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Nieto-Panqueva F, Vázquez-Acevedo M, Hamel PP, González-Halphen D. Identification of factors limiting the allotopic production of the Cox2 subunit of yeast cytochrome c oxidase. Genetics 2024; 227:iyae058. [PMID: 38626319 DOI: 10.1093/genetics/iyae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/18/2024] Open
Abstract
Mitochondrial genes can be artificially relocalized in the nuclear genome in a process known as allotopic expression, such is the case of the mitochondrial cox2 gene, encoding subunit II of cytochrome c oxidase (CcO). In yeast, cox2 can be allotopically expressed and is able to restore respiratory growth of a cox2-null mutant if the Cox2 subunit carries the W56R substitution within the first transmembrane stretch. However, the COX2W56R strain exhibits reduced growth rates and lower steady-state CcO levels when compared to wild-type yeast. Here, we investigated the impact of overexpressing selected candidate genes predicted to enhance internalization of the allotopic Cox2W56R precursor into mitochondria. The overproduction of Cox20, Oxa1, and Pse1 facilitated Cox2W56R precursor internalization, improving the respiratory growth of the COX2W56R strain. Overproducing TIM22 components had a limited effect on Cox2W56R import, while overproducing TIM23-related components showed a negative effect. We further explored the role of the Mgr2 subunit within the TIM23 translocator in the import process by deleting and overexpressing the MGR2 gene. Our findings indicate that Mgr2 is instrumental in modulating the TIM23 translocon to correctly sort Cox2W56R. We propose a biogenesis pathway followed by the allotopically produced Cox2 subunit based on the participation of the 2 different structural/functional forms of the TIM23 translocon, TIM23MOTOR and TIM23SORT, that must follow a concerted and sequential mode of action to insert Cox2W56R into the inner mitochondrial membrane in the correct Nout-Cout topology.
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Affiliation(s)
- Felipe Nieto-Panqueva
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-243, 04510 D.F. (Mexico), México
| | - Miriam Vázquez-Acevedo
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-243, 04510 D.F. (Mexico), México
| | - Patrice P Hamel
- Department of Molecular Genetics and Department of Biological Chemistry and Pharmacology, The Ohio State University, 582 Aronoff laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA
- School of BioScience and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632 014, India
| | - Diego González-Halphen
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-243, 04510 D.F. (Mexico), México
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2
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Jung SJ, Sridhara S, Ott M. Early steps in the biogenesis of mitochondrially encoded oxidative phosphorylation subunits. IUBMB Life 2024; 76:125-139. [PMID: 37712772 DOI: 10.1002/iub.2784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/10/2023] [Indexed: 09/16/2023]
Abstract
The complexes mediating oxidative phosphorylation (OXPHOS) in the inner mitochondrial membrane consist of proteins encoded in the nuclear or the mitochondrial DNA. The mitochondrially encoded membrane proteins (mito-MPs) represent the catalytic core of these complexes and follow complicated pathways for biogenesis. Owing to their overall hydrophobicity, mito-MPs are co-translationally inserted into the inner membrane by the Oxa1 insertase. After insertion, OXPHOS biogenesis factors mediate the assembly of mito-MPs into complexes and participate in the regulation of mitochondrial translation, while protein quality control factors recognize and degrade faulty or excess proteins. This review summarizes the current understanding of these early steps occurring during the assembly of mito-MPs by concentrating on results obtained in the model organism baker's yeast.
