane bilayer is controversially described in the literature. Here, we systematically review and examine the protein-membrane, protein-water, and protein-protein contacts of the nine helices of active Bax and Bak, and add a new set of topology data obtained by fluorescence and EPR methods. We conclude based on the consistent part of the datasets that the core/dimerization domain of Bax (Bak) is water exposed with only helices 4 and 5 in membrane contact, whereas the piercing/latch domain is in peripheral membrane contact, with helix 9 being transmembrane. Among the available structural models, those considering the dimerization/core domain at the rim of a toroidal pore are the most plausible to describe the active state of the proteins, although the structural flexibility of the piercing/latch domain does not allow unambiguous discrimination between the existing models.
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25
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Cichocki BA, Krumpe K, Vitali DG, Rapaport D. Pex19 is involved in importing dually targeted tail-anchored proteins to both mitochondria and peroxisomes. Traffic 2018; 19:770-785. [DOI: 10.1111/tra.12604] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Bogdan A. Cichocki
- Interfaculty Institute of Biochemistry; University of Tübingen; Tübingen Germany
| | - Katrin Krumpe
- Interfaculty Institute of Biochemistry; University of Tübingen; Tübingen Germany
| | - Daniela G. Vitali
- Interfaculty Institute of Biochemistry; University of Tübingen; Tübingen Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry; University of Tübingen; Tübingen Germany
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26
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Abstract
Proper localization of membrane proteins is essential for the function of biological membranes and for the establishment of organelle identity within a cell. Molecular machineries that mediate membrane protein biogenesis need to not only achieve a high degree of efficiency and accuracy, but also prevent off-pathway aggregation events that can be detrimental to cells. The posttranslational targeting of tail-anchored proteins (TAs) provides tractable model systems to probe these fundamental issues. Recent advances in understanding TA-targeting pathways reveal sophisticated molecular machineries that drive and regulate these processes. These findings also suggest how an interconnected network of targeting factors, cochaperones, and quality control machineries together ensures robust membrane protein biogenesis.
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Affiliation(s)
- Un Seng Chio
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125; , ,
| | - Hyunju Cho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125; , ,
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125; , ,
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27
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Figueiredo Costa B, Cassella P, Colombo SF, Borgese N. Discrimination between the endoplasmic reticulum and mitochondria by spontaneously inserting tail‐anchored proteins. Traffic 2018; 19:182-197. [DOI: 10.1111/tra.12550] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/18/2018] [Accepted: 01/18/2018] [Indexed: 01/16/2023]
Affiliation(s)
- Bruna Figueiredo Costa
- CNR Institute of Neuroscience and BIOMETRA DepartmentUniversità degli Studi di Milano Milan Italy
| | - Patrizia Cassella
- CNR Institute of Neuroscience and BIOMETRA DepartmentUniversità degli Studi di Milano Milan Italy
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28
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Abstract
Peroxisomes contain anabolic and catabolic enzymes including oxidases that produce hydrogen peroxide as a by-product. Peroxisomes also contain catalase to metabolize hydrogen peroxide. It has been recognized that catalase is localized to cytosol in addition to peroxisomes. A recent study has revealed that loss of VDAC2 shifts localization of BAK, a pro-apoptotic member of Bcl-2 family, from mitochondria to peroxisomes and cytosol, thereby leading to release of peroxisomal matrix proteins including catalase to the cytosol. A subset of BAK is localized to peroxisomes even in wild-type cells, regulating peroxisomal membrane permeability and catalase localization. The cytosolic catalase potentially acts as an antioxidant to eliminate extra-peroxisomal hydrogen peroxide.
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Affiliation(s)
- Non Miyata
- Department of Biology, Faculty of Sciences, Kyushu University, 819-0395, Nishi-ku, Fukuoka, Japan.,Department of Chemistry, Faculty of Sciences, Kyushu University, 819-0395, Nishi-ku, Fukuoka, Japan
| | - Kanji Okumoto
- Department of Biology, Faculty of Sciences, Kyushu University, 819-0395, Nishi-ku, Fukuoka, Japan.,Graduate School of Systems Life Sciences, Kyushu University, 819-0395, Nishi-ku, Fukuoka, Japan
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Kyushu University, 812-8582, Higashi-ku, Fukuoka, Japan.
