1
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Synthetic negative genome screen of the GPN-loop GTPase NPA3 in Saccharomyces cerevisiae. Curr Genet 2022; 68:343-360. [PMID: 35660944 DOI: 10.1007/s00294-022-01243-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/21/2022] [Accepted: 04/30/2022] [Indexed: 11/03/2022]
Abstract
The GPN-loop GTPase Npa3 is encoded by an essential gene in the yeast Saccharomyces cerevisiae. Npa3 plays a critical role in the assembly and nuclear accumulation of RNA polymerase II (RNAPII), a function that may explain its essentiality. Genetic interactions describe the extent to which a mutation in a particular gene affects a specific phenotype when co-occurring with an alteration in a second gene. Discovering synthetic negative genetic interactions has long been used as a tool to delineate the functional relatedness between pairs of genes participating in common or compensatory biological pathways. Previously, our group showed that nuclear targeting and transcriptional activity of RNAPII were unaffected in cells expressing exclusively a C-terminal truncated mutant version of Npa3 (npa3∆C) lacking the last 106 residues naturally absent from the single GPN protein in Archaea, but universally conserved in all Npa3 orthologs of eukaryotes. To gain insight into novel cellular functions for Npa3, we performed here a genome-wide Synthetic Genetic Array (SGA) study coupled to bulk fluorescence monitoring to identify negative genetic interactions of NPA3 by crossing an npa3∆C strain with a 4,389 nonessential gene-deletion collection. This genetic screen revealed previously unknown synthetic negative interactions between NPA3 and 15 genes. Our results revealed that the Npa3 C-terminal tail extension regulates the participation of this essential GTPase in previously unknown biological processes related to mitochondrial homeostasis and ribosome biogenesis.
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2
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Diederichs KA, Pitt AS, Varughese JT, Hackel TN, Buchanan SK, Shaw PL. Mechanistic insights into fungal mitochondrial outer membrane protein biogenesis. Curr Opin Struct Biol 2022; 74:102383. [DOI: 10.1016/j.sbi.2022.102383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/11/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
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3
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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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4
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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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5
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Diederichs KA, Buchanan SK, Botos I. Building Better Barrels - β-barrel Biogenesis and Insertion in Bacteria and Mitochondria. J Mol Biol 2021; 433:166894. [PMID: 33639212 PMCID: PMC8292188 DOI: 10.1016/j.jmb.2021.166894] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 01/20/2023]
Abstract
β-barrel proteins are folded and inserted into outer membranes by multi-subunit protein complexes that are conserved across different types of outer membranes. In Gram-negative bacteria this complex is the barrel-assembly machinery (BAM), in mitochondria it is the sorting and assembly machinery (SAM) complex, and in chloroplasts it is the outer envelope protein Oep80. Mitochondrial β-barrel precursor proteins are translocated from the cytoplasm to the intermembrane space by the translocase of the outer membrane (TOM) complex, and stabilized by molecular chaperones before interaction with the assembly machinery. Outer membrane bacterial BamA interacts with four periplasmic accessory proteins, whereas mitochondrial Sam50 interacts with two cytoplasmic accessory proteins. Despite these major architectural differences between BAM and SAM complexes, their core proteins, BamA and Sam50, seem to function the same way. Based on the new SAM complex structures, we propose that the mitochondrial β-barrel folding mechanism follows the budding model with barrel-switching aiding in the release of new barrels. We also built a new molecular model for Tom22 interacting with Sam37 to identify regions that could mediate TOM-SAM supercomplex formation.
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Affiliation(s)
- Kathryn A Diederichs
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Istvan Botos
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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6
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Takeda H, Tsutsumi A, Nishizawa T, Lindau C, Busto JV, Wenz LS, Ellenrieder L, Imai K, Straub SP, Mossmann W, Qiu J, Yamamori Y, Tomii K, Suzuki J, Murata T, Ogasawara S, Nureki O, Becker T, Pfanner N, Wiedemann N, Kikkawa M, Endo T. Mitochondrial sorting and assembly machinery operates by β-barrel switching. Nature 2021; 590:163-169. [PMID: 33408415 DOI: 10.1038/s41586-020-03113-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023]
Abstract
The mitochondrial outer membrane contains so-called β-barrel proteins, which allow communication between the cytosol and the mitochondrial interior1-3. Insertion of β-barrel proteins into the outer membrane is mediated by the multisubunit mitochondrial sorting and assembly machinery (SAM, also known as TOB)4-6. Here we use cryo-electron microscopy to determine the structures of two different forms of the yeast SAM complex at a resolution of 2.8-3.2 Å. The dimeric complex contains two copies of the β-barrel channel protein Sam50-Sam50a and Sam50b-with partially open lateral gates. The peripheral membrane proteins Sam35 and Sam37 cap the Sam50 channels from the cytosolic side, and are crucial for the structural and functional integrity of the dimeric complex. In the second complex, Sam50b is replaced by the β-barrel protein Mdm10. In cooperation with Sam50a, Sam37 recruits and traps Mdm10 by penetrating the interior of its laterally closed β-barrel from the cytosolic side. The substrate-loaded SAM complex contains one each of Sam50, Sam35 and Sam37, but neither Mdm10 nor a second Sam50, suggesting that Mdm10 and Sam50b function as placeholders for a β-barrel substrate released from Sam50a. Our proposed mechanism for dynamic switching of β-barrel subunits and substrate explains how entire precursor proteins can fold in association with the mitochondrial machinery for β-barrel assembly.
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Affiliation(s)
- Hironori Takeda
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kyoto, Japan
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Caroline Lindau
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jon V Busto
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lena-Sophie Wenz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Sanofi Deutschland GmbH, Frankfurt am Main, Germany
| | - Lars Ellenrieder
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Novartis Pharma AG, Basel, Switzerland
| | - Kenichiro Imai
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.,Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Sebastian P Straub
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,Sanofi-Aventis (Suisse) ag, Vernier, Switzerland
| | - Waltraut Mossmann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jian Qiu
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Yu Yamamori
- Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.,AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Junko Suzuki
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kyoto, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kyoto, Japan. .,Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kyoto, Japan.
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7
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Lundquist K, Billings E, Bi M, Wellnitz J, Noinaj N. The assembly of β-barrel membrane proteins by BAM and SAM. Mol Microbiol 2020; 115:425-435. [PMID: 33314350 DOI: 10.1111/mmi.14666] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/11/2020] [Indexed: 12/31/2022]
Abstract
Gram-negative bacteria, mitochondria, and chloroplasts all possess an outer membrane populated with a host of β-barrel outer-membrane proteins (βOMPs). These βOMPs play crucial roles in maintaining viability of their hosts, and therefore, it is essential to understand the biogenesis of this class of membrane proteins. In recent years, significant structural and functional advancements have been made toward elucidating this process, which is mediated by the β-barrel assembly machinery (BAM) in Gram-negative bacteria, and by the sorting and assembly machinery (SAM) in mitochondria. Structures of both BAM and SAM have now been reported, allowing a comparison and dissection of the two machineries, with other studies reporting on functional aspects of each. Together, these new insights provide compelling support for the proposed budding mechanism, where each nascent βOMP forms a hybrid-barrel intermediate with BAM/SAM in route to its biogenesis into the membrane. Here, we will review these recent studies and highlight their contributions toward understanding βOMP biogenesis in Gram-negative bacteria and in mitochondria. We will also weigh the evidence supporting each of the two leading mechanistic models for how BAM/SAM function, and offer an outlook on future studies within the field.
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Affiliation(s)
- Karl Lundquist
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Evan Billings
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Maxine Bi
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - James Wellnitz
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA.,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
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8
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Functions of the BamBCDE Lipoproteins Revealed by Bypass Mutations in BamA. J Bacteriol 2020; 202:JB.00401-20. [PMID: 32817097 DOI: 10.1128/jb.00401-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/13/2020] [Indexed: 12/27/2022] Open
Abstract
The heteropentomeric β-barrel assembly machine (BAM complex) is responsible for folding and inserting a diverse array of β-barrel outer membrane proteins (OMPs) into the outer membrane (OM) of Gram-negative bacteria. The BAM complex contains two essential proteins, the β-barrel OMP BamA and a lipoprotein BamD, whereas the auxiliary lipoproteins BamBCE are individually nonessential. Here, we identify and characterize three bamA mutations, the E-to-K change at position 470 (bamAE470K ), the A-to-P change at position 496 (bamAA496P ), and the A-to-S change at position 499 (bamAA499S ), that suppress the otherwise lethal ΔbamD, ΔbamB ΔbamC ΔbamE, and ΔbamC ΔbamD ΔbamE mutations. The viability of cells lacking different combinations of BAM complex lipoproteins provides the opportunity to examine the role of the individual proteins in OMP assembly. Results show that, in wild-type cells, BamBCE share a redundant function; at least one of these lipoproteins must be present to allow BamD to coordinate productively with BamA. Besides BamA regulation, BamD shares an additional essential function that is redundant with a second function of BamB. Remarkably, bamAE470K suppresses both, allowing the construction of a BAM complex composed solely of BamAE470K that is able to assemble OMPs in the absence of BamBCDE. This work demonstrates that the BAM complex lipoproteins do not participate in the catalytic folding of OMP substrates but rather function to increase the efficiency of the assembly process by coordinating and regulating the assembly of diverse OMP substrates.IMPORTANCE The folding and insertion of β-barrel outer membrane proteins (OMPs) are conserved processes in mitochondria, chloroplasts, and Gram-negative bacteria. In Gram-negative bacteria, OMPs are assembled into the outer membrane (OM) by the heteropentomeric β-barrel assembly machine (BAM complex). In this study, we probe the function of the individual BAM proteins and how they coordinate assembly of a diverse family of OMPs. Furthermore, we identify a gain-of-function bamA mutant capable of assembling OMPs independently of all four other BAM proteins. This work advances our understanding of OMP assembly and sheds light on how this process is distinct in Gram-negative bacteria.