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Affiliation(s)
- Sung-Jun Jung
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Martin Ott
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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3
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Nieto-Panqueva F, Rubalcava-Gracia D, Hamel PP, González-Halphen D. The constraints of allotopic expression. Mitochondrion 2023; 73:30-50. [PMID: 37739243 DOI: 10.1016/j.mito.2023.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Allotopic expression is the functional transfer of an organellar gene to the nucleus, followed by synthesis of the gene product in the cytosol and import into the appropriate organellar sub compartment. Here, we focus on mitochondrial genes encoding OXPHOS subunits that were naturally transferred to the nucleus, and critically review experimental evidence that claim their allotopic expression. We emphasize aspects that may have been overlooked before, i.e., when modifying a mitochondrial gene for allotopic expression━besides adapting the codon usage and including sequences encoding mitochondrial targeting signals━three additional constraints should be considered: (i) the average apparent free energy of membrane insertion (μΔGapp) of the transmembrane stretches (TMS) in proteins earmarked for the inner mitochondrial membrane, (ii) the final, functional topology attained by each membrane-bound OXPHOS subunit; and (iii) the defined mechanism by which the protein translocator TIM23 sorts cytosol-synthesized precursors. The mechanistic constraints imposed by TIM23 dictate the operation of two pathways through which alpha-helices in TMS are sorted, that eventually determine the final topology of membrane proteins. We used the biological hydrophobicity scale to assign an average apparent free energy of membrane insertion (μΔGapp) and a "traffic light" color code to all TMS of OXPHOS membrane proteins, thereby predicting which are more likely to be internalized into mitochondria if allotopically produced. We propose that the design of proteins for allotopic expression must make allowance for μΔGapp maximization of highly hydrophobic TMS in polypeptides whose corresponding genes have not been transferred to the nucleus in some organisms.
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Affiliation(s)
- Felipe Nieto-Panqueva
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Diana Rubalcava-Gracia
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico; Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrice P Hamel
- Department of Molecular Genetics and Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA; Vellore Institute of Technology (VIT), School of BioScience and Technology, Vellore, Tamil Nadu, India
| | - Diego González-Halphen
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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4
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Rodríguez-Caparrós A, Tani-ichi S, Casal Á, López-Ros J, Suñé C, Ikuta K, Hernández-Munain C. Interleukin-7 receptor signaling is crucial for enhancer-dependent TCRδ germline transcription mediated through STAT5 recruitment. Front Immunol 2022; 13:943510. [PMID: 36059467 PMCID: PMC9437428 DOI: 10.3389/fimmu.2022.943510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022] Open
Abstract
γδ T cells play important roles in immune responses by rapidly producing large quantities of cytokines. Recently, γδ T cells have been found to be involved in tissue homeostatic regulation, playing roles in thermogenesis, bone regeneration and synaptic plasticity. Nonetheless, the mechanisms involved in γδ T-cell development, especially the regulation of TCRδ gene transcription, have not yet been clarified. Previous studies have established that NOTCH1 signaling plays an important role in the Tcrg and Tcrd germline transcriptional regulation induced by enhancer activation, which is mediated through the recruitment of RUNX1 and MYB. In addition, interleukin-7 signaling has been shown to be required for Tcrg germline transcription, VγJγ rearrangement and γδ T-lymphocyte generation as well as for promoting T-cell survival. In this study, we discovered that interleukin-7 is required for the activation of enhancer-dependent Tcrd germline transcription during thymocyte development. These results indicate that the activation of both Tcrg and Tcrd enhancers during γδ T-cell development in the thymus depends on the same NOTCH1- and interleukin-7-mediated signaling pathways. Understanding the regulation of the Tcrd enhancer during thymocyte development might lead to a better understanding of the enhancer-dependent mechanisms involved in the genomic instability and chromosomal translocations that cause leukemia.
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Affiliation(s)
- Alonso Rodríguez-Caparrós
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Shizue Tani-ichi
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Áurea Casal
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Jennifer López-Ros
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Carlos Suñé
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Koichi Ikuta
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Cristina Hernández-Munain
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
- *Correspondence: Cristina Hernández-Munain,
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Liang L, Takamiya R, Miki Y, Heike K, Taketomi Y, Sugimoto N, Yamaguchi M, Shitara H, Nishito Y, Kobayashi T, Hirabayashi T, Murakami M. Group IVE cytosolic phospholipase A 2 limits psoriatic inflammation by mobilizing the anti-inflammatory lipid N-acylethanolamine. FASEB J 2022; 36:e22301. [PMID: 35478358 DOI: 10.1096/fj.202101958r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 12/17/2022]
Abstract
Psoriasis is an inflammatory disorder characterized by keratinocyte hyper-proliferation and Th17-type immune responses. However, the roles of bioactive lipids and the regulation of their biosynthesis in this chronic skin disease are not fully understood. Herein, we show that group IVE cytosolic phospholipase A2 (cPLA2 ε/PLA2G4E) plays a counterregulatory role against psoriatic inflammation by producing the anti-inflammatory lipid N-acylethanolamine (NAE). Lipidomics analysis of mouse skin revealed that NAE species and their precursors (N-acyl-phosphatidylethanolamine and glycerophospho-N-acylethanolamine) were robustly increased in parallel with the ongoing process of imiquimod (IMQ)-induced psoriasis, accompanied by a marked upregulation of cPLA2 ε in epidermal keratinocytes. Genetic deletion of cPLA2 ε exacerbated IMQ-induced ear swelling and psoriatic marker expression, with a dramatic reduction of NAE-related lipids in IMQ-treated, and even normal, skin. Stimulation of cultured human keratinocytes with psoriatic cytokines concomitantly increased PLA2G4E expression and NAE production, and supplementation with NAEs significantly attenuated the cytokine-induced upregulation of the psoriatic marker S100A9. Increased expression of cPLA2 ε was also evident in the epidermis of psoriatic patients. These findings reveal for the first time the in vivo role of cPLA2 ε, which is highly induced in the keratinocytes of the psoriatic skin, promotes the biosynthesis of NAE-related lipids, and contributes to limiting psoriatic inflammation.