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29
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Okumoto K, Ono T, Toyama R, Shimomura A, Nagata A, Fujiki Y. New splicing variants of mitochondrial Rho GTPase-1 (Miro1) transport peroxisomes. J Cell Biol 2017; 217:619-633. [PMID: 29222186 PMCID: PMC5800816 DOI: 10.1083/jcb.201708122] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/27/2017] [Accepted: 11/06/2017] [Indexed: 01/31/2023] Open
Abstract
The mechanisms underlying microtubule-dependent long-distance movement of peroxisomes in mammalian cells are unclear. Okumoto et al. identify splicing variants of human mitochondrial Rho GTPase-1 (Miro1) that localize to peroxisomes and that link these organelles to microtubule-dependent transport complexes including TRAK2. Microtubule-dependent long-distance movement of peroxisomes occurs in mammalian cells. However, its molecular mechanisms remain undefined. In this study, we identified three distinct splicing variants of human mitochondrial Rho GTPase-1 (Miro1), each containing amino acid sequence insertions 1 (named Miro1-var2), 2 (Miro1-var3), and both 1 and 2 (Miro1-var4), respectively, at upstream of the transmembrane domain. Miro1-var4 and Miro1-var2 are localized to peroxisomes in a manner dependent on the insertion 1 that is recognized by the cytosolic receptor Pex19p. Exogenous expression of Miro1-var4 induces accumulation of peroxisomes at the cell periphery and augments long-range movement of peroxisomes along microtubules. Depletion of all Miro1 variants by knocking down MIRO1 suppresses the long-distance movement of peroxisomes. Such abrogated movement is restored by reexpression of peroxisomal Miro1 variants. Collectively, our findings identify for the first time peroxisome-localized Miro1 variants as adapter proteins that link peroxisomes to the microtubule-dependent transport complexes including TRAK2 in the intracellular translocation of peroxisomes in mammalian cells.
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Affiliation(s)
- Kanji Okumoto
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan.,Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuaki Ono
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Ryusuke Toyama
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Ayako Shimomura
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Aiko Nagata
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Yukio Fujiki
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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30
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BCL-2 family proteins: changing partners in the dance towards death. Cell Death Differ 2017; 25:65-80. [PMID: 29149100 PMCID: PMC5729540 DOI: 10.1038/cdd.2017.186] [Citation(s) in RCA: 932] [Impact Index Per Article: 133.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/17/2017] [Accepted: 09/19/2017] [Indexed: 02/06/2023] Open
Abstract
The BCL-2 family of proteins controls cell death primarily by direct binding interactions that regulate mitochondrial outer membrane permeabilization (MOMP) leading to the irreversible release of intermembrane space proteins, subsequent caspase activation and apoptosis. The affinities and relative abundance of the BCL-2 family proteins dictate the predominate interactions between anti-apoptotic and pro-apoptotic BCL-2 family proteins that regulate MOMP. We highlight the core mechanisms of BCL-2 family regulation of MOMP with an emphasis on how the interactions between the BCL-2 family proteins govern cell fate. We address the critical importance of both the concentration and affinities of BCL-2 family proteins and show how differences in either can greatly change the outcome. Further, we explain the importance of using full-length BCL-2 family proteins (versus truncated versions or peptides) to parse out the core mechanisms of MOMP regulation by the BCL-2 family. Finally, we discuss how post-translational modifications and differing intracellular localizations alter the mechanisms of apoptosis regulation by BCL-2 family proteins. Successful therapeutic intervention of MOMP regulation in human disease requires an understanding of the factors that mediate the major binding interactions between BCL-2 family proteins in cells.
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31
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Lutfullahoğlu-Bal G, Keskin A, Seferoğlu AB, Dunn CD. Bacterial tail anchors can target to the mitochondrial outer membrane. Biol Direct 2017; 12:16. [PMID: 28738827 PMCID: PMC5525287 DOI: 10.1186/s13062-017-0187-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/10/2017] [Indexed: 01/15/2023] Open
Abstract
Background During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria. Currently, a widely conserved translocon allows proteins to pass from the cytosol into mitochondria, but how proteins encoded outside of mitochondria were first directed to these organelles at the dawn of eukaryogenesis is not clear. Because several proteins targeted by a carboxyl-terminal tail anchor (TA) appear to have the ability to insert spontaneously into the mitochondrial outer membrane (OM), it is possible that self-inserting, tail-anchored polypeptides obtained from bacteria might have formed the first gate allowing proteins to access mitochondria from the cytosol. Results Here, we tested whether bacterial TAs are capable of targeting to mitochondria. In a survey of proteins encoded by the proteobacterium Escherichia coli, predicted TA sequences were directed to specific subcellular locations within the yeast Saccharomyces cerevisiae. Importantly, TAs obtained from DUF883 family members ElaB and YqjD were abundantly localized to and inserted at the mitochondrial OM. Conclusions Our results support the notion that eukaryotic cells are able to utilize membrane-targeting signals present in bacterial proteins obtained by lateral gene transfer, and our findings make plausible a model in which mitochondrial protein translocation was first driven by tail-anchored proteins. Reviewers This article was reviewed by Michael Ryan and Thomas Simmen. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0187-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Abdurrahman Keskin
- Department of Molecular Biology and Genetics, Koç University, 34450 Sarıyer, İstanbul, Turkey.,Present Address: Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Ayşe Bengisu Seferoğlu
- Department of Molecular Biology and Genetics, Koç University, 34450 Sarıyer, İstanbul, Turkey
| | - Cory D Dunn
- Department of Molecular Biology and Genetics, Koç University, 34450 Sarıyer, İstanbul, Turkey. .,Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
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32
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Straub SP, Stiller SB, Wiedemann N, Pfanner N. Dynamic organization of the mitochondrial protein import machinery. Biol Chem 2017; 397:1097-1114. [PMID: 27289000 DOI: 10.1515/hsz-2016-0145] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 05/17/2016] [Indexed: 01/12/2023]
Abstract
Mitochondria contain elaborate machineries for the import of precursor proteins from the cytosol. The translocase of the outer mitochondrial membrane (TOM) performs the initial import of precursor proteins and transfers the precursors to downstream translocases, including the presequence translocase and the carrier translocase of the inner membrane, the mitochondrial import and assembly machinery of the intermembrane space, and the sorting and assembly machinery of the outer membrane. Although the protein translocases can function as separate entities in vitro, recent studies revealed a close and dynamic cooperation of the protein import machineries to facilitate efficient transfer of precursor proteins in vivo. In addition, protein translocases were found to transiently interact with distinct machineries that function in the respiratory chain or in the maintenance of mitochondrial membrane architecture. Mitochondrial protein import is embedded in a regulatory network that ensures protein biogenesis, membrane dynamics, bioenergetic activity and quality control.