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9
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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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The gain-of-function allele bamA E470K bypasses the essential requirement for BamD in β-barrel outer membrane protein assembly. Proc Natl Acad Sci U S A 2020; 117:18737-18743. [PMID: 32675245 DOI: 10.1073/pnas.2007696117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The outer membrane (OM) of gram-negative bacteria confers innate resistance to toxins and antibiotics. Integral β-barrel outer membrane proteins (OMPs) function to establish and maintain the selective permeability of the OM. OMPs are assembled into the OM by the β-barrel assembly machine (BAM), which is composed of one OMP-BamA-and four lipoproteins-BamB, C, D, and E. BamB, C, and E can be removed individually with only minor effects on barrier function; however, depletion of either BamA or BamD causes a global defect in OMP assembly and results in cell death. We have identified a gain-of-function mutation, bamA E470K , that bypasses the requirement for BamD. Although bamD::kan bamA E470K cells exhibit growth and OM barrier defects, they assemble OMPs with surprising robustness. Our results demonstrate that BamD does not play a catalytic role in OMP assembly, but rather functions to regulate the activity of BamA.
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11
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Diederichs KA, Ni X, Rollauer SE, Botos I, Tan X, King MS, Kunji ERS, Jiang J, Buchanan SK. Structural insight into mitochondrial β-barrel outer membrane protein biogenesis. Nat Commun 2020; 11:3290. [PMID: 32620929 PMCID: PMC7335169 DOI: 10.1038/s41467-020-17144-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/13/2020] [Indexed: 11/09/2022] Open
Abstract
In mitochondria, β-barrel outer membrane proteins mediate protein import, metabolite transport, lipid transport, and biogenesis. The Sorting and Assembly Machinery (SAM) complex consists of three proteins that assemble as a 1:1:1 complex to fold β-barrel proteins and insert them into the mitochondrial outer membrane. We report cryoEM structures of the SAM complex from Myceliophthora thermophila, which show that Sam50 forms a 16-stranded transmembrane β-barrel with a single polypeptide-transport-associated (POTRA) domain extending into the intermembrane space. Sam35 and Sam37 are located on the cytosolic side of the outer membrane, with Sam35 capping Sam50, and Sam37 interacting extensively with Sam35. Sam35 and Sam37 each adopt a GST-like fold, with no functional, structural, or sequence similarity to their bacterial counterparts. Structural analysis shows how the Sam50 β-barrel opens a lateral gate to accommodate its substrates.
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Affiliation(s)
- Kathryn A Diederichs
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Xiaodan Ni
- Laboratory of Membrane Proteins and Structural Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sarah E Rollauer
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
- Vertex Pharmaceuticals, 50 Northern Avenue, Boston, MA, 02210, USA
| | - Istvan Botos
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Xiaofeng Tan
- Laboratory of Membrane Proteins and Structural Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Martin S King
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Edmund R S Kunji
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Jiansen Jiang
- Laboratory of Membrane Proteins and Structural Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
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12
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Avendaño-Monsalve MC, Ponce-Rojas JC, Funes S. From cytosol to mitochondria: the beginning of a protein journey. Biol Chem 2020; 401:645-661. [DOI: 10.1515/hsz-2020-0110] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/24/2020] [Indexed: 01/18/2023]
Abstract
AbstractMitochondrial protein import is one of the key processes during mitochondrial biogenesis that involves a series of events necessary for recognition and delivery of nucleus-encoded/cytosol-synthesized mitochondrial proteins into the organelle. The past research efforts have mainly unraveled how membrane translocases ensure the correct protein sorting within the different mitochondrial subcompartments. However, early steps of recognition and delivery remain relatively uncharacterized. In this review, we discuss our current understanding about the signals on mitochondrial proteins, as well as in the mRNAs encoding them, which with the help of cytosolic chaperones and membrane receptors support protein targeting to the organelle in order to avoid improper localization. In addition, we discuss recent findings that illustrate how mistargeting of mitochondrial proteins triggers stress responses, aiming to restore cellular homeostasis.
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Affiliation(s)
- Maria Clara Avendaño-Monsalve
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n Ciudad Universitaria Coyoacán, México, Cd.Mx. 04510, Mexico
| | - José Carlos Ponce-Rojas
- Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Soledad Funes
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n Ciudad Universitaria Coyoacán, México, Cd.Mx. 04510, Mexico
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13
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Metzger MB, Scales JL, Dunklebarger MF, Loncarek J, Weissman AM. A protein quality control pathway at the mitochondrial outer membrane. eLife 2020; 9:51065. [PMID: 32118579 PMCID: PMC7136024 DOI: 10.7554/elife.51065] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/01/2020] [Indexed: 12/27/2022] Open
Abstract
Maintaining the essential functions of mitochondria requires mechanisms to recognize and remove misfolded proteins. However, quality control (QC) pathways for misfolded mitochondrial proteins remain poorly defined. Here, we establish temperature-sensitive (ts-) peripheral mitochondrial outer membrane (MOM) proteins as novel model QC substrates in Saccharomyces cerevisiae. The ts- proteins sen2-1HAts and sam35-2HAts are degraded from the MOM by the ubiquitin-proteasome system. Ubiquitination of sen2-1HAts is mediated by the ubiquitin ligase (E3) Ubr1, while sam35-2HAts is ubiquitinated primarily by San1. Mitochondria-associated degradation (MAD) of both substrates requires the SSA family of Hsp70s and the Hsp40 Sis1, providing the first evidence for chaperone involvement in MAD. In addition to a role for the Cdc48-Npl4-Ufd1 AAA-ATPase complex, Doa1 and a mitochondrial pool of the transmembrane Cdc48 adaptor, Ubx2, are implicated in their degradation. This study reveals a unique QC pathway comprised of a combination of cytosolic and mitochondrial factors that distinguish it from other cellular QC pathways.
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Affiliation(s)
- Meredith B Metzger
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, United States
| | - Jessica L Scales
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, United States
| | - Mitchell F Dunklebarger
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, United States
| | - Jadranka Loncarek
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, United States
| | - Allan M Weissman
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, United States
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14
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Alves R, Kastora SL, Gomes-Gonçalves A, Azevedo N, Rodrigues CF, Silva S, Demuyser L, Van Dijck P, Casal M, Brown AJP, Henriques M, Paiva S. Transcriptional responses of Candida glabrata biofilm cells to fluconazole are modulated by the carbon source. NPJ Biofilms Microbiomes 2020; 6:4. [PMID: 31993211 PMCID: PMC6978337 DOI: 10.1038/s41522-020-0114-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022] Open
Abstract
Candida glabrata is an important human fungal pathogen known to trigger serious infections in immune-compromised individuals. Its ability to form biofilms, which exhibit high tolerance to antifungal treatments, has been considered as an important virulence factor. However, the mechanisms involving antifungal resistance in biofilms and the impact of host niche environments on these processes are still poorly defined. In this study, we performed a whole-transcriptome analysis of C. glabrata biofilm cells exposed to different environmental conditions and constraints in order to identify the molecular pathways involved in fluconazole resistance and understand how acidic pH niches, associated with the presence of acetic acid, are able to modulate these responses. We show that fluconazole treatment induces gene expression reprogramming in a carbon source and pH-dependent manner. This is particularly relevant for a set of genes involved in DNA replication, ergosterol, and ubiquinone biosynthesis. We also provide additional evidence that the loss of mitochondrial function is associated with fluconazole resistance, independently of the growth condition. Lastly, we propose that C. glabrata Mge1, a cochaperone involved in iron metabolism and protein import into the mitochondria, is a key regulator of fluconazole susceptibility during carbon and pH adaptation by reducing the metabolic flux towards toxic sterol formation. These new findings suggest that different host microenvironments influence directly the physiology of C. glabrata, with implications on how this pathogen responds to antifungal treatment. Our analyses identify several pathways that can be targeted and will potentially prove to be useful for developing new antifungals to treat biofilm-based infections.