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Affiliation(s)
- Luyiyun Liang
- Laboratory of Microenvironmental and Metabolic Health Science, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Rina Takamiya
- Laboratory of Microenvironmental and Metabolic Health Science, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshimi Miki
- Laboratory of Microenvironmental and Metabolic Health Science, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kanako Heike
- Department of Biology, Faculty of Science, Ochanomizu University, Tokyo, Japan
| | - Yoshitaka Taketomi
- Laboratory of Microenvironmental and Metabolic Health Science, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Sugimoto
- Laboratory of Microenvironmental and Metabolic Health Science, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Midori Yamaguchi
- Laboratory for Transgenic Technology, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hiroshi Shitara
- Laboratory for Transgenic Technology, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yasumasa Nishito
- Laboratory for Transgenic Technology, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Tetsuyuki Kobayashi
- Department of Biology, Faculty of Science, Ochanomizu University, Tokyo, Japan
| | - Tetsuya Hirabayashi
- Laboratory of Biomembrane, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Makoto Murakami
- Laboratory of Microenvironmental and Metabolic Health Science, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
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6
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Efficient integration of transmembrane domains depends on the folding properties of the upstream sequences. Proc Natl Acad Sci U S A 2021; 118:2102675118. [PMID: 34373330 PMCID: PMC8379923 DOI: 10.1073/pnas.2102675118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The topology of membrane proteins is defined by the successive integration of α-helical transmembrane domains at the Sec61 translocon. For each polypeptide segment of ∼20 residues entering the translocon, their combined hydrophobicities were previously shown to define membrane integration. Here, we discovered that different sequences preceding a potential transmembrane domain substantially affect the hydrophobicity threshold. Sequences that are rapidly folding, intrinsically disordered, very short, or strongly binding chaperones allow efficient integration at low hydrophobicity. Folding deficient mutant domains and artificial sequences not binding chaperones interfered with membrane integration likely by remaining partially unfolded and exposing hydrophobic surfaces that compete with the translocon for the emerging transmembrane segment, reducing integration efficiency. Rapid folding or strong chaperone binding thus promote efficient integration. The topology of most membrane proteins is defined by the successive integration of α-helical transmembrane domains at the Sec61 translocon. The translocon provides a pore for the transfer of polypeptide segments across the membrane while giving them lateral access to the lipid. For each polypeptide segment of ∼20 residues, the combined hydrophobicities of its constituent amino acids were previously shown to define the extent of membrane integration. Here, we discovered that different sequences preceding a potential transmembrane domain substantially affect its hydrophobicity requirement for integration. Rapidly folding domains, sequences that are intrinsically disordered or very short or capable of binding chaperones with high affinity, allow for efficient transmembrane integration with low-hydrophobicity thresholds for both orientations in the membrane. In contrast, long protein fragments, folding-deficient mutant domains, and artificial sequences not binding chaperones interfered with membrane integration, requiring higher hydrophobicity. We propose that the latter sequences, as they compact on their hydrophobic residues, partially folded but unable to reach a native state, expose hydrophobic surfaces that compete with the translocon for the emerging transmembrane segment, reducing integration efficiency. The results suggest that rapid folding or strong chaperone binding is required for efficient transmembrane integration.