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33
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Ouellet M, Guillebaud G, Gervais V, Lupien St-Pierre D, Germain M. A novel algorithm identifies stress-induced alterations in mitochondrial connectivity and inner membrane structure from confocal images. PLoS Comput Biol 2017. [PMID: 28640814 PMCID: PMC5501662 DOI: 10.1371/journal.pcbi.1005612] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondria exist as a highly interconnected network that is exquisitely sensitive to variations in nutrient availability, as well as a large array of cellular stresses. Changes in length and connectivity of this network, as well as alterations in the mitochondrial inner membrane (cristae), regulate cell fate by controlling metabolism, proliferation, differentiation, and cell death. Given the key roles of mitochondrial dynamics, the process by which mitochondria constantly fuse and fragment, the measure of mitochondrial length and connectivity provides crucial information on the health and activity of various cell populations. However, despite the importance of accurately measuring mitochondrial networks, the tools required to rapidly and accurately provide this information are lacking. Here, we developed a novel probabilistic approach to automatically measure mitochondrial length distribution and connectivity from confocal images. This method accurately identified mitochondrial changes caused by starvation or the inhibition of mitochondrial function. In addition, we successfully used the algorithm to measure changes in mitochondrial inner membrane/matrix occurring in response to Complex III inhibitors. As cristae rearrangements play a critical role in metabolic regulation and cell survival, this provides a rapid method to screen for proteins or compounds affecting this process. The algorithm will thus provide a robust tool to dissect the molecular mechanisms underlying the key roles of mitochondria in the regulation of cell fate.
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Affiliation(s)
- Mathieu Ouellet
- Département de Chimie, Biochimie et Physique, Université du Québec à Trois-Rivières, Trois-Rivières, Quebec, Canada
- Groupe de Recherche en Signalisation Cellulaire, Université du Québec à Trois-Rivières, Trois-Rivières, Quebec, Canada
- Centre de Recherche Biomed, Université du Québec à Trois-Rivières, Trois-Rivières, Quebec, Canada
| | - Gérald Guillebaud
- Groupe de Recherche en Signalisation Cellulaire, Université du Québec à Trois-Rivières, Trois-Rivières, Quebec, Canada
- Centre de Recherche Biomed, Université du Québec à Trois-Rivières, Trois-Rivières, Quebec, Canada
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, Quebec, Canada
| | - Valerie Gervais
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, Quebec, Canada
| | - David Lupien St-Pierre
- Département de Génie Industriel, Université du Québec à Trois-Rivières, Trois-Rivières, Quebec, Canada
| | - Marc Germain
- Groupe de Recherche en Signalisation Cellulaire, Université du Québec à Trois-Rivières, Trois-Rivières, Quebec, Canada
- Centre de Recherche Biomed, Université du Québec à Trois-Rivières, Trois-Rivières, Quebec, Canada
- Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, Quebec, Canada
- * E-mail:
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34
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Costello JL, Castro IG, Camões F, Schrader TA, McNeall D, Yang J, Giannopoulou EA, Gomes S, Pogenberg V, Bonekamp NA, Ribeiro D, Wilmanns M, Jedd G, Islinger M, Schrader M. Predicting the targeting of tail-anchored proteins to subcellular compartments in mammalian cells. J Cell Sci 2017; 130:1675-1687. [PMID: 28325759 PMCID: PMC5450235 DOI: 10.1242/jcs.200204] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/14/2017] [Indexed: 12/22/2022] Open
Abstract
Tail-anchored (TA) proteins contain a single transmembrane domain (TMD) at the C-terminus that anchors them to the membranes of organelles where they mediate critical cellular processes. Accordingly, mutations in genes encoding TA proteins have been identified in a number of severe inherited disorders. Despite the importance of correctly targeting a TA protein to its appropriate membrane, the mechanisms and signals involved are not fully understood. In this study, we identify additional peroxisomal TA proteins, discover more proteins that are present on multiple organelles, and reveal that a combination of TMD hydrophobicity and tail charge determines targeting to distinct organelle locations in mammals. Specifically, an increase in tail charge can override a hydrophobic TMD signal and re-direct a protein from the ER to peroxisomes or mitochondria and vice versa. We show that subtle changes in those parameters can shift TA proteins between organelles, explaining why peroxisomes and mitochondria have many of the same TA proteins. This enabled us to associate characteristic physicochemical parameters in TA proteins with particular organelle groups. Using this classification allowed successful prediction of the location of uncharacterized TA proteins for the first time.