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Grants
- MR/M026663/1 Medical Research Council
- MR/N006364/1 Medical Research Council
- MR/N006364/2 Medical Research Council
- This study was supported by the Portuguese National Funding Agency for Science, Research and Technology FCT (grant PTDC/BIAMIC/5184/2014). RA received FCT PhD fellowship (PD/BD/113813/2015). The authors gratefully acknowledge Edinburgh Genomics for RNA-Seq library preparation and sequencing. The work on CBMA was supported by the strategic program UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569). The work on CEB was supported by PEst-OE/EQB/LA0023/2013, from FCT, “BioHealth - Biotechnology and Bioengineering approaches to improve health quality", Ref. NORTE-07-0124-FEDER-000027, co-funded by the Programa Operacional Regional do Norte (ON.2 – O Novo Norte), QREN, FEDER and the project “Consolidating Research Expertize and Resources on Cellular and Molecular Biotechnology at CEB/IBB”, Ref. FCOMP-01-0124-FEDER-027462. The work in Aberdeen was also supported by the European Research Council through the advanced grant “STRIFE” (C-2009-AdG-249793), by the UK Medical Research Council (MR/M026663/1) and by the Medical Research Council Center for Medical Mycology and the University of Aberdeen (MR/N006364/1). The work at KU Leuven was supported by the Federation of European Biochemical Societies (FEBS) through a short-term fellowship awarded to RA and by the Fund for Scientific Research Flanders (FWO; WO.009.16N).
- Federation of European Biochemical Societies (FEBS)
- Strategic program UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569)
- European Research Council through the advanced grant “STRIFE” (C-2009-AdG-249793), UK Medical Research Council (MR/M026663/1) and Medical Research Council Center for Medical Mycology and the University of Aberdeen (MR/N006364/1
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Affiliation(s)
- Rosana Alves
- Center of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Stavroula L. Kastora
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, UK
| | - Alexandra Gomes-Gonçalves
- Center of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Nuno Azevedo
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Center for Biological Engineering, University of Minho, Braga, Portugal
| | - Célia F. Rodrigues
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Center for Biological Engineering, University of Minho, Braga, Portugal
- LEPABE, Department of Chemical Engineering, University of Porto, Porto, Portugal
| | - Sónia Silva
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Center for Biological Engineering, University of Minho, Braga, Portugal
| | - Liesbeth Demuyser
- VIB-KU Leuven Center for Microbiology, Flanders, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
| | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Flanders, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
| | - Margarida Casal
- Center of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Alistair J. P. Brown
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, UK
- MRC Center for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, UK
| | - Mariana Henriques
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Center for Biological Engineering, University of Minho, Braga, Portugal
| | - Sandra Paiva
- Center of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
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15
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Jian F, Chen D, Chen L, Yan C, Lu B, Zhu Y, Chen S, Shi A, Chan DC, Song Z. Sam50 Regulates PINK1-Parkin-Mediated Mitophagy by Controlling PINK1 Stability and Mitochondrial Morphology. Cell Rep 2019; 23:2989-3005. [PMID: 29874585 DOI: 10.1016/j.celrep.2018.05.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 04/01/2018] [Accepted: 05/03/2018] [Indexed: 10/14/2022] Open
Abstract
PINK1 and Parkin mediate mitophagy, the cellular process that clears dysfunctional mitochondria. Mitophagy is regulated by mitochondrial dynamics, but the molecules linking these two processes remain poorly understood. Here, we show that Sam50, the core component of the sorting and assembly machinery (SAM), is a critical regulator of mitochondrial dynamics and PINK1-Parkin-mediated mitophagy. In response to Sam50 depletion, normal tubular mitochondria are first fragmented and subsequently merged into large spheres. Sam50 interacts with PINK1 to facilitate its processing and degradation. Depletion of Sam50 results in PINK1 accumulation, Parkin recruitment, and mitophagy. Interestingly, Sam50 deficiency induces a piecemeal mode of mitophagy that eliminates mitochondria "bit by bit" but spares mtDNA. In C. elegans, the Sam50 homolog gop-3 is required for the maintenance of mitochondrial morphology and mass. Our findings reveal that Sam50 directly links mitochondrial dynamics and mitophagy and that Sam50 depletion induces elimination of mitochondria without affecting mtDNA content.
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Affiliation(s)
- Fenglei Jian
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Dan Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine and the Collaborative Innovation Center for Brain Science, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Li Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Chaojun Yan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Bin Lu
- Attardi Institute of Mitochondrial Biomedicine, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yushan Zhu
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin, China
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Medical Research Institute, Wuhan University, Hubei, China
| | - Anbing Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medicine and the Collaborative Innovation Center for Brain Science, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - David C Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zhiyin Song
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China.
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16
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Mitochondrial diseases caused by dysfunctional mitochondrial protein import. Biochem Soc Trans 2018; 46:1225-1238. [PMID: 30287509 DOI: 10.1042/bst20180239] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/20/2018] [Accepted: 08/31/2018] [Indexed: 12/18/2022]
Abstract
Mitochondria are essential organelles which perform complex and varied functions within eukaryotic cells. Maintenance of mitochondrial health and functionality is thus a key cellular priority and relies on the organelle's extensive proteome. The mitochondrial proteome is largely encoded by nuclear genes, and mitochondrial proteins must be sorted to the correct mitochondrial sub-compartment post-translationally. This essential process is carried out by multimeric and dynamic translocation and sorting machineries, which can be found in all four mitochondrial compartments. Interestingly, advances in the diagnosis of genetic disease have revealed that mutations in various components of the human import machinery can cause mitochondrial disease, a heterogenous and often severe collection of disorders associated with energy generation defects and a multisystem presentation often affecting the cardiovascular and nervous systems. Here, we review our current understanding of mitochondrial protein import systems in human cells and the molecular basis of mitochondrial diseases caused by defects in these pathways.
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17
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Höhr AIC, Lindau C, Wirth C, Qiu J, Stroud DA, Kutik S, Guiard B, Hunte C, Becker T, Pfanner N, Wiedemann N. Membrane protein insertion through a mitochondrial β-barrel gate. Science 2018; 359:359/6373/eaah6834. [PMID: 29348211 DOI: 10.1126/science.aah6834] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/12/2017] [Accepted: 12/14/2017] [Indexed: 11/02/2022]
Abstract
The biogenesis of mitochondria, chloroplasts, and Gram-negative bacteria requires the insertion of β-barrel proteins into the outer membranes. Homologous Omp85 proteins are essential for membrane insertion of β-barrel precursors. It is unknown if precursors are threaded through the Omp85-channel interior and exit laterally or if they are translocated into the membrane at the Omp85-lipid interface. We have mapped the interaction of a precursor in transit with the mitochondrial Omp85-channel Sam50 in the native membrane environment. The precursor is translocated into the channel interior, interacts with an internal loop, and inserts into the lateral gate by β-signal exchange. Transport through the Omp85-channel interior followed by release through the lateral gate into the lipid phase may represent a basic mechanism for membrane insertion of β-barrel proteins.
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Affiliation(s)
- Alexandra I C Höhr
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Caroline Lindau
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Christophe Wirth
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Jian Qiu
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - David A Stroud
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Stephan Kutik
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Bernard Guiard
- Centre de Génétique Moléculaire, CNRS, 91190 Gif-sur-Yvette, France
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, 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, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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18
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Jores T, Klinger A, Groß LE, Kawano S, Flinner N, Duchardt-Ferner E, Wöhnert J, Kalbacher H, Endo T, Schleiff E, Rapaport D. Characterization of the targeting signal in mitochondrial β-barrel proteins. Nat Commun 2016; 7:12036. [PMID: 27345737 PMCID: PMC4931251 DOI: 10.1038/ncomms12036] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 05/24/2016] [Indexed: 01/15/2023] Open
Abstract
Mitochondrial β-barrel proteins are synthesized on cytosolic ribosomes and must be specifically targeted to the organelle before their integration into the mitochondrial outer membrane. The signal that assures such precise targeting and its recognition by the organelle remained obscure. In the present study we show that a specialized β-hairpin motif is this long searched for signal. We demonstrate that a synthetic β-hairpin peptide competes with the import of mitochondrial β-barrel proteins and that proteins harbouring a β-hairpin peptide fused to passenger domains are targeted to mitochondria. Furthermore, a β-hairpin motif from mitochondrial proteins targets chloroplast β-barrel proteins to mitochondria. The mitochondrial targeting depends on the hydrophobicity of the β-hairpin motif. Finally, this motif interacts with the mitochondrial import receptor Tom20. Collectively, we reveal that β-barrel proteins are targeted to mitochondria by a dedicated β-hairpin element, and this motif is recognized at the organelle surface by the outer membrane translocase. Mitochondrial β-barrel proteins are synthesized in the cytosol before being targeted to the organelle. Here, Jores et al. show that a specialized hydrophobic β-hairpin motif is the previously undefined targeting sequence and is recognized by the mitochondrial outer membrane translocase.