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7
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Edwards R, Gerlich S, Tokatlidis K. The biogenesis of mitochondrial intermembrane space proteins. Biol Chem 2021; 401:737-747. [PMID: 32061164 DOI: 10.1515/hsz-2020-0114] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 02/13/2020] [Indexed: 01/09/2023]
Abstract
The mitochondrial intermembrane space (IMS) houses a large spectrum of proteins with distinct and critical functions. Protein import into this mitochondrial sub-compartment is underpinned by an intriguing variety of pathways, many of which are still poorly understood. The constricted volume of the IMS and the topological segregation by the inner membrane cristae into a bulk area surrounded by the boundary inner membrane and the lumen within the cristae is an important factor that adds to the complexity of the protein import, folding and assembly processes. We discuss the main import pathways into the IMS, but also how IMS proteins are degraded or even retro-translocated to the cytosol in an integrated network of interactions that is necessary to maintain a healthy balance of IMS proteins under physiological and cellular stress conditions. We conclude this review by highlighting new and exciting perspectives in this area with a view to develop a better understanding of yet unknown, likely unconventional import pathways, how presequence-less proteins can be targeted and the basis for dual localisation in the IMS and the cytosol. Such knowledge is critical to understanding the dynamic changes of the IMS proteome in response to stress, and particularly important for maintaining optimal mitochondrial fitness.
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Affiliation(s)
- Ruairidh Edwards
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ Scotland, UK
| | - Sarah Gerlich
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ Scotland, UK.,Department for Chemistry, Institute for Biochemistry, University of Cologne, 50674 Cologne, Germany
| | - Kostas Tokatlidis
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ Scotland, UK
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8
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Lee S, Lee H, Yoo S, Ieva R, van der Laan M, von Heijne G, Kim H. The Mgr2 subunit of the TIM23 complex regulates membrane insertion of marginal stop-transfer signals in the mitochondrial inner membrane. FEBS Lett 2019; 594:1081-1087. [PMID: 31764998 DOI: 10.1002/1873-3468.13692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/04/2019] [Accepted: 11/12/2019] [Indexed: 11/08/2022]
Abstract
The TIM23 complex mediates membrane insertion of presequence-containing mitochondrial proteins via a stop-transfer mechanism. Stop-transfer signals consist of hydrophobic transmembrane segments and flanking charges. Mgr2 functions as a lateral gatekeeper of the TIM23 complex. However, it remains elusive which features of stop-transfer signals are discriminated by Mgr2. To determine the effects of Mgr2 on the TIM23-mediated stop-transfer pathway, we measured membrane insertion of model transmembrane segments of varied hydrophobicity and flanking charges in Mgr2-deletion or -overexpression yeast strains. We found that upon deletion of Mgr2, the threshold hydrophobicity for membrane insertion, as well as the requirement for matrix-facing positive charges, is reduced. These results imply that the Mgr2-mediated gatekeeper function is important for controlling membrane sorting of marginal stop-transfer signals.
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Affiliation(s)
- Seoeun Lee
- School of Biological Sciences, Seoul National University, South Korea
| | - Hunsang Lee
- School of Biological Sciences, Seoul National University, South Korea.,Donnelly Centre, Toronto, Canada
| | - Suji Yoo
- School of Biological Sciences, Seoul National University, South Korea
| | - Raffaele Ieva
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, France
| | - Martin van der Laan
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling, PZMS, Saarland University, Homburg, Germany
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Hyun Kim
- School of Biological Sciences, Seoul National University, South Korea
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9
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Rubalcava-Gracia D, García-Rincón J, Pérez-Montfort R, Hamel PP, González-Halphen D. Key within-membrane residues and precursor dosage impact the allotopic expression of yeast subunit II of cytochrome c oxidase. Mol Biol Cell 2019; 30:2358-2366. [PMID: 31318312 PMCID: PMC6741066 DOI: 10.1091/mbc.e18-12-0788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Experimentally relocating mitochondrial genes to the nucleus for functional expression (allotopic expression) is a challenging process. The high hydrophobicity of mitochondria-encoded proteins seems to be one of the main factors preventing this allotopic expression. We focused on subunit II of cytochrome c oxidase (Cox2) to study which modifications may enable or improve its allotopic expression in yeast. Cox2 can be imported from the cytosol into mitochondria in the presence of the W56R substitution, which decreases the protein hydrophobicity and allows partial respiratory rescue of a cox2-null strain. We show that the inclusion of a positive charge is more favorable than substitutions that only decrease the hydrophobicity. We also searched for other determinants enabling allotopic expression in yeast by examining the COX2 gene in organisms where it was transferred to the nucleus during evolution. We found that naturally occurring variations at within-membrane residues in the legume Glycine max Cox2 could enable yeast COX2 allotopic expression. We also evidence that directing high doses of allotopically synthesized Cox2 to mitochondria seems to be counterproductive because the subunit aggregates at the mitochondrial surface. Our findings are relevant to the design of allotopic expression strategies and contribute to the understanding of gene retention in organellar genomes.