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Affiliation(s)
| | - Inês G Castro
- Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Fátima Camões
- Centre for Cell Biology/Institute of Biomedicine & Department of Biology, University of Aveiro, Aveiro 3810-193, Portugal
| | | | | | - Jing Yang
- Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore
| | | | - Sílvia Gomes
- Centre for Cell Biology/Institute of Biomedicine & Department of Biology, University of Aveiro, Aveiro 3810-193, Portugal
| | | | - Nina A Bonekamp
- Centre for Cell Biology/Institute of Biomedicine & Department of Biology, University of Aveiro, Aveiro 3810-193, Portugal
| | - Daniela Ribeiro
- Centre for Cell Biology/Institute of Biomedicine & Department of Biology, University of Aveiro, Aveiro 3810-193, Portugal
| | | | - Gregory Jedd
- Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore
| | - Markus Islinger
- Institute of Neuroanatomy, Center for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Mannheim 68167, Germany
| | - Michael Schrader
- Biosciences, University of Exeter, Exeter EX4 4QD, UK
- Centre for Cell Biology/Institute of Biomedicine & Department of Biology, University of Aveiro, Aveiro 3810-193, Portugal
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35
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Birkinshaw RW, Czabotar PE. The BCL-2 family of proteins and mitochondrial outer membrane permeabilisation. Semin Cell Dev Biol 2017; 72:152-162. [PMID: 28396106 DOI: 10.1016/j.semcdb.2017.04.001] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/03/2017] [Accepted: 04/06/2017] [Indexed: 01/24/2023]
Abstract
Apoptosis is a form of programmed cell death critical for the development and homeostasis of multicellular organisms. A key event within the mitochondrial pathway to apoptosis is the permeabilisation of the mitochondrial outer membrane (MOM), a point of no return in apoptotic progression. This event is governed by a complex interplay of interactions between BCL-2 family members. Here we discuss the roles of opposing factions within the family. We focus on the structural details of these interactions, how they promote or prevent apoptosis and recent developments towards understanding the conformational changes of BAK and BAX that lead to MOM permeabilisation. These interactions and structural insights are of particular interest for drug discovery, as highlighted by the development of therapeutics that target pro-survival family members and restore apoptosis in cancer cells.
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Affiliation(s)
- Richard W Birkinshaw
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia.
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36
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Prasai K. Regulation of mitochondrial structure and function by protein import: A current review. ACTA ACUST UNITED AC 2017; 24:107-122. [PMID: 28400074 DOI: 10.1016/j.pathophys.2017.03.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 12/14/2022]
Abstract
By generating the majority of a cell's ATP, mitochondria permit a vast range of reactions necessary for life. Mitochondria also perform other vital functions including biogenesis and assembly of iron-sulfur proteins, maintenance of calcium homeostasis, and activation of apoptosis. Accordingly, mitochondrial dysfunction has been linked with the pathology of many clinical conditions including cancer, type 2 diabetes, cardiomyopathy, and atherosclerosis. The ongoing maintenance of mitochondrial structure and function requires the import of nuclear-encoded proteins and for this reason, mitochondrial protein import is indispensible for cell viability. As mitochondria play central roles in determining if cells live or die, a comprehensive understanding of mitochondrial structure, protein import, and function is necessary for identifying novel drugs that may destroy harmful cells while rescuing or protecting normal ones to preserve tissue integrity. This review summarizes our current knowledge on mitochondrial architecture, mitochondrial protein import, and mitochondrial function. Our current comprehension of how mitochondrial functions maintain cell homeostasis and how cell death occurs as a result of mitochondrial stress are also discussed.
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Affiliation(s)
- Kanchanjunga Prasai
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130, USA.