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Affiliation(s)
- Tobias Jores
- Interfaculty Institute of Biochemistry, University of Tuebingen, Hoppe-Seyler-Str. 4, 72076 Tuebingen, Germany
| | - Anna Klinger
- Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Lucia E Groß
- Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Shin Kawano
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Nadine Flinner
- Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tuebingen, Hoppe-Seyler-Str. 4, 72076 Tuebingen, Germany
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.,Cluster of Excellence Frankfurt, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tuebingen, Hoppe-Seyler-Str. 4, 72076 Tuebingen, Germany
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19
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Wenz LS, Ellenrieder L, Qiu J, Bohnert M, Zufall N, van der Laan M, Pfanner N, Wiedemann N, Becker T. Sam37 is crucial for formation of the mitochondrial TOM-SAM supercomplex, thereby promoting β-barrel biogenesis. J Cell Biol 2015; 210:1047-54. [PMID: 26416958 PMCID: PMC4586741 DOI: 10.1083/jcb.201504119] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Sam37 promotes biogenesis of mitochondrial proteins by linking outer membrane translocases into a supercomplex Biogenesis of mitochondrial β-barrel proteins requires two preprotein translocases, the general translocase of the outer membrane (TOM) and the sorting and assembly machinery (SAM). TOM and SAM form a supercomplex that promotes transfer of β-barrel precursors. The SAM core complex contains the channel protein Sam50, which cooperates with Sam35 in precursor recognition, and the peripheral membrane protein Sam37. The molecular function of Sam37 has been unknown. We report that Sam37 is crucial for formation of the TOM–SAM supercomplex. Sam37 interacts with the receptor domain of Tom22 on the cytosolic side of the mitochondrial outer membrane and links TOM and SAM complexes. Sam37 thus promotes efficient transfer of β-barrel precursors to the SAM complex. We conclude that Sam37 functions as a coupling factor of the translocase supercomplex of the mitochondrial outer membrane.
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Affiliation(s)
- Lena-Sophie Wenz
- Institute of Biochemistry and Molecular Biology, 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, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jian Qiu
- Institute of Biochemistry and Molecular Biology, 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, University of Freiburg, 79104 Freiburg, Germany
| | - Maria Bohnert
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Nicole Zufall
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Martin van der Laan
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, 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, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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20
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O'Neil PK, Rollauer SE, Noinaj N, Buchanan SK. Fitting the Pieces of the β-Barrel Assembly Machinery Complex. Biochemistry 2015; 54:6303-11. [PMID: 26394220 PMCID: PMC4631317 DOI: 10.1021/acs.biochem.5b00852] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
β-Barrel membrane proteins are found in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria; however, exactly how they are folded and inserted remains unknown. Over the past decade, both functional and structural studies have greatly contributed to addressing this elusive mechanism. It is known that a conserved core machinery is required for each organelle, though the overall composition varies significantly. The vast majority of studies that aimed to understand the biogenesis of β-barrel membrane proteins has been conducted in Gram-negative bacteria. Here, it is the task of a multicomponent complex known as the β-barrel assembly machinery (BAM) complex to fold and insert new β-barrel membrane proteins into the outer membrane. In this review, we will discuss recent discoveries with the goal of utilizing all reported structural and functional studies to piece together a current structural model for the fully assembled BAM complex.
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Affiliation(s)
- Patrick K O'Neil
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - Sarah E Rollauer
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - Susan K Buchanan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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21
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Ulrich T, Oberhettinger P, Autenrieth IB, Rapaport D. Yeast Mitochondria as a Model System to Study the Biogenesis of Bacterial β-Barrel Proteins. Methods Mol Biol 2015; 1329:17-31. [PMID: 26427673 DOI: 10.1007/978-1-4939-2871-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Beta-barrel proteins are found in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. The evolutionary conservation in the biogenesis of these proteins allows mitochondria to assemble bacterial β-barrel proteins in their functional form. In this chapter, we describe exemplarily how the capacity of yeast mitochondria to process the trimeric autotransporter YadA can be used to study the role of bacterial periplasmic chaperones in this process.
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Affiliation(s)
- Thomas Ulrich
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Straße 4, Tübingen, 72076, Germany
| | - Philipp Oberhettinger
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, 72076, Germany
| | - Ingo B Autenrieth
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, 72076, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Straße 4, Tübingen, 72076, Germany.
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22
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Schuler MH, Di Bartolomeo F, Böttinger L, Horvath SE, Wenz LS, Daum G, Becker T. Phosphatidylcholine affects the role of the sorting and assembly machinery in the biogenesis of mitochondrial β-barrel proteins. J Biol Chem 2015; 290:26523-32. [PMID: 26385920 DOI: 10.1074/jbc.m115.687921] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 11/06/2022] Open
Abstract
Two protein translocases drive the import of β-barrel precursor proteins into the mitochondrial outer membrane: The translocase of the outer membrane (TOM complex) promotes transport of the precursor to the intermembrane space, whereas the sorting and assembly machinery (SAM complex) mediates subsequent folding of the β-barrel and its integration into the target membrane. The non-bilayer-forming phospholipids phosphatidylethanolamine (PE) and cardiolipin (CL) are required for the biogenesis of β-barrel proteins. Whether bilayer-forming phospholipids such as phosphatidylcholine (PC), the most abundant phospholipid of the mitochondrial outer membrane, play a role in the import of β-barrel precursors is unclear. In this study, we show that PC is required for stability and function of the SAM complex during the biogenesis of β-barrel proteins. PC further promotes the SAM-dependent assembly of the TOM complex, indicating a general role of PC for the function of the SAM complex. In contrast to PE-deficient mitochondria precursor accumulation at the TOM complex is not affected by depletion of PC. We conclude that PC and PE affect the function of distinct protein translocases in mitochondrial β-barrel biogenesis.
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Affiliation(s)
- Max-Hinderk Schuler
- From the Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | | | - Lena Böttinger
- From the Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Susanne E Horvath
- From the Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Lena-Sophie Wenz
- From the Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Günther Daum
- Institute for Biochemistry, Graz University of Technology, NaWi Graz, A-8010 Graz, Austria,
| | - Thomas Becker
- From the Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany, BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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23
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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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24
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Abstract
The vast majority of outer membrane (OM) proteins in Gram-negative bacteria belongs to the class of membrane-embedded β-barrel proteins. Besides Gram-negative bacteria, the presence of β-barrel proteins is restricted to the OM of the eukaryotic organelles mitochondria and chloroplasts that were derived from prokaryotic ancestors. The assembly of these proteins into the corresponding OM is in each case facilitated by a dedicated protein complex that contains a highly conserved central β-barrel protein termed BamA/YaeT/Omp85 in Gram-negative bacteria and Tob55/Sam50 in mitochondria. However, little is known about the exact mechanism by which these complexes mediate the integration of β-barrel precursors into the lipid bilayer. Interestingly, previous studies showed that during evolution, these complexes retained the ability to functionally assemble β-barrel proteins from different origins. In this review we summarize the current knowledge on the biogenesis pathway of β-barrel proteins in Gram-negative bacteria, mitochondria and chloroplasts and focus on the commonalities and divergences that evolved between the different β-barrel assembly machineries.
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Affiliation(s)
- Thomas Ulrich
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany.
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25
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Höhr AIC, Straub SP, Warscheid B, Becker T, Wiedemann N. Assembly of β-barrel proteins in the mitochondrial outer membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:74-88. [PMID: 25305573 DOI: 10.1016/j.bbamcr.2014.10.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/25/2014] [Accepted: 10/01/2014] [Indexed: 12/15/2022]
Abstract
Mitochondria evolved through endosymbiosis of a Gram-negative progenitor with a host cell to generate eukaryotes. Therefore, the outer membrane of mitochondria and Gram-negative bacteria contain pore proteins with β-barrel topology. After synthesis in the cytosol, β-barrel precursor proteins are first transported into the mitochondrial intermembrane space. Folding and membrane integration of β-barrel proteins depend on the mitochondrial sorting and assembly machinery (SAM) located in the outer membrane, which is related to the β-barrel assembly machinery (BAM) in bacteria. The SAM complex recognizes β-barrel proteins by a β-signal in the C-terminal β-strand that is required to initiate β-barrel protein insertion into the outer membrane. In addition, the SAM complex is crucial to form membrane contacts with the inner mitochondrial membrane by interacting with the mitochondrial contact site and cristae organizing system (MICOS) and shares a subunit with the endoplasmic reticulum-mitochondria encounter structure (ERMES) that links the outer mitochondrial membrane to the endoplasmic reticulum (ER).
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Affiliation(s)
- Alexandra I C Höhr
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Sebastian P Straub
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany; Abteilung Biochemie und Funktionelle Proteomik, Institut für Biologie II, Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany
| | - Nils Wiedemann
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany.
