1
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Yoshii SR, Barral Y. Fission-independent compartmentalization of mitochondria during budding yeast cell division. J Cell Biol 2024; 223:e202211048. [PMID: 38180475 PMCID: PMC10783438 DOI: 10.1083/jcb.202211048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 07/14/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
Lateral diffusion barriers compartmentalize membranes to generate polarity or asymmetrically partition membrane-associated macromolecules. Budding yeasts assemble such barriers in the endoplasmic reticulum (ER) and the outer nuclear envelope at the bud neck to retain aging factors in the mother cell and generate naïve and rejuvenated daughter cells. However, little is known about whether other organelles are similarly compartmentalized. Here, we show that the membranes of mitochondria are laterally compartmentalized at the bud neck and near the cell poles. The barriers in the inner mitochondrial membrane are constitutive, whereas those in the outer membrane form in response to stresses. The strength of mitochondrial diffusion barriers is regulated positively by spatial cues from the septin axis and negatively by retrograde (RTG) signaling. These data indicate that mitochondria are compartmentalized in a fission-independent manner. We propose that these diffusion barriers promote mitochondrial polarity and contribute to mitochondrial quality control.
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Affiliation(s)
- Saori R. Yoshii
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yves Barral
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
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2
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Chen S, Allen G, Panasenko OO, Collart MA. Not4-dependent targeting of MMF1 mRNA to mitochondria limits its expression via ribosome pausing, Egd1 ubiquitination, Caf130, no-go-decay and autophagy. Nucleic Acids Res 2023; 51:5022-5039. [PMID: 37094076 PMCID: PMC10250226 DOI: 10.1093/nar/gkad299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 04/11/2023] [Indexed: 04/26/2023] Open
Abstract
The Ccr4-Not complex is a conserved multi protein complex with diverse roles in the mRNA life cycle. Recently we determined that the Not1 and Not4 subunits of Ccr4-Not inversely regulate mRNA solubility and thereby impact dynamics of co-translation events. One mRNA whose solubility is limited by Not4 is MMF1 encoding a mitochondrial matrix protein. In this work we uncover a mechanism that limits MMF1 overexpression and depends upon its co-translational targeting to the mitochondria. We have named this mechanism Mito-ENCay. This mechanism relies on Not4 promoting ribosome pausing during MMF1 translation, and hence the co-translational docking of the MMF1 mRNA to mitochondria via the mitochondrial targeting sequence of the Mmf1 nascent chain, the Egd1 chaperone, the Om14 mitochondrial outer membrane protein and the co-translational import machinery. Besides co-translational Mitochondrial targeting, Mito-ENCay depends upon Egd1 ubiquitination by Not4, the Caf130 subunit of the Ccr4-Not complex, the mitochondrial outer membrane protein Cis1, autophagy and no-go-decay.
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Affiliation(s)
- Siyu Chen
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | - George Allen
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | - Olesya O Panasenko
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
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3
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Zhou J, Jung M, Dimmer KS, Rapaport D. The multi-factor modulated biogenesis of the mitochondrial multi-span protein Om14. J Biophys Biochem Cytol 2022; 221:213056. [PMID: 35262629 PMCID: PMC8916117 DOI: 10.1083/jcb.202112030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/26/2022] [Accepted: 02/03/2022] [Indexed: 12/14/2022] Open
Abstract
The mitochondrial outer membrane (MOM) harbors proteins that traverse the membrane via several helical segments and are called multi-span proteins. To obtain new insights into the biogenesis of these proteins, we utilized yeast mitochondria and the multi-span protein Om14. Testing different truncation variants, we show that while only the full-length protein contains all the information that assures perfect targeting specificity, shorter variants are targeted to mitochondria with compromised fidelity. Employing a specific insertion assay and various deletion strains, we show that proteins exposed to the cytosol do not contribute significantly to the biogenesis process. We further demonstrate that Mim1 and Porin support optimal membrane integration of Om14 but none of them are absolutely required. Unfolding of newly synthesized Om14, its optimal hydrophobicity, and higher fluidity of the membrane enhanced the import capacity of Om14. Collectively, these findings suggest that MOM multi-span proteins follow different biogenesis pathways in which proteinaceous elements and membrane behavior contribute to a variable extent to the combined efficiency.
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Affiliation(s)
- Jialin Zhou
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Martin Jung
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Kai S Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
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4
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Fu J, Zhou M, Gritsenko MA, Nakayasu ES, Song L, Luo ZQ. Legionella pneumophila modulates host energy metabolism by ADP-ribosylation of ADP/ATP translocases. eLife 2022; 11:73611. [PMID: 35084332 PMCID: PMC8820735 DOI: 10.7554/elife.73611] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
The intracellular pathogen Legionella pneumophila delivers more than 330 effectors into host cells by its Dot/Icm secretion system. Those effectors direct the biogenesis of the Legionella-containing vacuole (LCV) that permits its intracellular survival and replication. It has long been documented that the LCV is associated with mitochondria and a number of Dot/Icm effectors have been shown to target to this organelle. Yet, the biochemical function and host cell target of most of these effectors remain unknown. Here, we found that the Dot/Icm substrate Ceg3 (Lpg0080) is a mono-ADP-ribosyltransferase that localizes to the mitochondria in host cells where it attacks ADP/ATP translocases by ADP-ribosylation, and blunts their ADP/ATP exchange activity. The modification occurs on the second arginine residue in the -RRRMMM- element, which is conserved among all known ADP/ATP carriers from different organisms. Our results reveal modulation of host energy metabolism as a virulence mechanism for L. pneumophila.