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37
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Abstract
Mitochondria are essential organelles with numerous functions in cellular metabolism and homeostasis. Most of the >1,000 different mitochondrial proteins are synthesized as precursors in the cytosol and are imported into mitochondria by five transport pathways. The protein import machineries of the mitochondrial membranes and aqueous compartments reveal a remarkable variability of mechanisms for protein recognition, translocation, and sorting. The protein translocases do not operate as separate entities but are connected to each other and to machineries with functions in energetics, membrane organization, and quality control. Here, we discuss the versatility and dynamic organization of the mitochondrial protein import machineries. Elucidating the molecular mechanisms of mitochondrial protein translocation is crucial for understanding the integration of protein translocases into a large network that controls organelle biogenesis, function, and dynamics.
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Affiliation(s)
- Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, and BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany; ,
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, and BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany; ,
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38
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Hosoi KI, Miyata N, Mukai S, Furuki S, Okumoto K, Cheng EH, Fujiki Y. The VDAC2-BAK axis regulates peroxisomal membrane permeability. J Cell Biol 2017; 216:709-722. [PMID: 28174205 PMCID: PMC5350511 DOI: 10.1083/jcb.201605002] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 09/23/2016] [Accepted: 01/12/2017] [Indexed: 11/22/2022] Open
Abstract
Peroxisomal biogenesis disorders (PBDs) are fatal genetic diseases consisting of 14 complementation groups (CGs). We previously isolated a peroxisome-deficient Chinese hamster ovary cell mutant, ZP114, which belongs to none of these CGs. Using a functional screening strategy, VDAC2 was identified as rescuing the peroxisomal deficiency of ZP114 where VDAC2 expression was not detected. Interestingly, knockdown of BAK or overexpression of the BAK inhibitors BCL-XL and MCL-1 restored peroxisomal biogenesis in ZP114 cells. Although VDAC2 is not localized to the peroxisome, loss of VDAC2 shifts the localization of BAK from mitochondria to peroxisomes, resulting in peroxisomal deficiency. Introduction of peroxisome-targeted BAK harboring the Pex26p transmembrane region into wild-type cells resulted in the release of peroxisomal matrix proteins to cytosol. Moreover, overexpression of BAK activators PUMA and BIM permeabilized peroxisomes in a BAK-dependent manner. Collectively, these findings suggest that BAK plays a role in peroxisomal permeability, similar to mitochondrial outer membrane permeabilization.
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Affiliation(s)
- Ken-Ichiro Hosoi
- Department of Biology, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan.,Graduate School of Systems Life Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Non Miyata
- Department of Biology, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Satoru Mukai
- Department of Biology, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Satomi Furuki
- Department of Biology, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan.,Graduate School of Systems Life Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kanji Okumoto
- Department of Biology, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan.,Graduate School of Systems Life Sciences, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Emily H Cheng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
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39
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Evidence for Amino Acid Snorkeling from a High-Resolution, In Vivo Analysis of Fis1 Tail-Anchor Insertion at the Mitochondrial Outer Membrane. Genetics 2016; 205:691-705. [PMID: 28007883 PMCID: PMC5289845 DOI: 10.1534/genetics.116.196428] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/12/2016] [Indexed: 01/03/2023] Open
Abstract
Proteins localized to mitochondria by a carboxyl-terminal tail anchor (TA) play roles in apoptosis, mitochondrial dynamics, and mitochondrial protein import. To reveal characteristics of TAs that may be important for mitochondrial targeting, we focused our attention upon the TA of the Saccharomyces cerevisiaeFis1 protein. Specifically, we generated a library of Fis1p TA variants fused to the Gal4 transcription factor, then, using next-generation sequencing, revealed which Fis1p TA mutations inhibited membrane insertion and allowed Gal4p activity in the nucleus. Prompted by our global analysis, we subsequently analyzed the ability of individual Fis1p TA mutants to localize to mitochondria. Our findings suggest that the membrane-associated domain of the Fis1p TA may be bipartite in nature, and we encountered evidence that the positively charged patch at the carboxyl terminus of Fis1p is required for both membrane insertion and organelle specificity. Furthermore, lengthening or shortening of the Fis1p TA by up to three amino acids did not inhibit mitochondrial targeting, arguing against a model in which TA length directs insertion of TAs to distinct organelles. Most importantly, positively charged residues were more acceptable at several positions within the membrane-associated domain of the Fis1p TA than negatively charged residues. These findings, emerging from the first high-resolution analysis of an organelle targeting sequence by deep mutational scanning, provide strong, in vivo evidence that lysine and arginine can “snorkel,” or become stably incorporated within a lipid bilayer by placing terminal charges of their side chains at the membrane interface.