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Affiliation(s)
- Diana Rubalcava-Gracia
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Juan García-Rincón
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Ruy Pérez-Montfort
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Patrice Paul Hamel
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
| | - Diego González-Halphen
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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Mitochondrial presequence import: Multiple regulatory knobs fine-tune mitochondrial biogenesis and homeostasis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:930-944. [PMID: 30802482 DOI: 10.1016/j.bbamcr.2019.02.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 12/22/2022]
Abstract
Mitochondria are pivotal organelles for cellular signaling and metabolism, and their dysfunction leads to severe cellular stress. About 60-70% of the mitochondrial proteome consists of preproteins synthesized in the cytosol with an amino-terminal cleavable presequence targeting signal. The TIM23 complex transports presequence signals towards the mitochondrial matrix. Ultimately, the mature protein segments are either transported into the matrix or sorted to the inner membrane. To ensure accurate preprotein import into distinct mitochondrial sub-compartments, the TIM23 machinery adopts specific functional conformations and interacts with different partner complexes. Regulatory subunits modulate the translocase dynamics, tailoring the import reaction to the incoming preprotein. The mitochondrial membrane potential and the ATP generated via oxidative phosphorylation are key energy sources in driving the presequence import pathway. Thus, mitochondrial dysfunctions have rapid repercussions on biogenesis. Cellular mechanisms exploit the presequence import pathway to monitor mitochondrial dysfunctions and mount transcriptional and proteostatic responses to restore functionality.
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11
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Rubalcava-Gracia D, Vázquez-Acevedo M, Funes S, Pérez-Martínez X, González-Halphen D. Mitochondrial versus nuclear gene expression and membrane protein assembly: the case of subunit 2 of yeast cytochrome c oxidase. Mol Biol Cell 2018; 29:820-833. [PMID: 29437907 PMCID: PMC5905295 DOI: 10.1091/mbc.e17-09-0560] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/12/2018] [Accepted: 02/01/2018] [Indexed: 12/24/2022] Open
Abstract
Deletion of the yeast mitochondrial gene COX2, encoding subunit 2 (mtCox2) of cytochrome c oxidase (CcO), results in a respiratory-incompetent Δcox2 strain. For a cytosol-synthesized Cox2 to restore respiratory growth, it must carry the W56R mutation (cCox2W56R). Nevertheless, only a fraction of cCox2W56R is matured in mitochondria, allowing ∼60% steady-state accumulation of CcO. This can be attributed either to the point mutation or to an inefficient biogenesis of cCox2W56R. We generated a strain expressing the mutant protein mtCox2W56R inside mitochondria which should follow the canonical biogenesis of mitochondria-encoded Cox2. This strain exhibited growth rates, CcO steady-state levels, and CcO activity similar to those of the wild type; therefore, the efficiency of Cox2 biogenesis is the limiting step for successful allotopic expression. Upon coexpression of cCox2W56R and mtCox2, each protein assembled into CcO independently from its genetic origin, resulting in a mixed population of CcO with most complexes containing the mtCox2 version. Notably, the presence of the mtCox2 enhances cCox2W56R incorporation. We provide proof of principle that an allotopically expressed Cox2 may complement a phenotype due to a mutant mitochondrial COX2 gene. These results are relevant to developing a rational design of genes for allotopic expression intended to treat human mitochondrial diseases.