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26
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Ulrich T, Oberhettinger P, Schütz M, Holzer K, Ramms AS, Linke D, Autenrieth IB, Rapaport D. Evolutionary conservation in biogenesis of β-barrel proteins allows mitochondria to assemble a functional bacterial trimeric autotransporter protein. J Biol Chem 2014; 289:29457-70. [PMID: 25190806 DOI: 10.1074/jbc.m114.565655] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Yersinia adhesin A (YadA) belongs to a class of bacterial adhesins that form trimeric structures. Their mature form contains a passenger domain and a C-terminal β-domain that anchors the protein in the outer membrane (OM). Little is known about how precursors of such proteins cross the periplasm and assemble into the OM. In the present study we took advantage of the evolutionary conservation in the biogenesis of β-barrel proteins between bacteria and mitochondria. We previously observed that upon expression in yeast cells, bacterial β-barrel proteins including the transmembrane domain of YadA assemble into the mitochondrial OM. In the current study we found that when expressed in yeast cells both the monomeric and trimeric forms of full-length YadA were detected in mitochondria but only the trimeric species was fully integrated into the OM. The oligomeric form was exposed on the surface of the organelle in its native conformation and maintained its capacity to adhere to host cells. The co-expression of YadA with a mitochondria-targeted form of the bacterial periplasmic chaperone Skp, but not with SurA or SecB, resulted in enhanced levels of both forms of YadA. Taken together, these results indicate that the proper assembly of trimeric autotransporter can occur also in a system lacking the lipoproteins of the BAM machinery and is specifically enhanced by the chaperone Skp.
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Affiliation(s)
- Thomas Ulrich
- From the Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Philipp Oberhettinger
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany, and
| | - Monika Schütz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany, and
| | - Katharina Holzer
- From the Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Anne S Ramms
- From the Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Dirk Linke
- Department of Protein Evolution, Max-Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ingo B Autenrieth
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany, and
| | - Doron Rapaport
- From the Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany,
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27
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Misra R, Stikeleather R, Gabriele R. In vivo roles of BamA, BamB and BamD in the biogenesis of BamA, a core protein of the β-barrel assembly machine of Escherichia coli. J Mol Biol 2014; 427:1061-74. [PMID: 24792419 DOI: 10.1016/j.jmb.2014.04.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/18/2014] [Accepted: 04/22/2014] [Indexed: 11/24/2022]
Abstract
Assembly of the β-barrel outer membrane proteins (OMPs) is an essential cellular process in Gram-negative bacteria and in the mitochondria and chloroplasts of eukaryotes--two organelles of bacterial origin. Central to this process is the conserved β-barrel OMP that belongs to the Omp85 superfamily. In Escherichia coli, BamA is the core β-barrel OMP and, together with four outer membrane lipoproteins, BamBCDE, constitutes the β-barrel assembly machine (BAM). In this paper, we investigated the roles of BamD, an essential lipoprotein, and BamB in BamA biogenesis. Depletion of BamD caused impairment in BamA biogenesis and cessation of cell growth. These defects of BamD depletion were partly reversed by single-amino-acid substitutions mapping within the β-barrel domain of BamA. However, in the absence of BamB, the positive effects of the β-barrel substitutions on BamA biogenesis under BamD depletion conditions were nullified. By employing a BamA protein bearing one such substitution, F474L, it was demonstrated that the mutant BamA protein could not only assemble without BamD but also facilitate the assembly of wild-type BamA expressed in trans. Based on these data, we propose a model in which the Bam lipoproteins, which are localized to the outer membrane by the BAM-independent Lol pathway, aid in the creation of new BAM complexes by serving as outer membrane receptors and folding factors for nascent BamA molecules. The newly assembled BAM holocomplex then catalyzes the assembly of substrate OMPs and BamA. These in vivo findings are corroborated by recently published in vitro data.
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Affiliation(s)
- Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Ryan Stikeleather
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Rebecca Gabriele
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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28
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Flinner N, Ellenrieder L, Stiller SB, Becker T, Schleiff E, Mirus O. Mdm10 is an ancient eukaryotic porin co-occurring with the ERMES complex. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:3314-3325. [PMID: 24135058 DOI: 10.1016/j.bbamcr.2013.10.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 09/20/2013] [Accepted: 10/07/2013] [Indexed: 12/17/2022]
Abstract
Mitochondrial β-barrel proteins fulfill central functions in the outer membrane like metabolite exchange catalyzed by the voltage-dependent anion channel (VDAC) and protein biogenesis by the central components of the preprotein translocase of the outer membrane (Tom40) or of the sorting and assembly machinery (Sam50). The mitochondrial division and morphology protein Mdm10 is another essential outer membrane protein with proposed β-barrel fold, which has so far only been found in Fungi. Mdm10 is part of the endoplasmic reticulum mitochondria encounter structure (ERMES), which tethers the ER to mitochondria and associates with the SAM complex. In here, we provide evidence that Mdm10 phylogenetically belongs to the VDAC/Tom40 superfamily. Contrary to Tom40 and VDAC, Mdm10 exposes long loops towards both sides of the membrane. Analyses of single loop deletion mutants of Mdm10 in the yeast Saccharomyces cerevisiae reveal that the loops are dispensable for Mdm10 function. Sequences similar to fungal Mdm10 can be found in species from Excavates to Fungi, but neither in Metazoa nor in plants. Strikingly, the presence of Mdm10 coincides with the appearance of the other ERMES components. Mdm10's presence in both unikonts and bikonts indicates an introduction at an early time point in eukaryotic evolution.
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Affiliation(s)
- Nadine Flinner
- JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Lars Ellenrieder
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, D-79104 Freiburg, Germany
| | - Sebastian B Stiller
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, D-79104 Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, D-79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, D-79104 Freiburg, Germany
| | - Enrico Schleiff
- JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | - Oliver Mirus
- JWGU Frankfurt am Main, Cluster of Excellence Macromolecular Complexes, Centre of Membrane Proteomics, Department of Biosciences, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
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29
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Kulawiak B, Höpker J, Gebert M, Guiard B, Wiedemann N, Gebert N. The mitochondrial protein import machinery has multiple connections to the respiratory chain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:612-26. [PMID: 23274250 DOI: 10.1016/j.bbabio.2012.12.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/12/2012] [Accepted: 12/17/2012] [Indexed: 01/09/2023]
Abstract
The mitochondrial inner membrane harbors the complexes of the respiratory chain and protein translocases required for the import of mitochondrial precursor proteins. These complexes are functionally interdependent, as the import of respiratory chain precursor proteins across and into the inner membrane requires the membrane potential. Vice versa the membrane potential is generated by the proton pumping complexes of the respiratory chain. Besides this basic codependency four different systems for protein import, processing and assembly show further connections to the respiratory chain. The mitochondrial intermembrane space import and assembly machinery oxidizes cysteine residues within the imported precursor proteins and is able to donate the liberated electrons to the respiratory chain. The presequence translocase of the inner membrane physically interacts with the respiratory chain. The mitochondrial processing peptidase is homologous to respiratory chain subunits and the carrier translocase of the inner membrane even shares a subunit with the respiratory chain. In this review we will summarize the import of mitochondrial precursor proteins and highlight these special links between the mitochondrial protein import machinery and the respiratory chain. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Affiliation(s)
- Bogusz Kulawiak
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, Freiburg, Germany
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30
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Misra R. Assembly of the β-Barrel Outer Membrane Proteins in Gram-Negative Bacteria, Mitochondria, and Chloroplasts. ISRN MOLECULAR BIOLOGY 2012; 2012:708203. [PMID: 27335668 PMCID: PMC4890855 DOI: 10.5402/2012/708203] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 10/22/2012] [Indexed: 01/12/2023]
Abstract
In the last decade, there has been an explosion of publications on the assembly of β-barrel outer membrane proteins (OMPs), which carry out diverse cellular functions, including solute transport, protein secretion, and assembly of protein and lipid components of the outer membrane. Of the three outer membrane model systems—Gram-negative bacteria, mitochondria and chloroplasts—research on bacterial and mitochondrial systems has so far led the way in dissecting the β-barrel OMP assembly pathways. Many exciting discoveries have been made, including the identification of β-barrel OMP assembly machineries in bacteria and mitochondria, and potentially the core assembly component in chloroplasts. The atomic structures of all five components of the bacterial β-barrel assembly machinery (BAM) complex, except the β-barrel domain of the core BamA protein, have been solved. Structures reveal that these proteins contain domains/motifs known to facilitate protein-protein interactions, which are at the heart of the assembly pathways. While structural information has been valuable, most of our current understanding of the β-barrel OMP assembly pathways has come from genetic, molecular biology, and biochemical analyses. This paper provides a comparative account of the β-barrel OMP assembly pathways in Gram-negative bacteria, mitochondria, and chloroplasts.