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Affiliation(s)
- Jiaqi Fu
- Department of Biological Science, Purdue University, West Lafayette, United States
| | - Mowei Zhou
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, United States
| | - Marina A Gritsenko
- Biological Science Division, Pacific Northwest National Laboratory, Richland, United States
| | - Ernesto S Nakayasu
- Biological Science Division, Pacific Northwest National Laboratory, Richland, United States
| | - Lei Song
- Department of Respiratory Medicine, Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Department of Biological Science, Purdue University, West Lafayette, United States
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5
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Shvetsova A, Masud AJ, Schneider L, Bergmann U, Monteuuis G, Miinalainen IJ, Hiltunen JK, Kastaniotis AJ. A hunt for OM45 synthetic petite interactions in Saccharomyces cerevisiae reveals a role for Miro GTPase Gem1p in cristae structure maintenance. Microbiologyopen 2021; 10:e1238. [PMID: 34713605 PMCID: PMC8501180 DOI: 10.1002/mbo3.1238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 11/28/2022] Open
Abstract
Om45 is a major protein of the yeast's outer mitochondrial membrane under respiratory conditions. However, the cellular role of the protein has remained obscure. Previously, deletion mutant phenotypes have not been found, and clear amino acid sequence similarities that would allow inferring its functional role are not available. In this work, we describe synthetic petite mutants of GEM1 and UGO1 that depend on the presence of OM45 for respiratory growth, as well as the identification of several multicopy suppressors of the synthetic petite phenotypes. In the analysis of our mutants, we demonstrate that Om45p and Gem1p have a collaborative role in the maintenance of mitochondrial morphology, cristae structure, and mitochondrial DNA maintenance. A group of multicopy suppressors rescuing the synthetic lethal phenotypes of the mutants on non-fermentable carbon sources additionally supports this result. Our results imply that the synthetic petite phenotypes we observed are due to the disturbance of the inner mitochondrial membrane and point to this mitochondrial sub-compartment as the main target of action of Om45p, Ugo1p, and the yeast Miro GTPase Gem1p.
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Affiliation(s)
- Antonina Shvetsova
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - Ali J. Masud
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - Laura Schneider
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - Ulrich Bergmann
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - Geoffray Monteuuis
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
- Present address:
Department of Biochemistry and Developmental BiologyUniversity of HelsinkiHelsinkiFinland
| | - Ilkka J. Miinalainen
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - J. Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
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6
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Drwesh L, Rapaport D. Biogenesis pathways of α-helical mitochondrial outer membrane proteins. Biol Chem 2021; 401:677-686. [PMID: 32017702 DOI: 10.1515/hsz-2019-0440] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/21/2020] [Indexed: 01/23/2023]
Abstract
Mitochondria harbor in their outer membrane (OM) proteins of different topologies. These proteins are encoded by the nuclear DNA, translated on cytosolic ribosomes and inserted into their target organelle by sophisticated protein import machineries. Recently, considerable insights have been accumulated on the insertion pathways of proteins into the mitochondrial OM. In contrast, little is known regarding the early cytosolic stages of their biogenesis. It is generally presumed that chaperones associate with these proteins following their synthesis in the cytosol, thereby keeping them in an import-competent conformation and preventing their aggregation and/or mis-folding and degradation. In this review, we outline the current knowledge about the biogenesis of different mitochondrial OM proteins with various topologies, and highlight the recent findings regarding their import pathways starting from early cytosolic events until their recognition on the mitochondrial surface that lead to their final insertion into the mitochondrial OM.
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Affiliation(s)
- Layla Drwesh
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
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7
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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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8
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A Farnesylated Coxiella burnetii Effector Forms a Multimeric Complex at the Mitochondrial Outer Membrane during Infection. Infect Immun 2017; 85:IAI.01046-16. [PMID: 28242621 DOI: 10.1128/iai.01046-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/17/2017] [Indexed: 01/16/2023] Open
Abstract
Coxiella burnetii, the causative agent of Q fever, establishes a unique lysosome-derived intracellular niche termed the Coxiella-containing vacuole (CCV). The Dot/Icm-type IVB secretion system is essential for the biogenesis of the CCV and the intracellular replication of Coxiella Effector proteins, translocated into the host cell through this apparatus, act to modulate host trafficking and signaling processes to facilitate CCV development. Here we investigated the role of CBU0077, a conserved Coxiella effector that had previously been observed to localize to lysosomal membranes. CBU0077 was dispensable for the intracellular replication of Coxiella in HeLa and THP-1 cells and did not appear to participate in CCV biogenesis. Intriguingly, native and epitope-tagged CBU0077 produced by Coxiella displayed specific punctate localization at host cell mitochondria. As such, we designated CBU0077 MceA (mitochondrial Coxiellaeffector protein A). Analysis of ectopically expressed MceA truncations revealed that the capacity to traffic to mitochondria is encoded within the first 84 amino acids of this protein. MceA is farnesylated by the host cell; however, this does not impact mitochondrial localization. Examination of mitochondria isolated from infected cells revealed that MceA is specifically integrated into the mitochondrial outer membrane and forms a complex of approximately 120 kDa. Engineering Coxiella to express either MceA tagged with 3×FLAG or MceA tagged with 2×hemagglutinin allowed us to perform immunoprecipitation experiments that showed that MceA forms a homo-oligomeric species at the mitochondrial outer membrane during infection. This research reveals that mitochondria are a bona fide target of Coxiella effectors and MceA is a complex-forming effector at the mitochondrial outer membrane during Coxiella infection.
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9
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Konstantinov YM, Dietrich A, Weber-Lotfi F, Ibrahim N, Klimenko ES, Tarasenko VI, Bolotova TA, Koulintchenko MV. DNA import into mitochondria. BIOCHEMISTRY (MOSCOW) 2016; 81:1044-1056. [DOI: 10.1134/s0006297916100035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Ellenrieder L, Opaliński Ł, Becker L, Krüger V, Mirus O, Straub SP, Ebell K, Flinner N, Stiller SB, Guiard B, Meisinger C, Wiedemann N, Schleiff E, Wagner R, Pfanner N, Becker T. Separating mitochondrial protein assembly and endoplasmic reticulum tethering by selective coupling of Mdm10. Nat Commun 2016; 7:13021. [PMID: 27721450 PMCID: PMC5476798 DOI: 10.1038/ncomms13021] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 08/25/2016] [Indexed: 01/19/2023] Open
Abstract
The endoplasmic reticulum–mitochondria encounter structure (ERMES) connects the mitochondrial outer membrane with the ER. Multiple functions have been linked to ERMES, including maintenance of mitochondrial morphology, protein assembly and phospholipid homeostasis. Since the mitochondrial distribution and morphology protein Mdm10 is present in both ERMES and the mitochondrial sorting and assembly machinery (SAM), it is unknown how the ERMES functions are connected on a molecular level. Here we report that conserved surface areas on opposite sides of the Mdm10 β-barrel interact with SAM and ERMES, respectively. We generated point mutants to separate protein assembly (SAM) from morphology and phospholipid homeostasis (ERMES). Our study reveals that the β-barrel channel of Mdm10 serves different functions. Mdm10 promotes the biogenesis of α-helical and β-barrel proteins at SAM and functions as integral membrane anchor of ERMES, demonstrating that SAM-mediated protein assembly is distinct from ER-mitochondria contact sites. The protein Mdm10 is known to be present in the endoplasmic reticulum-mitochondria encounter structure (ERMES) and in mitochondrial sorting and assembly machinery (SAM). Here, the authors examine how this protein interacts with SAM and EMRES, showing that the SAM-mediated protein machinery is independent of ERMES.