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Affiliation(s)
- Diana Rubalcava-Gracia
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad México, D. F., Mexico
| | - Miriam Vázquez-Acevedo
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad México, D. F., Mexico
| | - Soledad Funes
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad México, D. F., Mexico
| | - Xochitl Pérez-Martínez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad México, D. F., Mexico
| | - Diego González-Halphen
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad México, D. F., Mexico
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12
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Kirscht A, Sonntag Y, Kjellbom P, Johanson U. A structural preview of aquaporin 8 via homology modeling of seven vertebrate isoforms. BMC STRUCTURAL BIOLOGY 2018; 18:2. [PMID: 29454339 PMCID: PMC5816522 DOI: 10.1186/s12900-018-0081-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 01/25/2018] [Indexed: 11/10/2022]
Abstract
Background Aquaporins (AQPs) facilitate the passage of small neutral polar molecules across membranes of the cell. In animals there are four distinct AQP subfamilies, whereof AQP8 homologues constitute one of the smallest subfamilies with just one member in man. AQP8 conducts water, ammonia, urea, glycerol and H2O2 through various membranes of animal cells. This passive channel has been connected to a number of phenomena, such as volume change of mitochondria, ammonia neurotoxicity, and mitochondrial dysfunction related to oxidative stress. Currently, there is no experimentally determined structure of an AQP8, hence the structural understanding of this subfamily is limited. The recently solved structure of the plant AQP, AtTIP2;1, which has structural and functional features in common with AQP8s, has opened up for construction of homology models that are likely to be more accurate than previous models. Results Here we present homology models of seven vertebrate AQP8s. Modeling based on the AtTIP2;1 structure alone resulted in reasonable models except for the pore being blocked by a phenylalanine that is not present in AtTIP2;1. To achieve an open pore, these models were supplemented with models based on the bacterial water specific AQP, EcAqpZ, creating a chimeric monomeric model for each AQP8 isoform. The selectivity filter (also named the aromatic/arginine region), which defines the permeant substrate profile, comprises five amino acid residues in AtTIP2;1, including a histidine coming from loop C. Compared to AtTIP2;1, the selectivity filters of modelled AQP8s only deviates in that they are slightly more narrow and more hydrophobic due to a phenylalanine replacing the histidine from loop C. Interestingly, the models do not exclude the existence of a side pore beneath loop C similar to that described in the structure of AtTIP2;1. Conclusions Our models concur that AQP8s are likely to have an AtTIP2;1-like selectivity filter. The detailed description of the expected configuration of residues in the selectivity filters of AQP8s provides an excellent starting point for planning of as well as rationalizing the outcome of mutational studies. Our strategy to compile hybrid models based on several templates may prove useful also for other AQPs for which structural information is limited. Electronic supplementary material The online version of this article (10.1186/s12900-018-0081-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Kirscht
- Division of Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden
| | - Yonathan Sonntag
- Division of Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden
| | - Per Kjellbom
- Division of Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden
| | - Urban Johanson
- Division of Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, Box 124, SE-221 00, Lund, Sweden.
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13
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Lee S, Lee H, Yoo S, Kim H. Molecular insights into the m-AAA protease-mediated dislocation of transmembrane helices in the mitochondrial inner membrane. J Biol Chem 2017; 292:20058-20066. [PMID: 29030426 DOI: 10.1074/jbc.m117.796763] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 09/29/2017] [Indexed: 11/06/2022] Open
Abstract
Protein complexes involved in respiration, ATP synthesis, and protein import reside in the mitochondrial inner membrane; thus, proper regulation of these proteins is essential for cell viability. The m-AAA protease, a conserved hetero-hexameric AAA (ATPase associated with diverse cellular activities) protease, composed of the Yta10 and Yta12 proteins, regulates mitochondrial proteostasis by mediating protein maturation and degradation. It also recognizes and mediates the dislocation of membrane-embedded substrates, including foreign transmembrane (TM) segments, but the molecular mechanism involved in these processes remains elusive. This study investigated the role of the TM domains in the m-AAA protease by systematic replacement of one TM domain at a time in yeast. Our data indicated that replacement of the Yta10 TM2 domain abolishes membrane dislocation for only a subset of substrates, whereas replacement of the Yta12 TM2 domain impairs membrane dislocation for all tested substrates, suggesting different roles of the TM domains in each m-AAA protease subunit. Furthermore, m-AAA protease-mediated membrane dislocation was impaired in the presence of a large downstream hydrophilic moiety in a membrane substrate. This finding suggested that the m-AAA protease cannot dislocate large hydrophilic domains across the membrane, indicating that the membrane dislocation probably occurs in a lipid environment. In summary, this study highlights previously underappreciated biological roles of TM domains of the m-AAA proteases in mediating the recognition and dislocation of membrane-embedded substrates.