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Affiliation(s)
- Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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31
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Klein A, Israel L, Lackey SWK, Nargang FE, Imhof A, Baumeister W, Neupert W, Thomas DR. Characterization of the insertase for β-barrel proteins of the outer mitochondrial membrane. ACTA ACUST UNITED AC 2012; 199:599-611. [PMID: 23128244 PMCID: PMC3494861 DOI: 10.1083/jcb.201207161] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Isolation of the intact TOB complex reveals a 1:1:1 stoichiometry of Tob55, Tob38, and Tob37 with a 140-kD molecular mass, providing new insight into complex structure and function. The TOB–SAM complex is an essential component of the mitochondrial outer membrane that mediates the insertion of β-barrel precursor proteins into the membrane. We report here its isolation and determine its size, composition, and structural organization. The complex from Neurospora crassa was composed of Tob55–Sam50, Tob38–Sam35, and Tob37–Sam37 in a stoichiometry of 1:1:1 and had a molecular mass of 140 kD. A very minor fraction of the purified complex was associated with one Mdm10 protein. Using molecular homology modeling for Tob55 and cryoelectron microscopy reconstructions of the TOB complex, we present a model of the TOB–SAM complex that integrates biochemical and structural data. We discuss our results and the structural model in the context of a possible mechanism of the TOB insertase.
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Affiliation(s)
- Astrid Klein
- Max-Planck Institut für Biochemie, Abteilung für zelluläre Biochemie, D-82152 Martinsried, Germany
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32
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Abstract
A protein's function is intimately linked to its correct subcellular location, yet the machinery required for protein synthesis is predominately cytosolic. How proteins are trafficked through the confines of the cell and integrated into the appropriate cellular compartments has puzzled and intrigued researchers for decades. Indeed, studies exploring this premise revealed elaborate cellular protein translocation and sorting systems, which ensure that all proteins are shuttled to the appropriate cellular destination, where they fulfill their specific functions. This holds true for mitochondria, where sophisticated molecular machines serve to recognize incoming precursor proteins and integrate them into the functional framework of the organelle. We summarize the recent progress in our understanding of mitochondrial protein sorting and the machineries and mechanisms that mediate and regulate this highly dynamic cellular process essential for survival of virtually all eukaryotic cells.
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33
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Shiota T, Maruyama M, Miura M, Tamura Y, Yamano K, Esaki M, Endo T. The Tom40 assembly process probed using the attachment of different intramitochondrial sorting signals. Mol Biol Cell 2012; 23:3936-47. [PMID: 22933571 PMCID: PMC3469510 DOI: 10.1091/mbc.e12-03-0202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The β-barrel protein Tom40 functions as a protein-conducting channel in the mitochondrial outer membrane. By attaching mitochondrial presequences for various mitochondrial destinations to Tom40, it is possible to follow its sorting process. The results provide insight into the mechanism for the precise delivery of β-barrel proteins to the outer membrane. The TOM40 complex is a protein translocator in the mitochondrial outer membrane and consists of several different subunits. Among them, Tom40 is a central subunit that constitutes a protein-conducting channel by forming a β-barrel structure. To probe the nature of the assembly process of Tom40 in the outer membrane, we attached various mitochondrial presequences to Tom40 that possess sorting information for the intermembrane space (IMS), inner membrane, and matrix and would compete with the inherent Tom40 assembly process. We analyzed the mitochondrial import of those fusion proteins in vitro. Tom40 crossed the outer membrane and/or inner membrane even in the presence of various sorting signals. N-terminal anchorage of the attached presequence to the inner membrane did not prevent Tom40 from associating with the TOB/SAM complex, although it impaired its efficient release from the TOB complex in vitro but not in vivo. The IMS or matrix-targeting presequence attached to Tom40 was effective in substituting for the requirement for small Tim proteins in the IMS for the translocation of Tom40 across the outer membrane. These results provide insight into the mechanism responsible for the precise delivery of β-barrel proteins to the outer mitochondrial membrane.
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Affiliation(s)
- Takuya Shiota
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
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34
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Bohnert M, Wenz LS, Zerbes RM, Horvath SE, Stroud DA, von der Malsburg K, Müller JM, Oeljeklaus S, Perschil I, Warscheid B, Chacinska A, Veenhuis M, van der Klei IJ, Daum G, Wiedemann N, Becker T, Pfanner N, van der Laan M. Role of mitochondrial inner membrane organizing system in protein biogenesis of the mitochondrial outer membrane. Mol Biol Cell 2012; 23:3948-56. [PMID: 22918945 PMCID: PMC3469511 DOI: 10.1091/mbc.e12-04-0295] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mitochondrial inner membrane organizing system (MINOS) is a large protein complex required for maintaining inner membrane architecture. We report that MINOS independently interacts with both preprotein translocases of the outer mitochondrial membrane and plays a role in the biogenesis of β-barrel proteins of the outer membrane. Mitochondria contain two membranes, the outer membrane and the inner membrane with folded cristae. The mitochondrial inner membrane organizing system (MINOS) is a large protein complex required for maintaining inner membrane architecture. MINOS interacts with both preprotein transport machineries of the outer membrane, the translocase of the outer membrane (TOM) and the sorting and assembly machinery (SAM). It is unknown, however, whether MINOS plays a role in the biogenesis of outer membrane proteins. We have dissected the interaction of MINOS with TOM and SAM and report that MINOS binds to both translocases independently. MINOS binds to the SAM complex via the conserved polypeptide transport–associated domain of Sam50. Mitochondria lacking mitofilin, the large core subunit of MINOS, are impaired in the biogenesis of β-barrel proteins of the outer membrane, whereas mutant mitochondria lacking any of the other five MINOS subunits import β-barrel proteins in a manner similar to wild-type mitochondria. We show that mitofilin is required at an early stage of β-barrel biogenesis that includes the initial translocation through the TOM complex. We conclude that MINOS interacts with TOM and SAM independently and that the core subunit mitofilin is involved in biogenesis of outer membrane β-barrel proteins.
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Affiliation(s)
- Maria Bohnert
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
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35
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Dudek J, Rehling P, van der Laan M. Mitochondrial protein import: common principles and physiological networks. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:274-85. [PMID: 22683763 DOI: 10.1016/j.bbamcr.2012.05.028] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/24/2012] [Accepted: 05/28/2012] [Indexed: 11/28/2022]
Abstract
Most mitochondrial proteins are encoded in the nucleus. They are synthesized as precursor forms in the cytosol and must be imported into mitochondria with the help of different protein translocases. Distinct import signals within precursors direct each protein to the mitochondrial surface and subsequently onto specific transport routes to its final destination within these organelles. In this review we highlight common principles of mitochondrial protein import and address different mechanisms of protein integration into mitochondrial membranes. Over the last years it has become clear that mitochondrial protein translocases are not independently operating units, but in fact closely cooperate with each other. We discuss recent studies that indicate how the pathways for mitochondrial protein biogenesis are embedded into a functional network of various other physiological processes, such as energy metabolism, signal transduction, and maintenance of mitochondrial morphology. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Jan Dudek
- Abteilung Biochemie II, Universität Göttingen, 37073 Göttingen, Germany
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36
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Dynamic association of BAM complex modules includes surface exposure of the lipoprotein BamC. J Mol Biol 2012; 422:545-55. [PMID: 22683355 DOI: 10.1016/j.jmb.2012.05.035] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Revised: 05/09/2012] [Accepted: 05/30/2012] [Indexed: 11/21/2022]
Abstract
The β-barrel assembly machinery (BAM) complex drives the assembly of β-barrel proteins into the outer membrane of gram-negative bacteria. It is composed of five subunits: BamA, BamB, BamC, BamD, and BamE. We find that the BAM complex isolated from the outer membrane of Escherichia coli consists of a core complex of BamA:B:C:D:E and, in addition, a BamA:B module and a BamC:D module. In the absence of BamC, these modules are destabilized, resulting in increased protease susceptibility of BamD and BamB. While the N-terminus of BamC carries a highly conserved region crucial for stable interaction with BamD, immunofluorescence, immunoprecipitation, and protease-sensitivity assays show that the C-terminal domain of BamC, composed of two helix-grip motifs, is exposed on the surface of E. coli. This unexpected topology of a bacterial lipoprotein is reminiscent of the analogous protein subunits from the mitochondrial β-barrel insertion machinery, the SAM complex. The modular arrangement and topological features provide new insight into the architecture of the BAM complex, towards a better understanding of the mechanism driving β-barrel membrane protein assembly.