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Affiliation(s)
- Lars Ellenrieder
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany.,Faculty of Biology, University of Freiburg, Freiburg D-79104, Germany
| | - Łukasz Opaliński
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany
| | - Lars Becker
- Division of Biophysics, School of Biology/Chemistry, University of Osnabrück, Osnabrück D-49034, Germany
| | - Vivien Krüger
- Division of Biophysics, School of Biology/Chemistry, University of Osnabrück, Osnabrück D-49034, Germany
| | - Oliver Mirus
- Molecular Cell Biology of Plants, University of Frankfurt, Frankfurt D-60438, Germany
| | - Sebastian P Straub
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany.,Faculty of Biology, University of Freiburg, Freiburg D-79104, Germany
| | - Katharina Ebell
- Division of Biophysics, School of Biology/Chemistry, University of Osnabrück, Osnabrück D-49034, Germany
| | - Nadine Flinner
- Molecular Cell Biology of Plants, University of Frankfurt, Frankfurt D-60438, Germany
| | - Sebastian B Stiller
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany
| | - Bernard Guiard
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Gif-sur-Yvette 91190, France
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg D-79104, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg D-79104, Germany
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, University of Frankfurt, Frankfurt D-60438, Germany.,Buchmann Institute of Molecular Life Sciences, Cluster of Excellence Macromolecular Complexes, University of Frankfurt, Frankfurt D-60438, Germany
| | - Richard Wagner
- Division of Biophysics, School of Biology/Chemistry, University of Osnabrück, Osnabrück D-49034, Germany.,Life Sciences &Chemistry, Focus Area Health, Jacobs University Bremen, Bremen D-28759, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg D-79104, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg D-79104, Germany
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11
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Ra EA, Lee TA, Won Kim S, Park A, Choi HJ, Jang I, Kang S, Hee Cheon J, Cho JW, Eun Lee J, Lee S, Park B. TRIM31 promotes Atg5/Atg7-independent autophagy in intestinal cells. Nat Commun 2016; 7:11726. [PMID: 27216961 PMCID: PMC4890305 DOI: 10.1038/ncomms11726] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 04/26/2016] [Indexed: 01/08/2023] Open
Abstract
Autophagy is responsible for the bulk degradation of cytosolic constituents and plays an essential role in the intestinal epithelium by controlling beneficial host-bacterial relationships. Atg5 and Atg7 are thought to be critical for autophagy. However, Atg5- or Atg7-deficient cells still form autophagosomes and autolysosomes, and are capable of removing proteins or bacteria. Here, we report that human TRIM31 (tripartite motif), an intestine-specific protein localized in mitochondria, is essential for promoting lipopolysaccharide-induced Atg5/Atg7-independent autophagy. TRIM31 directly interacts with phosphatidylethanolamine in a palmitoylation-dependent manner, leading to induction of autolysosome formation. Depletion of endogenous TRIM31 significantly increases the number of intestinal epithelial cells containing invasive bacteria. Crohn's disease patients display TRIM31 downregulation. Human cytomegalovirus-infected intestinal cells show a decrease in TRIM31 expression as well as a significant increase in bacterial load, reversible by the introduction of wild-type TRIM31. We provide insight into an alternative autophagy pathway that protects against intestinal pathogenic bacterial infection.
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Affiliation(s)
- Eun A. Ra
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Taeyun A. Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Seung Won Kim
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, South Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Areum Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Hyun jin Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Insook Jang
- Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, South Korea
| | - Sujin Kang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Jae Hee Cheon
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, South Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Jin Won Cho
- Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, South Korea
| | - Ji Eun Lee
- Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, South Korea
- Samsung Genome Institute (SGI), Samsung Medical Center, Seoul 06351, South Korea
| | - Sungwook Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Boyoun Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
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12
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Nucleic acid import into mitochondria: New insights into the translocation pathways. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:3165-81. [DOI: 10.1016/j.bbamcr.2015.09.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/16/2015] [Accepted: 09/10/2015] [Indexed: 11/18/2022]
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13
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Genome-Wide Screens in Saccharomyces cerevisiae Highlight a Role for Cardiolipin in Biogenesis of Mitochondrial Outer Membrane Multispan Proteins. Mol Cell Biol 2015; 35:3200-11. [PMID: 26149385 DOI: 10.1128/mcb.00107-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/26/2015] [Indexed: 11/20/2022] Open
Abstract
A special group of mitochondrial outer membrane (MOM) proteins spans the membrane several times via multiple helical segments. Such multispan proteins are synthesized on cytosolic ribosomes before their targeting to mitochondria and insertion into the MOM. Previous work recognized the import receptor Tom70 and the mitochondrial import (MIM) complex, both residents of the MOM, as required for optimal biogenesis of these proteins. However, their involvement is not sufficient to explain either the entire import pathway or its regulation. To identify additional factors that are involved in the biogenesis of MOM multispan proteins, we performed complementary high-throughput visual and growth screens in Saccharomyces cerevisiae. Cardiolipin (CL) synthase (Crd1) appeared as a candidate in both screens. Our results indeed demonstrate lower steady-state levels of the multispan proteins Ugo1, Scm4, and Om14 in mitochondria from crd1Δ cells. Importantly, MOM single-span proteins were not affected by this mutation. Furthermore, organelles lacking Crd1 had a lower in vitro capacity to import newly synthesized Ugo1 and Scm4 molecules. Crd1, which is located in the mitochondrial inner membrane, condenses phosphatidylglycerol together with CDP-diacylglycerol to obtain de novo synthesized CL molecules. Hence, our findings suggest that CL is an important component in the biogenesis of MOM multispan proteins.