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Affiliation(s)
- Seoeun Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Hunsang Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea; Donnelly Centre, Toronto, Ontario M5S 3E1, Canada
| | - Suji Yoo
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Hyun Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
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14
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Straub SP, Stiller SB, Wiedemann N, Pfanner N. Dynamic organization of the mitochondrial protein import machinery. Biol Chem 2017; 397:1097-1114. [PMID: 27289000 DOI: 10.1515/hsz-2016-0145] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 05/17/2016] [Indexed: 01/12/2023]
Abstract
Mitochondria contain elaborate machineries for the import of precursor proteins from the cytosol. The translocase of the outer mitochondrial membrane (TOM) performs the initial import of precursor proteins and transfers the precursors to downstream translocases, including the presequence translocase and the carrier translocase of the inner membrane, the mitochondrial import and assembly machinery of the intermembrane space, and the sorting and assembly machinery of the outer membrane. Although the protein translocases can function as separate entities in vitro, recent studies revealed a close and dynamic cooperation of the protein import machineries to facilitate efficient transfer of precursor proteins in vivo. In addition, protein translocases were found to transiently interact with distinct machineries that function in the respiratory chain or in the maintenance of mitochondrial membrane architecture. Mitochondrial protein import is embedded in a regulatory network that ensures protein biogenesis, membrane dynamics, bioenergetic activity and quality control.
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15
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Sánchez-Vásquez L, Vázquez-Acevedo M, de la Mora J, Vega-deLuna F, Cardol P, Remacle C, Dreyfus G, González-Halphen D. Near-neighbor interactions of the membrane-embedded subunits of the mitochondrial ATP synthase of a chlorophycean alga. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:497-509. [DOI: 10.1016/j.bbabio.2017.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/25/2017] [Accepted: 04/29/2017] [Indexed: 12/24/2022]
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16
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Abstract
Mitochondria are essential organelles with numerous functions in cellular metabolism and homeostasis. Most of the >1,000 different mitochondrial proteins are synthesized as precursors in the cytosol and are imported into mitochondria by five transport pathways. The protein import machineries of the mitochondrial membranes and aqueous compartments reveal a remarkable variability of mechanisms for protein recognition, translocation, and sorting. The protein translocases do not operate as separate entities but are connected to each other and to machineries with functions in energetics, membrane organization, and quality control. Here, we discuss the versatility and dynamic organization of the mitochondrial protein import machineries. Elucidating the molecular mechanisms of mitochondrial protein translocation is crucial for understanding the integration of protein translocases into a large network that controls organelle biogenesis, function, and dynamics.
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Affiliation(s)
- Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, and BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany; ,
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, and BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany; ,
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17
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Mitochondrial OXA Translocase Plays a Major Role in Biogenesis of Inner-Membrane Proteins. Cell Metab 2016; 23:901-8. [PMID: 27166948 PMCID: PMC4873616 DOI: 10.1016/j.cmet.2016.04.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 01/02/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023]
Abstract
The mitochondrial inner membrane harbors three protein translocases. Presequence translocase and carrier translocase are essential for importing nuclear-encoded proteins. The oxidase assembly (OXA) translocase is required for exporting mitochondrial-encoded proteins; however, different views exist about its relevance for nuclear-encoded proteins. We report that OXA plays a dual role in the biogenesis of nuclear-encoded mitochondrial proteins. First, a systematic analysis of OXA-deficient mitochondria led to an unexpected expansion of the spectrum of OXA substrates imported via the presequence pathway. Second, biogenesis of numerous metabolite carriers depends on OXA, although they are not imported by the presequence pathway. We show that OXA is crucial for the biogenesis of the Tim18-Sdh3 module of the carrier translocase. The export translocase OXA is thus required for the import of metabolite carriers by promoting assembly of the carrier translocase. We conclude that OXA is of central importance for the biogenesis of the mitochondrial inner membrane.