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40
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Ellenrieder L, Mårtensson CU, Becker T. Biogenesis of mitochondrial outer membrane proteins, problems and diseases. Biol Chem 2016; 396:1199-213. [PMID: 25980382 DOI: 10.1515/hsz-2015-0170] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 05/08/2015] [Indexed: 12/25/2022]
Abstract
Proteins of the mitochondrial outer membrane are synthesized as precursors on cytosolic ribosomes and sorted via internal targeting sequences to mitochondria. Two different types of integral outer membrane proteins exist: proteins with a transmembrane β-barrel and proteins embedded by a single or multiple α-helices. The import pathways of these two types of membrane proteins differ fundamentally. Precursors of β-barrel proteins are first imported across the outer membrane via the translocase of the outer membrane (TOM complex). The TOM complex is coupled to the sorting and assembly machinery (SAM complex), which catalyzes folding and membrane insertion of these precursors. The mitochondrial import machinery (MIM complex) promotes import of proteins with multiple α-helical membrane spans. Depending on the topology precursors of proteins with a single α-helical membrane anchor are imported via several distinct routes. We summarize current models and open questions of biogenesis of mitochondrial outer membrane proteins and discuss the impact of malfunctions of protein sorting on the development of diseases.
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41
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Luna-Vargas MP, Chipuk JE. The deadly landscape of pro-apoptotic BCL-2 proteins in the outer mitochondrial membrane. FEBS J 2016; 283:2676-89. [PMID: 26662859 PMCID: PMC4907887 DOI: 10.1111/febs.13624] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/11/2015] [Accepted: 12/08/2015] [Indexed: 01/06/2023]
Abstract
Apoptosis is a biological process that removes damaged, excess or infected cells through a genetically controlled mechanism. This process plays a crucial role in organismal development, immunity and tissue homeostasis, and alterations in apoptosis contribute to human diseases including cancer and auto-immunity. In the past two decades, significant efforts have focused on understanding the function of the BCL-2 proteins, a complex family of pro-survival and pro-apoptotic α-helical proteins that directly control the mitochondrial pathway of apoptosis. Diverse structural investigations of the BCL-2 family members have broadened our mechanistic understanding of their individual functions. However, an often over-looked aspect of the mitochondrial pathway of apoptosis is how the BCL-2 family specifically interacts with and targets the outer mitochondrial membrane to initiate apoptosis. Structural information on the relationship between the BCL-2 family and the outer mitochondrial membrane is missing; likewise, knowledge of the biophysical mechanisms by which the outer mitochondrial membrane affects and effects apoptosis is lacking. In this mini-review, we provide a current overview of the BCL-2 family members and discuss the latest structural insights into BAK/BAX activation and oligomerization in the context of the outer mitochondrial membrane and mitochondrial biology.
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Affiliation(s)
- Mark P.A. Luna-Vargas
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Jerry E. Chipuk
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- The Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
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42
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Itakura E, Zavodszky E, Shao S, Wohlever ML, Keenan RJ, Hegde RS. Ubiquilins Chaperone and Triage Mitochondrial Membrane Proteins for Degradation. Mol Cell 2016; 63:21-33. [PMID: 27345149 PMCID: PMC4942676 DOI: 10.1016/j.molcel.2016.05.020] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/04/2016] [Accepted: 05/16/2016] [Indexed: 12/14/2022]
Abstract
We investigated how mitochondrial membrane proteins remain soluble in the cytosol until their delivery to mitochondria or degradation at the proteasome. We show that Ubiquilin family proteins bind transmembrane domains in the cytosol to prevent aggregation and temporarily allow opportunities for membrane targeting. Over time, Ubiquilins recruit an E3 ligase to ubiquitinate bound clients. The attached ubiquitin engages Ubiquilin's UBA domain, normally bound to an intramolecular UBL domain, and stabilizes the Ubiquilin-client complex. This conformational change precludes additional chances at membrane targeting for the client, while simultaneously freeing Ubiquilin's UBL domain for targeting to the proteasome. Loss of Ubiquilins by genetic ablation or sequestration in polyglutamine aggregates leads to accumulation of non-inserted mitochondrial membrane protein precursors. These findings define Ubiquilins as a family of chaperones for cytosolically exposed transmembrane domains and explain how they use ubiquitin to triage clients for degradation via coordinated intra- and intermolecular interactions.
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Affiliation(s)
- Eisuke Itakura
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Department of Biology, Faculty of Science, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Eszter Zavodszky
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sichen Shao
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Matthew L Wohlever
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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VDAC2-specific cellular functions and the underlying structure. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2503-14. [PMID: 27116927 DOI: 10.1016/j.bbamcr.2016.04.020] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/20/2016] [Accepted: 04/20/2016] [Indexed: 01/30/2023]
Abstract
Voltage Dependent Anion-selective Channel 2 (VDAC2) contributes to oxidative metabolism by sharing a role in solute transport across the outer mitochondrial membrane (OMM) with other isoforms of the VDAC family, VDAC1 and VDAC3. Recent studies revealed that VDAC2 also has a distinctive role in mediating sarcoplasmic reticulum to mitochondria local Ca(2+) transport at least in cardiomyocytes, which is unlikely to be explained simply by the expression level of VDAC2. Furthermore, a strictly isoform-dependent VDAC2 function was revealed in the mitochondrial import and OMM-permeabilizing function of pro-apoptotic Bcl-2 family proteins, primarily Bak in many cell types. In addition, emerging evidence indicates a variety of other isoform-specific engagements for VDAC2. Since VDAC isoforms display 75% sequence similarity, the distinctive structure underlying VDAC2-specific functions is an intriguing problem. In this paper we summarize studies of VDAC2 structure and functions, which suggest a fundamental and exclusive role for VDAC2 in health and disease. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou.