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14
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Horvath SE, Rampelt H, Oeljeklaus S, Warscheid B, van der Laan M, Pfanner N. Role of membrane contact sites in protein import into mitochondria. Protein Sci 2015; 24:277-97. [PMID: 25514890 DOI: 10.1002/pro.2625] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 12/08/2014] [Indexed: 12/13/2022]
Abstract
Mitochondria import more than 1,000 different proteins from the cytosol. The proteins are synthesized as precursors on cytosolic ribosomes and are translocated by protein transport machineries of the mitochondrial membranes. Five main pathways for protein import into mitochondria have been identified. Most pathways use the translocase of the outer mitochondrial membrane (TOM) as the entry gate into mitochondria. Depending on specific signals contained in the precursors, the proteins are subsequently transferred to different intramitochondrial translocases. In this article, we discuss the connection between protein import and mitochondrial membrane architecture. Mitochondria possess two membranes. It is a long-standing question how contact sites between outer and inner membranes are formed and which role the contact sites play in the translocation of precursor proteins. A major translocation contact site is formed between the TOM complex and the presequence translocase of the inner membrane (TIM23 complex), promoting transfer of presequence-carrying preproteins to the mitochondrial inner membrane and matrix. Recent findings led to the identification of contact sites that involve the mitochondrial contact site and cristae organizing system (MICOS) of the inner membrane. MICOS plays a dual role. It is crucial for maintaining the inner membrane cristae architecture and forms contacts sites to the outer membrane that promote translocation of precursor proteins into the intermembrane space and outer membrane of mitochondria. The view is emerging that the mitochondrial protein translocases do not function as independent units, but are embedded in a network of interactions with machineries that control mitochondrial activity and architecture.
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Affiliation(s)
- Susanne E Horvath
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104, Freiburg, Germany
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15
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Lesnik C, Cohen Y, Atir-Lande A, Schuldiner M, Arava Y. OM14 is a mitochondrial receptor for cytosolic ribosomes that supports co-translational import into mitochondria. Nat Commun 2014; 5:5711. [PMID: 25487825 PMCID: PMC4268710 DOI: 10.1038/ncomms6711] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 10/30/2014] [Indexed: 11/13/2022] Open
Abstract
It is well established that import of proteins into mitochondria can occur after their complete synthesis by cytosolic ribosomes. Recently, an additional model was revived, proposing that some proteins are imported co-translationally. This model entails association of ribosomes with the mitochondrial outer membrane, shown to be mediated through the ribosome-associated chaperone nascent chain-associated complex (NAC). However, the mitochondrial receptor of this complex is unknown. Here, we identify the Saccharomyces cerevisiae outer membrane protein OM14 as a receptor for NAC. OM14Δ mitochondria have significantly lower amounts of associated NAC and ribosomes, and ribosomes from NAC[Δ] cells have reduced levels of associated OM14. Importantly, mitochondrial import assays reveal a significant decrease in import efficiency into OM14Δ mitochondria, and OM14-dependent import necessitates NAC. Our results identify OM14 as the first mitochondrial receptor for ribosome-associated NAC and reveal its importance for import. These results provide a strong support for an additional, co-translational mode of import into mitochondria. Mitochondrial proteins can be imported post-translationally; however, a role for co-translational import has recently provoked renewed interest. Lesnik et al. identify OM14 as a mitochondrial ribosome receptor required for efficient co-translational import of mitochondrial proteins.
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Affiliation(s)
- Chen Lesnik
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yifat Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Avigail Atir-Lande
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yoav Arava
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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16
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Wenz LS, Opaliński L, Schuler MH, Ellenrieder L, Ieva R, Böttinger L, Qiu J, van der Laan M, Wiedemann N, Guiard B, Pfanner N, Becker T. The presequence pathway is involved in protein sorting to the mitochondrial outer membrane. EMBO Rep 2014; 15:678-85. [PMID: 24781695 DOI: 10.1002/embr.201338144] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The mitochondrial outer membrane contains integral α-helical and β-barrel proteins that are imported from the cytosol. The machineries importing β-barrel proteins have been identified, however, different views exist on the import of α-helical proteins. It has been reported that the biogenesis of Om45, the most abundant signal-anchored protein, does not depend on proteinaceous components, but involves direct insertion into the outer membrane. We show that import of Om45 occurs via the translocase of the outer membrane and the presequence translocase of the inner membrane. Assembly of Om45 in the outer membrane involves the MIM machinery. Om45 thus follows a new mitochondrial biogenesis pathway that uses elements of the presequence import pathway to direct a protein to the outer membrane.