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37
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Mitochondrial sorting and assembly machinery subunit Sam37 in Candida albicans: insight into the roles of mitochondria in fitness, cell wall integrity, and virulence. EUKARYOTIC CELL 2012; 11:532-44. [PMID: 22286093 DOI: 10.1128/ec.05292-11] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Recent studies indicate that mitochondrial functions impinge on cell wall integrity, drug tolerance, and virulence of human fungal pathogens. However, the mechanistic aspects of these processes are poorly understood. We focused on the mitochondrial outer membrane SAM (Sorting and Assembly Machinery) complex subunit Sam37 in Candida albicans. Inactivation of SAM37 in C. albicans leads to a large reduction in fitness, a phenotype not conserved with the model yeast Saccharomyces cerevisiae. Our data indicate that slow growth of the sam37ΔΔ mutant results from mitochondrial DNA loss, a new function for Sam37 in C. albicans, and from reduced activity of the essential SAM complex subunit Sam35. The sam37ΔΔ mutant was hypersensitive to drugs that target the cell wall and displayed altered cell wall structure, supporting a role for Sam37 in cell wall integrity in C. albicans. The sensitivity of the mutant to membrane-targeting antifungals was not significantly altered. The sam37ΔΔ mutant was avirulent in the mouse model, and bioinformatics showed that the fungal Sam37 proteins are distant from their animal counterparts and could thus represent potential drug targets. Our study provides the first direct evidence for a link between mitochondrial function and cell wall integrity in C. albicans and is further relevant for understanding mitochondrial function in fitness, antifungal drug tolerance, and virulence of this major pathogen. Beyond the relevance to fungal pathogenesis, this work also provides new insight into the mitochondrial and cellular roles of the SAM complex in fungi.
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Jiang JH, Davies JK, Lithgow T, Strugnell RA, Gabriel K. Targeting of Neisserial PorB to the mitochondrial outer membrane: an insight on the evolution of β-barrel protein assembly machines. Mol Microbiol 2011; 82:976-87. [DOI: 10.1111/j.1365-2958.2011.07880.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Liu Z, Li X, Zhao P, Gui J, Zheng W, Zhang Y. Tracing the evolution of the mitochondrial protein import machinery. Comput Biol Chem 2011; 35:336-40. [PMID: 22099629 DOI: 10.1016/j.compbiolchem.2011.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 10/01/2011] [Indexed: 10/16/2022]
Abstract
Mitochondria are eukaryotic organelles originated from a single bacterial endosymbiosis about 2 billion years ago. One of the earliest events in the evolution of mitochondria was the acquisition of a mechanism that facilitated the import of proteins from cytosol. The mitochondrial protein import machinery consists of dozens of subunits, and they are of modular design. However, to date, it is not clear when certain component was added to the machinery. Using extensive homology searches, the evolutionary history of the mitochondrial protein import machinery was reconstructed. The results indicated that 6 of the 35 subunits have homologs in prokaryote, suggesting that they were prokaryotic origin; the major subunit gains were occurred in the earliest stage of eukaryotic evolution; subsequent to the gain of these conserved set of subunits, the mitochondrial protein import machinery components diversified along the eukaryotic lineages and a number of lineage-specific subunits can be observed. Furthermore, protein import systems of mitochondria-like organelles (hydrogenosomes and mitosomes) have dramatically reduced their subunit contents, however, they share most of the prokaryotic origin components with mitochondrion.
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Affiliation(s)
- Zhen Liu
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064 Chengdu, People's Republic of China.
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Lackey SWK, Wideman JG, Kennedy EK, Go NE, Nargang FE. The Neurospora crassa TOB complex: analysis of the topology and function of Tob38 and Tob37. PLoS One 2011; 6:e25650. [PMID: 21980517 PMCID: PMC3182244 DOI: 10.1371/journal.pone.0025650] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 09/07/2011] [Indexed: 11/18/2022] Open
Abstract
The TOB or SAM complex is responsible for assembling several proteins into the mitochondrial outer membrane, including all β-barrel proteins. We have identified several forms of the complex in Neurospora crassa. One form contains Tob55, Tob38, and Tob37; another contains these three subunits plus the Mdm10 protein; while additional complexes contain only Tob55. As previously shown for Tob55, both Tob37 and Tob38 are essential for viability of the organism. Mitochondria deficient in Tob37 or Tob38 have reduced ability to assemble β-barrel proteins. The function of two hydrophobic domains in the C-terminal region of the Tob37 protein was investigated. Mutant Tob37 proteins lacking either or both of these regions are able to restore viability to cells lacking the protein. One of the domains was found to anchor the protein to the outer mitochondrial membrane but was not necessary for targeting or association of the protein with mitochondria. Examination of the import properties of mitochondria containing Tob37 with deletions of the hydrophobic domains reveals that the topology of Tob37 may be important for interactions between specific classes of β-barrel precursors and the TOB complex.
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Affiliation(s)
| | - Jeremy G. Wideman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Erin K. Kennedy
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Nancy E. Go
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Frank E. Nargang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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Stroud DA, Becker T, Qiu J, Stojanovski D, Pfannschmidt S, Wirth C, Hunte C, Guiard B, Meisinger C, Pfanner N, Wiedemann N. Biogenesis of mitochondrial β-barrel proteins: the POTRA domain is involved in precursor release from the SAM complex. Mol Biol Cell 2011; 22:2823-33. [PMID: 21680715 PMCID: PMC3154879 DOI: 10.1091/mbc.e11-02-0148] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The mitochondrial outer membrane contains proteinaceous machineries for the translocation of precursor proteins. The sorting and assembly machinery (SAM) is required for the insertion of β-barrel proteins into the outer membrane. Sam50 is the channel-forming core subunit of the SAM complex and belongs to the BamA/Sam50/Toc75 family of proteins that have been conserved from Gram-negative bacteria to mitochondria and chloroplasts. These proteins contain one or more N-terminal polypeptide transport-associated (POTRA) domains. POTRA domains can bind precursor proteins, however, different views exist on the role of POTRA domains in the biogenesis of β-barrel proteins. It has been suggested that the single POTRA domain of mitochondrial Sam50 plays a receptor-like function at the SAM complex. We established a system to monitor the interaction of chemical amounts of β-barrel precursor proteins with the SAM complex of wild-type and mutant yeast in organello. We report that the SAM complex lacking the POTRA domain of Sam50 efficiently binds β-barrel precursors, but is impaired in the release of the precursors. These results indicate the POTRA domain of Sam50 is not essential for recognition of β-barrel precursors but functions in a subsequent step to promote the release of precursor proteins from the SAM complex.
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Affiliation(s)
- David A Stroud
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
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Kozjak-Pavlovic V, Ott C, Götz M, Rudel T. Neisserial Omp85 protein is selectively recognized and assembled into functional complexes in the outer membrane of human mitochondria. J Biol Chem 2011; 286:27019-26. [PMID: 21652692 DOI: 10.1074/jbc.m111.232249] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As a consequence of their bacterial origin, mitochondria contain β-barrel proteins in their outer membrane (OMM). These proteins require the translocase of the outer membrane (TOM) complex and the conserved sorting and assembly machinery (SAM) complex for transport and integration into the OMM. The SAM complex and the β-barrel assembly machinery (BAM) required for biogenesis of β-barrel proteins in bacteria are evolutionarily related. Despite this homology, we show that bacterial β-barrel proteins are not universally recognized and integrated into the OMM of human mitochondria. Selectivity exists both at the level of the TOM and the SAM complex. Of all of the proteins we tested, human mitochondria imported only β-barrel proteins originating from Neisseria sp., and only Omp85, the central component of the neisserial BAM complex, integrated into the OMM. PorB proteins from different Neisseria, although imported by the TOM, were not recognized by the SAM complex and formed membrane complexes only when functional Omp85 was present at the same time in mitochondria. Omp85 alone was capable of integrating other bacterial β-barrel proteins in human mitochondria, but could not substitute for the function of its mitochondrial homolog Sam50. Thus, signals and machineries for transport and assembly of β-barrel proteins in bacteria and human mitochondria differ enough to allow only a certain type of β-barrel proteins to be targeted and integrated in mitochondrial membranes in human cells.
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Affiliation(s)
- Vera Kozjak-Pavlovic
- Biozentrum, Department of Microbiology, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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Delage L, Leblanc C, Nyvall Collén P, Gschloessl B, Oudot MP, Sterck L, Poulain J, Aury JM, Cock JM. In silico survey of the mitochondrial protein uptake and maturation systems in the brown alga Ectocarpus siliculosus. PLoS One 2011; 6:e19540. [PMID: 21611166 PMCID: PMC3097184 DOI: 10.1371/journal.pone.0019540] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/31/2011] [Indexed: 01/24/2023] Open
Abstract
The acquisition of mitochondria was a key event in eukaryote evolution. The aim of this study was to identify homologues of the components of the mitochondrial protein import machinery in the brown alga Ectocarpus and to use this information to investigate the evolutionary history of this fundamental cellular process. Detailed searches were carried out both for components of the protein import system and for related peptidases. Comparative and phylogenetic analyses were used to investigate the evolution of mitochondrial proteins during eukaryote diversification. Key observations include phylogenetic evidence for very ancient origins for many protein import components (Tim21, Tim50, for example) and indications of differences between the outer membrane receptors that recognize the mitochondrial targeting signals, suggesting replacement, rearrangement and/or emergence of new components across the major eukaryotic lineages. Overall, the mitochondrial protein import components analysed in this study confirmed a high level of conservation during evolution, indicating that most are derived from very ancient, ancestral proteins. Several of the protein import components identified in Ectocarpus, such as Tim21, Tim50 and metaxin, have also been found in other stramenopiles and this study suggests an early origin during the evolution of the eukaryotes.