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44
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Liu Y, Yagita Y, Fujiki Y. Assembly of Peroxisomal Membrane Proteins via the Direct Pex19p-Pex3p Pathway. Traffic 2016; 17:433-55. [PMID: 26777132 DOI: 10.1111/tra.12376] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 02/03/2023]
Abstract
Correct targeting of peroxisomal membrane proteins (PMPs) is essential for the formation and maintenance of functional peroxisomes. Activities of Pex19p to interact with PMPs on one hand and Pex3p on the other, including formation of ternary complexes between Pex19p, PMP and Pex3p, strongly support posttranslational translocation of PMPs via the Pex19p- and Pex3p-dependent direct pathway, termed the class I pathway. However, it remains elusive whether Pex19p-PMP complexes are indeed capable of being imported into peroxisomal membranes through the interaction between Pex19p and Pex3p. We resolve this issue by investigating the targeting process of several topologically distinct PMPs, including multimembrane spanning PMPs. We show here that Pex19p forms cytosolic complexes with PMPs and directly translocates them to peroxisomes. Using a semi-intact mammalian cell-based import assay system, we prove that PMPs in the cytosolic complexes are imported into peroxisomes via the interaction between cargo-loaded Pex19p and Pex3p. Furthermore, we demonstrate for the first time that peroxisomal targeting of ATAD1, an N-terminally signal-anchored protein that resides on both mitochondria and peroxisomes, is also achieved through the Pex19p- and Pex3p-dependent class I pathway. Together, our results suggest that translocation of PMPs via the class I pathway is a common event in mammalian cells.
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Affiliation(s)
- Yuqiong Liu
- Graduate School of Systems Life Sciences, Kyushu University Graduate School, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yuichi Yagita
- Department of Biology, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka, 819-0395, Japan.,Present address: Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
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Otera H, Miyata N, Kuge O, Mihara K. Drp1-dependent mitochondrial fission via MiD49/51 is essential for apoptotic cristae remodeling. J Cell Biol 2016; 212:531-44. [PMID: 26903540 PMCID: PMC4772499 DOI: 10.1083/jcb.201508099] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/26/2016] [Indexed: 11/25/2022] Open
Abstract
Drp1-dependent mitochondrial fission through MiD49 and MiD51, but not through Mff, is essential for cristae remodeling to facilitate cytochrome c release during the early phase of intrinsic apoptosis. Mitochondrial fission facilitates cytochrome c release from the intracristae space into the cytoplasm during intrinsic apoptosis, although how the mitochondrial fission factor Drp1 and its mitochondrial receptors Mff, MiD49, and MiD51 are involved in this reaction remains elusive. Here, we analyzed the functional division of these receptors with their knockout (KO) cell lines. In marked contrast to Mff-KO cells, MiD49/MiD51-KO and Drp1-KO cells completely resisted cristae remodeling and cytochrome c release during apoptosis. This phenotype in MiD49/51-KO cells, but not Drp1-KO cells, was completely abolished by treatments disrupting cristae structure such as OPA1 depletion. Unexpectedly, OPA1 oligomers generally thought to resist cytochrome c release by stabilizing the cristae structure were similarly disassembled in Drp1-KO and MiD49/51-KO cells, indicating that disassembly of OPA1 oligomers is not directly linked to cristae remodeling for cytochrome c release. Together, these results indicate that Drp1-dependent mitochondrial fission through MiD49/MiD51 regulates cristae remodeling during intrinsic apoptosis.
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Affiliation(s)
- Hidenori Otera
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Non Miyata
- Department of Chemistry, Faculty of Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Osamu Kuge
- Department of Chemistry, Faculty of Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Katsuyoshi Mihara
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 819-0395, Japan
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Fueller J, Egorov MV, Walther KA, Sabet O, Mallah J, Grabenbauer M, Kinkhabwala A. Subcellular Partitioning of Protein Tyrosine Phosphatase 1B to the Endoplasmic Reticulum and Mitochondria Depends Sensitively on the Composition of Its Tail Anchor. PLoS One 2015; 10:e0139429. [PMID: 26431424 PMCID: PMC4592070 DOI: 10.1371/journal.pone.0139429] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 09/14/2015] [Indexed: 01/15/2023] Open
Abstract
The canonical protein tyrosine phosphatase PTP1B is an important regulator of diverse cellular signaling networks. PTP1B has long been thought to exert its influence solely from its perch on the endoplasmic reticulum (ER); however, an additional subpopulation of PTP1B has recently been detected in mitochondria extracted from rat brain tissue. Here, we show that PTP1B’s mitochondrial localization is general (observed across diverse mammalian cell lines) and sensitively dependent on the transmembrane domain length, C-terminal charge and hydropathy of its short (≤35 amino acid) tail anchor. Our electron microscopy of specific DAB precipitation revealed that PTP1B localizes via its tail anchor to the outer mitochondrial membrane (OMM), with fluorescence lifetime imaging microscopy establishing that this OMM pool contributes to the previously reported cytoplasmic interaction of PTP1B with endocytosed epidermal growth factor receptor. We additionally examined the mechanism of PTP1B’s insertion into the ER membrane through heterologous expression of PTP1B’s tail anchor in wild-type yeast and yeast mutants of major conserved ER insertion pathways: In none of these yeast strains was ER targeting significantly impeded, providing in vivo support for the hypothesis of spontaneous membrane insertion (as previously demonstrated in vitro). Further functional elucidation of the newly recognized mitochondrial pool of PTP1B will likely be important for understanding its complex roles in cellular responses to external stimuli, cell proliferation and diseased states.