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Affiliation(s)
- Lena-Sophie Wenz
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany Faculty of Biology, Universität Freiburg, Freiburg, Germany
| | - Lukasz Opaliński
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany
| | - Max-Hinderk Schuler
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany
| | - Lars Ellenrieder
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany Faculty of Biology, Universität Freiburg, Freiburg, Germany
| | - Raffaele Ieva
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany
| | - Lena Böttinger
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany Faculty of Biology, Universität Freiburg, Freiburg, Germany
| | - Jian Qiu
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany Spemann Graduate School of Biology and Medicine, Universität Freiburg, Freiburg, Germany
| | - Martin van der Laan
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
| | - Nils Wiedemann
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
| | - Bernard Guiard
- Centre de Génétique Moléculaire, CNRS, Gif-sur-Yvette, France
| | - Nikolaus Pfanner
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
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17
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Sahi C, Kominek J, Ziegelhoffer T, Yu HY, Baranowski M, Marszalek J, Craig EA. Sequential duplications of an ancient member of the DnaJ-family expanded the functional chaperone network in the eukaryotic cytosol. Mol Biol Evol 2013; 30:985-98. [PMID: 23329686 DOI: 10.1093/molbev/mst008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Across eukaryotes, Hsp70-based chaperone machineries display an underlying unity in their sequence, structure, and biochemical mechanism of action, while working in a myriad of cellular processes. In good part, this extraordinary functional versatility is derived from the ability of a single Hsp70 to interact with an array of J-protein cochaperones to form a functional chaperone network. Among J-proteins, the DnaJ-type is the most prevalent, being present in all three kingdoms and in several different compartments of eukaryotic cells. However, because these ancient DnaJ-type proteins diverged at the base of the eukaryotic phylogeny, little is understood about the evolutionary basis of their diversification and thus the functional expansion of the chaperone network. Here, we report results of evolutionary and experimental analyses of two more recent members of the cytosolic DnaJ family of Saccharomyces cerevisiae, Xdj1 and Apj1, which emerged by sequential duplications of the ancient YDJ1 in Ascomycota. Sequence comparison and molecular modeling revealed that both Xdj1 and Apj1 maintained a domain organization similar to that of multifunctional Ydj1. However, despite these similarities, both Xdj1 and Apj1 evolved highly specialized functions. Xdj1 plays a unique role in the translocation of proteins from the cytosol into mitochondria. Apj1's specialized role is related to degradation of sumolyated proteins. Together these data provide the first clear example of cochaperone duplicates that evolved specialized functions, allowing expansion of the chaperone functional network, while maintaining the overall structural organization of their parental gene.
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Affiliation(s)
- Chandan Sahi
- Department of Biochemistry, University of Wisconsin-Madison, USA
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18
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Lauffer S, Mäbert K, Czupalla C, Pursche T, Hoflack B, Rödel G, Krause-Buchholz U. Saccharomyces cerevisiae porin pore forms complexes with mitochondrial outer membrane proteins Om14p and Om45p. J Biol Chem 2012; 287:17447-17458. [PMID: 22461620 DOI: 10.1074/jbc.m111.328328] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Numerous transport processes occur between the two mitochondrial (mt) membranes due to the diverse functions and metabolic processes of the mt organelle. The metabolite and ion transport through the mt outer membrane (OM) is widely assumed to be mediated by the porin pore, whereas in the mt inner membrane (IM) specific carriers are responsible for transport processes. Here, we provide evidence by means of Blue Native (BN)-PAGE analysis, co-immunoprecipitation, and tandem affinity purification that the two mt OM proteins Om14p and Om45p associate with the porin pore. Porin molecules seem to assemble independently to build the core unit. A subpopulation of these core units interacts with Om14p and Om45p. With preparative tandem affinity purification followed by MS analysis, we could identify interaction partners of this OM complex, which are mainly localized within the mt IM and function as carriers for diverse molecules. We propose a model for the role of the two OM proteins in addressing the porin pore to bind to specific channels in the mt IM to facilitate transport of metabolites.
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Affiliation(s)
- Susann Lauffer
- Institute of Genetics, Technische Universität Dresden, 01062 Dresden and.
| | - Katrin Mäbert
- Institute of Genetics, Technische Universität Dresden, 01062 Dresden and
| | - Cornelia Czupalla
- Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Theresia Pursche
- Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Bernard Hoflack
- Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Gerhard Rödel
- Institute of Genetics, Technische Universität Dresden, 01062 Dresden and
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19
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Dimmer KS, Papić D, Schumann B, Sperl D, Krumpe K, Walther DM, Rapaport D. A crucial role of Mim2 in the biogenesis of mitochondrial outer membrane proteins. J Cell Sci 2012; 125:3464-73. [DOI: 10.1242/jcs.103804] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Most of the mitochondrial outer membrane (MOM) proteins contain helical transmembrane domains. Some of the single span proteins and all known multiple span proteins are inserted into the membrane in a pathway which depends on the MOM protein Mitochondrial Import 1 (Mim1). So far it has been unknown whether additional proteins are required for this process. Here we describe the identification and characterization of Mim2, a novel protein of the mitochondrial outer membrane that has a crucial role in the biogenesis of MOM helical proteins. Mim2 physically and genetically interacts with Mim1 and both proteins form the MIM complex. Cells lacking Mim2 exhibit a severely reduced growth rate and lower steady state levels of helical MOM proteins. In addition, absence of Mim2 leads to compromised assembly of the translocase of the outer mitochondrial membrane (TOM complex), hampered mitochondrial protein import, and defects in mitochondrial morphology. In summary, the current study demonstrates that Mim2 is a novel central player in the biogenesis of MOM proteins.
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20
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Becker T, Wenz LS, Krüger V, Lehmann W, Müller JM, Goroncy L, Zufall N, Lithgow T, Guiard B, Chacinska A, Wagner R, Meisinger C, Pfanner N. The mitochondrial import protein Mim1 promotes biogenesis of multispanning outer membrane proteins. ACTA ACUST UNITED AC 2011; 194:387-95. [PMID: 21825073 PMCID: PMC3153637 DOI: 10.1083/jcb.201102044] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Mim1 complex imports α-helical mitochondrial outer membrane proteins with multiple transmembrane segments. The mitochondrial outer membrane contains translocase complexes for the import of precursor proteins. The translocase of the outer membrane complex functions as a general preprotein entry gate, whereas the sorting and assembly machinery complex mediates membrane insertion of β-barrel proteins of the outer membrane. Several α-helical outer membrane proteins are known to carry multiple transmembrane segments; however, only limited information is available on the biogenesis of these proteins. We report that mitochondria lacking the mitochondrial import protein 1 (Mim1) are impaired in the biogenesis of multispanning outer membrane proteins, whereas overexpression of Mim1 stimulates their import. The Mim1 complex cooperates with the receptor Tom70 in binding of precursor proteins and promotes their insertion and assembly into the outer membrane. We conclude that the Mim1 complex plays a central role in the import of α-helical outer membrane proteins with multiple transmembrane segments.