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Affiliation(s)
- Ludovic Delage
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Catherine Leblanc
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Pi Nyvall Collén
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Bernhard Gschloessl
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Marie-Pierre Oudot
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lieven Sterck
- VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
| | - Julie Poulain
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, Evry, France
- Centre National de la Recherche Scientifique, UMR 8030, Evry, France
- Université d'Evry, Evry, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, Evry, France
- Centre National de la Recherche Scientifique, UMR 8030, Evry, France
- Université d'Evry, Evry, France
| | - J. Mark Cock
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
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Midzak A, Rone M, Aghazadeh Y, Culty M, Papadopoulos V. Mitochondrial protein import and the genesis of steroidogenic mitochondria. Mol Cell Endocrinol 2011; 336:70-9. [PMID: 21147195 PMCID: PMC3057322 DOI: 10.1016/j.mce.2010.12.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 12/03/2010] [Accepted: 12/05/2010] [Indexed: 11/23/2022]
Abstract
The principal site of regulation of steroid hormone biosynthesis is the transfer of cholesterol from the outer to inner mitochondrial membrane. Hormonal stimulation of steroidogenic cells promotes this mitochondrial lipid import through a multi-protein complex, termed the transduceosome, spanning the two membranes. The transduceosome complex is assembled from multiple proteins, such as the steroidogenic acute regulatory (STAR) protein and translocator protein (TSPO), and requires their targeting to the mitochondria for transduceosome function. The vast majority of mitochondrial proteins, including those participating in cholesterol import, are encoded in the nucleus. Their subsequent mitochondrial incorporation is performed through a series of protein import machineries located in the outer and inner mitochondrial membranes. Here we review our current knowledge of the mitochondrial cholesterol import machinery of the transduceosome. This is complemented with descriptions of mitochondrial protein import machineries and mechanisms by which these machineries assemble the transduceosome in steroidogenic mitochondria.
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Affiliation(s)
- Andrew Midzak
- Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H3G 1A4, Canada
| | - Malena Rone
- Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H3G 1A4, Canada
| | - Yassaman Aghazadeh
- Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H3G 1A4, Canada
| | - Martine Culty
- Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, H3G 1A4, Canada
| | - Vassilios Papadopoulos
- Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Correspondence at The Research Institute of the McGill University Health Center, Montreal General Hospital, 1650 Cedar Avenue, C10-148, Montreal, Quebec H3G 1A4, Canada. Tel: 514-934-1934 ext. 44580; Fax: 514-934-8261;
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Müller JEN, Papic D, Ulrich T, Grin I, Schütz M, Oberhettinger P, Tommassen J, Linke D, Dimmer KS, Autenrieth IB, Rapaport D. Mitochondria can recognize and assemble fragments of a beta-barrel structure. Mol Biol Cell 2011; 22:1638-47. [PMID: 21460184 PMCID: PMC3093317 DOI: 10.1091/mbc.e10-12-0943] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The signal that directs newly synthesized mitochondrial β-barrel proteins from the cytosol to the organelle is poorly defined. The findings of this study demonstrate that, rather than a linear sequence, the structural information in four β-strands is sufficient for the mitochondria to recognize and assemble β-barrel protein. β-barrel proteins are found in the outer membranes of eukaryotic organelles of endosymbiotic origin as well as in the outer membrane of Gram-negative bacteria. Precursors of mitochondrial β-barrel proteins are synthesized in the cytosol and have to be targeted to the organelle. Currently, the signal that assures their specific targeting to mitochondria is poorly defined. To characterize the structural features needed for specific mitochondrial targeting and to test whether a full β-barrel structure is required, we expressed in yeast cells the β-barrel domain of the trimeric autotransporter Yersinia adhesin A (YadA). Trimeric autotransporters are found only in prokaryotes, where they are anchored to the outer membrane by a single 12-stranded β-barrel structure to which each monomer is contributing four β-strands. Importantly, we found that YadA is solely localized to the mitochondrial outer membrane, where it exists in a native trimeric conformation. These findings demonstrate that, rather than a linear sequence or a complete β-barrel structure, four β-strands are sufficient for the mitochondria to recognize and assemble a β-barrel protein. Remarkably, the evolutionary origin of mitochondria from bacteria enables them to import and assemble even proteins belonging to a class that is absent in eukaryotes.
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Affiliation(s)
- Jonas E N Müller
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
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Dukanovic J, Rapaport D. Multiple pathways in the integration of proteins into the mitochondrial outer membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:971-80. [DOI: 10.1016/j.bbamem.2010.06.021] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 06/22/2010] [Accepted: 06/23/2010] [Indexed: 11/25/2022]
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Gebert N, Ryan MT, Pfanner N, Wiedemann N, Stojanovski D. Mitochondrial protein import machineries and lipids: A functional connection. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1002-11. [DOI: 10.1016/j.bbamem.2010.08.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 08/02/2010] [Accepted: 08/02/2010] [Indexed: 01/01/2023]
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Biogenesis of Mitochondria: Dual Role of Tom7 in Modulating Assembly of the Preprotein Translocase of the Outer Membrane. J Mol Biol 2011; 405:113-24. [DOI: 10.1016/j.jmb.2010.11.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 10/25/2010] [Accepted: 11/02/2010] [Indexed: 11/21/2022]
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Dagley MJ, Gentle IE, Beilharz TH, Pettolino FA, Djordjevic JT, Lo TL, Uwamahoro N, Rupasinghe T, Tull DL, McConville M, Beaurepaire C, Nantel A, Lithgow T, Mitchell AP, Traven A. Cell wall integrity is linked to mitochondria and phospholipid homeostasis in Candida albicans through the activity of the post-transcriptional regulator Ccr4-Pop2. Mol Microbiol 2010; 79:968-89. [PMID: 21299651 DOI: 10.1111/j.1365-2958.2010.07503.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cell wall is essential for viability of fungi and is an effective drug target in pathogens such as Candida albicans. The contribution of post-transcriptional gene regulators to cell wall integrity in C. albicans is unknown. We show that the C. albicans Ccr4-Pop2 mRNA deadenylase, a regulator of mRNA stability and translation, is required for cell wall integrity. The ccr4/pop2 mutants display reduced wall β-glucans and sensitivity to the echinocandin caspofungin. Moreover, the deadenylase mutants are compromised for filamentation and virulence. We demonstrate that defective cell walls in the ccr4/pop2 mutants are linked to dysfunctional mitochondria and phospholipid imbalance. To further understand mitochondrial function in cell wall integrity, we screened a Saccharomyces cerevisiae collection of mitochondrial mutants. We identify several mitochondrial proteins required for caspofungin tolerance and find a connection between mitochondrial phospholipid homeostasis and caspofungin sensitivity. We focus on the mitochondrial outer membrane SAM complex subunit Sam37, demonstrating that it is required for both trafficking of phospholipids between the ER and mitochondria and cell wall integrity. Moreover, in C. albicans also Sam37 is essential for caspofungin tolerance. Our study provides the basis for an integrative view of mitochondrial function in fungal cell wall biogenesis and resistance to echinocandin antifungal drugs.
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Affiliation(s)
- Michael J Dagley
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
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50
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Yamano K, Tanaka-Yamano S, Endo T. Tom7 regulates Mdm10-mediated assembly of the mitochondrial import channel protein Tom40. J Biol Chem 2010; 285:41222-31. [PMID: 21036907 DOI: 10.1074/jbc.m110.163238] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
β-barrel membrane proteins in the mitochondrial outer membrane use the TOM40 complex to enter mitochondria and then the TOB/SAM complex to be assembled into the outer membrane. Tom7, a subunit of the TOM40 complex, regulates association of Mdm10 with the TOB complex. Here, we analyzed the role of Tom7 in assembly of β-barrel proteins, including Tom40, a central channel subunit of the TOM40 complex, and porin. Depletion of Tom7 decreased transient accumulation of Tom40 at the level of the TOB complex and retarded assembly of porin in vitro. On the other hand, overexpression of Tom7 resulted in enhanced accumulation of in vitro imported Tom40 in the TOB complex, yet it did not affect the in vitro assembly of porin. Site-specific photocross-linking in vivo revealed that Tom7 directly interacts with Tom40 through its transmembrane segment and with Mdm10. These results collectively show that Tom7 recruits Mdm10, enhancing its association with the MMM1 complex, to regulate timing of the release of Tom40 from the TOB complex for subsequent assembly into the TOM40 complex.
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Affiliation(s)
- Koji Yamano
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
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