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Affiliation(s)
- Julia Fueller
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Mikhail V. Egorov
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
- Institute of Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany
| | - Kirstin A. Walther
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Ola Sabet
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Jana Mallah
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Markus Grabenbauer
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
- Institute of Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany
| | - Ali Kinkhabwala
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
- * E-mail:
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47
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Motifs of VDAC2 required for mitochondrial Bak import and tBid-induced apoptosis. Proc Natl Acad Sci U S A 2015; 112:E5590-9. [PMID: 26417093 DOI: 10.1073/pnas.1510574112] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Voltage-dependent anion channel (VDAC) proteins are major components of the outer mitochondrial membrane. VDAC has three isoforms with >70% sequence similarity and redundant roles in metabolite and ion transport. However, only Vdac2(-/-) (V2(-/-)) mice are embryonic lethal, indicating a unique and fundamental function of VDAC2 (V2). Recently, a specific V2 requirement was demonstrated for mitochondrial Bak import and truncated Bid (tBid)-induced apoptosis. To determine the relevant domain(s) of V2 involved, VDAC1 (V1) and V2 chimeric constructs were created and used to rescue V2(-/-) fibroblasts. Surprisingly, the commonly cited V2-specific N-terminal extension and cysteines were found to be dispensable for Bak import and high tBid sensitivity. In gain-of-function studies, V2 (123-179) was the minimal sequence sufficient to render V1 competent to support Bak insertion. Furthermore, in loss-of-function experiments, T168 and D170 were identified as critical residues. These motifs are conserved in zebrafish V2 (zfV2) that also rescued V2-deficient fibroblasts. Because high-resolution structures of zfV2 and mammalian V1 have become available, we could superimpose these structures and recognized that the critical V2-specific residues help to create a distinctive open "pocket" on the cytoplasmic surface that could facilitate Bak recruitment.
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48
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Bohnert M, Pfanner N, van der Laan M. Mitochondrial machineries for insertion of membrane proteins. Curr Opin Struct Biol 2015; 33:92-102. [DOI: 10.1016/j.sbi.2015.07.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/13/2015] [Accepted: 07/27/2015] [Indexed: 01/08/2023]
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49
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Cooperation of protein machineries in mitochondrial protein sorting. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1119-29. [DOI: 10.1016/j.bbamcr.2015.01.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/16/2015] [Accepted: 01/20/2015] [Indexed: 02/07/2023]
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50
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Alsop AE, Fennell SC, Bartolo RC, Tan IKL, Dewson G, Kluck RM. Dissociation of Bak α1 helix from the core and latch domains is required for apoptosis. Nat Commun 2015; 6:6841. [PMID: 25880232 DOI: 10.1038/ncomms7841] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 03/03/2015] [Indexed: 02/06/2023] Open
Abstract
During apoptosis, Bak permeabilizes mitochondria after undergoing major conformational changes, including poorly defined N-terminal changes. Here, we characterize those changes using 11 antibodies that were epitope mapped using peptide arrays and mutagenesis. After Bak activation by Bid, epitopes throughout the α1 helix are exposed indicating complete dissociation of α1 from α2 in the core and from α6-α8 in the latch. Moreover, disulfide tethering of α1 to α2 or α6 blocks cytochrome c release, suggesting that α1 dissociation is required for further conformational changes during apoptosis. Assaying epitope exposure when α1 is tethered shows that Bid triggers α2 movement, followed by α1 dissociation. However, α2 reaches its final position only after α1 dissociates from the latch. Thus, α1 dissociation is a key step in unfolding Bak into three major components, the N terminus, the core (α2-α5) and the latch (α6-α8).
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Affiliation(s)
- Amber E Alsop
- 1] The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Stephanie C Fennell
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Ray C Bartolo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Iris K L Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Grant Dewson
- 1] The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ruth M Kluck
- 1] The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
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