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Affiliation(s)
- Thomas Becker
- Institute for Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Freiburg, Germany
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21
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Papic D, Krumpe K, Dukanovic J, Dimmer KS, Rapaport D. Multispan mitochondrial outer membrane protein Ugo1 follows a unique Mim1-dependent import pathway. ACTA ACUST UNITED AC 2011; 194:397-405. [PMID: 21825074 PMCID: PMC3153653 DOI: 10.1083/jcb.201102041] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The mitochondrial outer membrane (MOM) harbors several multispan proteins that execute various functions. Despite their importance, the mechanisms by which these proteins are recognized and inserted into the outer membrane remain largely unclear. In this paper, we address this issue using yeast mitochondria and the multispan protein Ugo1. Using a specific insertion assay and analysis by native gel electrophoresis, we show that the import receptor Tom70, but not its partner Tom20, is involved in the initial recognition of the Ugo1 precursor. Surprisingly, the import pore formed by the translocase of the outer membrane complex appears not to be required for the insertion process. Conversely, the multifunctional outer membrane protein mitochondrial import 1 (Mim1) plays a central role in mediating the insertion of Ugo1. Collectively, these results suggest that Ugo1 is inserted into the MOM by a novel pathway in which Tom70 and Mim1 contribute to the efficiency and selectivity of the process.
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Affiliation(s)
- Drazen Papic
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
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22
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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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23
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Imai K, Fujita N, Gromiha MM, Horton P. Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins. BMC Genomics 2011; 12:79. [PMID: 21272379 PMCID: PMC3045335 DOI: 10.1186/1471-2164-12-79] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 01/28/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The outer membranes of mitochondria are thought to be homologous to the outer membranes of Gram negative bacteria, which contain 100's of distinct families of β-barrel membrane proteins (BOMPs) often forming channels for transport of nutrients or drugs. However, only four families of mitochondrial BOMPs (MBOMPs) have been confirmed to date. Although estimates as high as 100 have been made in the past, the number of yet undiscovered MBOMPs is an open question. Fortunately, the recent discovery of a membrane integration signal (the β-signal) for MBOMPs gave us an opportunity to look for undiscovered MBOMPs. RESULTS We present the results of a comprehensive survey of eukaryotic protein sequences intended to identify new MBOMPs. Our search employs recent results on β-signals as well as structural information and a novel BOMP predictor trained on both bacterial and mitochondrial BOMPs. Our principal finding is circumstantial evidence suggesting that few MBOMPs remain to be discovered, if one assumes that, like known MBOMPs, novel MBOMPs will be monomeric and β-signal dependent. In addition to this, our analysis of MBOMP homologs reveals some exceptions to the current model of the β-signal, but confirms its consistent presence in the C-terminal region of MBOMP proteins. We also report a β-signal independent search for MBOMPs against the yeast and Arabidopsis proteomes. We find no good candidates MBOMPs in yeast but the Arabidopsis results are less conclusive. CONCLUSIONS Our results suggest there are no remaining MBOMPs left to discover in yeast; and if one assumes all MBOMPs are β-signal dependent, few MBOMP families remain undiscovered in any sequenced organism.
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Affiliation(s)
- Kenichiro Imai
- AIST, Computational Biology Research Center, Tokyo, Aomi 135-0064, Japan
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24
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Tong J, Dolezal P, Selkrig J, Crawford S, Simpson AGB, Noinaj N, Buchanan SK, Gabriel K, Lithgow T. Ancestral and derived protein import pathways in the mitochondrion of Reclinomonas americana. Mol Biol Evol 2010; 28:1581-91. [PMID: 21081480 DOI: 10.1093/molbev/msq305] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The evolution of mitochondria from ancestral bacteria required that new protein transport machinery be established. Recent controversy over the evolution of these new molecular machines hinges on the degree to which ancestral bacterial transporters contributed during the establishment of the new protein import pathway. Reclinomonas americana is a unicellular eukaryote with the most gene-rich mitochondrial genome known, and the large collection of membrane proteins encoded on the mitochondrial genome of R. americana includes a bacterial-type SecY protein transporter. Analysis of expressed sequence tags shows R. americana also has components of a mitochondrial protein translocase or "translocase in the inner mitochondrial membrane complex." Along with several other membrane proteins encoded on the mitochondrial genome Cox11, an assembly factor for cytochrome c oxidase retains sequence features suggesting that it is assembled by the SecY complex in R. americana. Despite this, protein import studies show that the RaCox11 protein is suited for import into mitochondria and functional complementation if the gene is transferred into the nucleus of yeast. Reclinomonas americana provides direct evidence that bacterial protein transport pathways were retained, alongside the evolving mitochondrial protein import machinery, shedding new light on the process of mitochondrial evolution.
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Affiliation(s)
- Janette Tong
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, Australia
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25
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Kerner J, Lee K, Hoppel CL. Post-translational modifications of mitochondrial outer membrane proteins. Free Radic Res 2010; 45:16-28. [DOI: 10.3109/10715762.2010.515218] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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26
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Ohlmeier S, Hiltunen JK, Bergmann U. Protein phosphorylation in mitochondria - A study on fermentative and respiratory growth of Saccharomyces cerevisiae. Electrophoresis 2010; 31:2869-81. [DOI: 10.1002/elps.200900759] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Minor modifications and major adaptations: the evolution of molecular machines driving mitochondrial protein import. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:947-54. [PMID: 20659421 DOI: 10.1016/j.bbamem.2010.07.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Revised: 07/17/2010] [Accepted: 07/20/2010] [Indexed: 11/23/2022]
Abstract
Bacterial endosymbionts gave rise to mitochondria in a process that depended on the acquisition of protein import pathways. Modification and in some cases major re-tooling of the endosymbiont's cellular machinery produced these pathways, establishing mitochondria as organelles common to all eukaryotic cells. The legacy of this evolutionary tinkering can be seen in the homologies and structural similarities between mitochondrial protein import machinery and modern day bacterial proteins. Comparative analysis of these systems is revealing both possible routes for the evolution of the mitochondrial membrane translocases and a greater understanding of the mechanisms behind mitochondrial protein import. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
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28
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Saliola M, D'Amici S, Sponziello M, Mancini P, Tassone P, Falcone C. The transdehydrogenase genes KlNDE1 and KlNDI1 regulate the expression of KlGUT2 in the yeast Kluyveromyces lactis. FEMS Yeast Res 2010; 10:518-26. [PMID: 20491935 DOI: 10.1111/j.1567-1364.2010.00631.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
KlNDE1 and KlNDI1 code for two inner mitochondrial membrane transdehydrogenases involved in the maintenance of the intracellular NAD(P)H redox balance. The function of these genes during the utilization of fermentative and respiratory carbon sources was studied. During growth in glucose, deletion of KlNDE1 and KlNDI1 led to an altered kinetic of ethanol and glycerol accumulation compared with the wild type; in addition, KlndiDelta was unable to grow in respiratory substrates. Northern analysis and GFP-fusion experiments showed that KlNDE1 and KlNDI1 regulate the expression of KlGUT2, a component of the glycerol-3-phosphate shuttle. Moreover, both genes seem to be involved in the biogenesis of the mitochondrial tubular network.
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Affiliation(s)
- Michele Saliola
- Department of Cell and Developmental Biology, University of Rome La Sapienza, Rome, Italy.
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29
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Two Modular Forms of the Mitochondrial Sorting and Assembly Machinery Are Involved in Biogenesis of α-Helical Outer Membrane Proteins. J Mol Biol 2010; 396:540-9. [DOI: 10.1016/j.jmb.2009.12.026] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 12/11/2009] [Accepted: 12/13/2009] [Indexed: 11/19/2022]
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30
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Abstract
Mitochondria possess a dedicated-chaperone system in the intermembrane space, the small Tims that are ubiquitous in all eukaryotes from yeast to man. They escort membrane proteins to the outer or the inner membrane for proper insertion. These mitochondrial chaperones do not require external energy to perform their function and have structural similarities to other ATP-independent chaperones. Here, we discuss their structural properties and how these relate to their chaperoning function in the mitochondrial intermembrane space.
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Affiliation(s)
- Nikos Petrakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (IMBB-FORTH), Heraklion, Crete, Greece
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31
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Rijken PJ, De Kruijff B, De Kroon AIPM. Phosphatidylcholine is essential for efficient functioning of the mitochondrial glycerol-3-phosphate dehydrogenase Gut2 inSaccharomyces cerevisiae. Mol Membr Biol 2009; 24:269-81. [PMID: 17520483 DOI: 10.1080/09687860701210732] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Gut2, the mitochondrial glycerol-3-phosphate dehydrogenase, was previously shown to become preferentially labelled with photoactivatable phosphatidylcholine (PC), pointing to a functional relation between these molecules. In the present study we analyzed whether Gut2 functioning depends on the PC content of yeast cells, using PC biosynthetic mutants in which the PC content was lowered. PC depletion was found to reduce growth on glycerol and to increase glycerol excretion, both indicating that PC is needed for optimal Gut2 functioning in vivo. Using several in vitro approaches the nature of the dependence of Gut2 functioning on cellular PC contents was investigated. The results of these experiments suggest that it is unlikely that the effects observed in vivo are due to changes in cellular Gut2 content, in specific activity of Gut2 in isolated mitochondria, or in the membrane association of Gut2, upon lowering the PC level. The in vivo effects are more likely an indirect result of PC depletion-induced changes in the cellular context in which Gut2 functions, that are not manifested in the in vitro systems used.
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Affiliation(s)
- Pieter J Rijken
- Department Biochemistry of Membranes, Bijvoet Institute and Institute of Biomembranes, Utrecht University, The Netherlands.
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Lueder F, Lithgow T. The three domains of the mitochondrial outer membrane protein Mim1 have discrete functions in assembly of the TOM complex. FEBS Lett 2009; 583:1475-80. [PMID: 19345216 DOI: 10.1016/j.febslet.2009.03.064] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Revised: 03/18/2009] [Accepted: 03/27/2009] [Indexed: 11/28/2022]
Abstract
The assembly of mitochondrial outer membrane proteins is an essential process, mediated by the SAM complex and a set of additional protein modules. We show that one of these, Mim1, is anchored in the outer membrane with its N-terminus exposed to the cytosol and its C-terminus in the mitochondrial intermembrane space. Using an in vitro assay to measure the multi-step pathway for assembly of Tom40 into the TOM complex, we find that an "early reaction" mediated by the SAM complex is regulated by the N-terminal domain of Mim1. In addition, a "late reaction" catalysed by the Sam37 subunit of the SAM complex is also influenced by Mim1. Thus, Mim1 participates at multiple stages in the assembly of the TOM complex.
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Affiliation(s)
- Franziska Lueder
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
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Distler AM, Kerner J, Hoppel CL. Proteomics of mitochondrial inner and outer membranes. Proteomics 2009; 8:4066-82. [PMID: 18763707 DOI: 10.1002/pmic.200800102] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
For the proteomic study of mitochondrial membranes, documented high quality mitochondrial preparations are a necessity to ensure proper localization. Despite the state-of-the-art technologies currently in use, there is no single technique that can be used for all studies of mitochondrial membrane proteins. Herein, we use examples to highlight solubilization techniques, different chromatographic methods, and developments in gel electrophoresis for proteomic analysis of mitochondrial membrane proteins. Blue-native gel electrophoresis has been successful not only for dissection of the inner membrane oxidative phosphorylation system, but also for the components of the outer membrane such as those involved in protein import. Identification of PTMs such as phosphorylation, acetylation, and nitration of mitochondrial membrane proteins has been greatly improved by the use of affinity techniques. However, understanding of the biological effect of these modifications is an area for further exploration. The rapid development of proteomic methods for both identification and quantitation, especially for modifications, will greatly impact the understanding of the mitochondrial membrane proteome.
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Affiliation(s)
- Anne M Distler
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
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Gatsos X, Perry AJ, Anwari K, Dolezal P, Wolynec PP, Likić VA, Purcell AW, Buchanan SK, Lithgow T. Protein secretion and outer membrane assembly in Alphaproteobacteria. FEMS Microbiol Rev 2008; 32:995-1009. [PMID: 18759741 PMCID: PMC2635482 DOI: 10.1111/j.1574-6976.2008.00130.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 06/23/2008] [Accepted: 07/18/2008] [Indexed: 11/17/2022] Open
Abstract
The assembly of beta-barrel proteins into membranes is a fundamental process that is essential in Gram-negative bacteria, mitochondria and plastids. Our understanding of the mechanism of beta-barrel assembly is progressing from studies carried out in Escherichia coli and Neisseria meningitidis. Comparative sequence analysis suggests that while many components mediating beta-barrel protein assembly are conserved in all groups of bacteria with outer membranes, some components are notably absent. The Alphaproteobacteria in particular seem prone to gene loss and show the presence or absence of specific components mediating the assembly of beta-barrels: some components of the pathway appear to be missing from whole groups of bacteria (e.g. Skp, YfgL and NlpB), other proteins are conserved but are missing characteristic domains (e.g. SurA). This comparative analysis is also revealing important structural signatures that are vague unless multiple members from a protein family are considered as a group (e.g. tetratricopeptide repeat (TPR) motifs in YfiO, beta-propeller signatures in YfgL). Given that the process of the beta-barrel assembly is conserved, analysis of outer membrane biogenesis in Alphaproteobacteria, the bacterial group that gave rise to mitochondria, also promises insight into the assembly of beta-barrel proteins in eukaryotes.
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Affiliation(s)
- Xenia Gatsos
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Andrew J Perry
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Khatira Anwari
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Pavel Dolezal
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - P Peter Wolynec
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Vladimir A Likić
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Trevor Lithgow
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
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Saliola M, Sponziello M, D'Amici S, Lodi T, Falcone C. Characterization of KlGUT2, a gene of the glycerol-3-phosphate shuttle, in Kluyveromyces lactis. FEMS Yeast Res 2008; 8:697-705. [PMID: 18503541 DOI: 10.1111/j.1567-1364.2008.00386.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
KlGUT2 encodes the mitochondrial component of the glycerol-3-phosphate shuttle in Kluyveromyces lactis, a dehydrogenase involved in the maintenance of the NADH redox balance and in glycerol utilization. Deletion of KlGUT2 led to glycerol accumulation during growth in glucose and growth retardation in ethanol. In addition, KlGUT2 deletion altered the expression of other mitochondrial dehydrogenases that contribute to the maintenance of the intracellular redox balance, suggesting a rerouting of ethanol oxidation from the cytoplasm to the mitochondria. Finally, Northern analysis showed that KlGUT2 has two transcripts: one constitutively expressed and dependent on HGT1, the high-affinity hexose transporter gene, and the other induced under respiratory conditions.
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Affiliation(s)
- Michele Saliola
- Department of Cell and Developmental Biology, University of Rome La Sapienza, Piazzale Aldo Moro, Rome, Italy.
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Walther DM, Rapaport D. Biogenesis of mitochondrial outer membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1793:42-51. [PMID: 18501716 DOI: 10.1016/j.bbamcr.2008.04.013] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 04/15/2008] [Accepted: 04/25/2008] [Indexed: 11/29/2022]
Abstract
Mitochondria are surrounded by two distinct membranes: the outer and the inner membrane. The mitochondrial outer membrane mediates numerous interactions between the mitochondrial metabolic and genetic systems and the rest of the eukaryotic cell. Proteins of this membrane are nuclear-encoded and synthesized as precursor proteins in the cytosol. They are targeted to the mitochondria and inserted into their target membrane via various pathways. This review summarizes our current knowledge of the sorting signals for this specific targeting and describes the mechanisms by which the mitochondrial import machineries recognize precursor proteins, mediate their membrane integration and facilitate assembly into functional complexes.
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Affiliation(s)
- Dirk M Walther
- Interfakultäres Institut für Biochemie, Hoppe-Seyler-Str. 4, University of Tübingen, 72076 Tübingen, Germany
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The Transmembrane Segment of Tom20 Is Recognized by Mim1 for Docking to the Mitochondrial TOM Complex. J Mol Biol 2008; 376:694-704. [DOI: 10.1016/j.jmb.2007.12.021] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Revised: 12/09/2007] [Accepted: 12/11/2007] [Indexed: 11/18/2022]
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Becker T, Pfannschmidt S, Guiard B, Stojanovski D, Milenkovic D, Kutik S, Pfanner N, Meisinger C, Wiedemann N. Biogenesis of the Mitochondrial TOM Complex. J Biol Chem 2008; 283:120-127. [DOI: 10.1074/jbc.m706997200] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Stojanovski D, Guiard B, Kozjak-Pavlovic V, Pfanner N, Meisinger C. Alternative function for the mitochondrial SAM complex in biogenesis of alpha-helical TOM proteins. ACTA ACUST UNITED AC 2007; 179:881-93. [PMID: 18039934 PMCID: PMC2099199 DOI: 10.1083/jcb.200706043] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The mitochondrial outer membrane contains two preprotein translocases: the general translocase of outer membrane (TOM) and the β-barrel–specific sorting and assembly machinery (SAM). TOM functions as the central entry gate for nuclear-encoded proteins. The channel-forming Tom40 is a β-barrel protein, whereas all Tom receptors and small Tom proteins are membrane anchored by a transmembrane α-helical segment in their N- or C-terminal portion. Synthesis of Tom precursors takes place in the cytosol, and their import occurs via preexisting TOM complexes. The precursor of Tom40 is then transferred to SAM for membrane insertion and assembly. Unexpectedly, we find that the biogenesis of α-helical Tom proteins with a membrane anchor in the C-terminal portion is SAM dependent. Each SAM protein is necessary for efficient membrane integration of the receptor Tom22, whereas assembly of the small Tom proteins depends on Sam37. Thus, the substrate specificity of SAM is not restricted to β-barrel proteins but also includes the majority of α-helical Tom proteins.
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Affiliation(s)
- Diana Stojanovski
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Universität Freiburg, D-79104 Freiburg, Germany
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40
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Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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