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18
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Revisiting trends on mitochondrial mega-channels for the import of proteins and nucleic acids. J Bioenerg Biomembr 2016; 49:75-99. [DOI: 10.1007/s10863-016-9662-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/25/2016] [Indexed: 12/14/2022]
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19
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Gumbart JC, Chipot C. Decrypting protein insertion through the translocon with free-energy calculations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1663-71. [PMID: 26896694 DOI: 10.1016/j.bbamem.2016.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 12/23/2022]
Abstract
Protein insertion into a membrane is a complex process involving numerous players. The most prominent of these players is the Sec translocon complex, a conserved protein-conducting channel present in the cytoplasmic membrane of bacteria and the membrane of the endoplasmic reticulum in eukaryotes. The last decade has seen tremendous leaps forward in our understanding of how insertion is managed by the translocon and its partners, coming from atomic-detailed structures, innovative experiments, and well-designed simulations. In this review, we discuss how experiments and simulations, hand-in-hand, teased out the secrets of the translocon-facilitated membrane insertion process. In particular, we focus on the role of free-energy calculations in elucidating membrane insertion. Amazingly, despite all its apparent complexity, protein insertion into membranes is primarily driven by simple thermodynamic and kinetic principles. This article is part of a Special Issue entitled: Membrane proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique and University of Illinois at Urbana-Champaign, UMR n° 7565, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy, France; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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20
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Turakhiya U, von der Malsburg K, Gold VAM, Guiard B, Chacinska A, van der Laan M, Ieva R. Protein Import by the Mitochondrial Presequence Translocase in the Absence of a Membrane Potential. J Mol Biol 2016; 428:1041-1052. [PMID: 26827728 DOI: 10.1016/j.jmb.2016.01.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/15/2015] [Accepted: 01/01/2016] [Indexed: 11/17/2022]
Abstract
The highly organized mitochondrial inner membrane harbors enzymes that produce the bulk of cellular ATP via oxidative phosphorylation. The majority of inner membrane protein precursors are synthesized in the cytosol. Precursors with a cleavable presequence are imported by the presequence translocase (TIM23 complex), while other precursors containing internal targeting signals are imported by the carrier translocase (TIM22 complex). Both TIM23 and TIM22 are activated by the transmembrane electrochemical potential. Many small inner membrane proteins, however, do not resemble canonical TIM23 or TIM22 substrates and their mechanism of import is unknown. We report that subunit e of the F1Fo-ATP synthase, a small single-spanning inner membrane protein that is critical for inner membrane organization, is imported by TIM23 in a process that does not require activation by the membrane potential. Absence of positively charged residues at the matrix-facing amino-terminus of subunit e facilitates membrane potential-independent import. Instead, engineered positive charges establish a dependence of the import reaction on the electrochemical potential. Our results have two major implications. First, they reveal an unprecedented pathway of protein import into the mitochondrial inner membrane, which is mediated by TIM23. Second, they directly demonstrate the role of the membrane potential in driving the electrophoretic transport of positively charged protein segments across the inner membrane.
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Affiliation(s)
- Uma Turakhiya
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School for Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Karina von der Malsburg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Vicki A M Gold
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Bernard Guiard
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France
| | - Agnieszka Chacinska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Martin van der Laan
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany
| | - Raffaele Ieva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Paul Sabatier, 31077 Toulouse, France.
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21
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Santos HJ, Imai K, Hanadate Y, Fukasawa Y, Oda T, Mi-Ichi F, Nozaki T. Screening and discovery of lineage-specific mitosomal membrane proteins in Entamoeba histolytica. Mol Biochem Parasitol 2016; 209:10-17. [PMID: 26792249 DOI: 10.1016/j.molbiopara.2016.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 11/17/2022]
Abstract
Entamoeba histolytica, an anaerobic intestinal parasite causing dysentery and extra-intestinal abscesses in humans, possesses highly reduced and divergent mitochondrion-related organelles (MROs) called mitosomes. This organelle lacks many features associated with canonical aerobic mitochondria and even other MROs such as hydrogenosomes. The Entamoeba mitosome has been found to have a compartmentalized sulfate activation pathway, which was recently implicated to have a role in amebic stage conversion. It also features a unique shuttle system via Tom60, which delivers proteins from the cytosol to the mitosome. In addition, only Entamoeba mitosomes possess a novel subclass of β-barrel outer membrane protein called MBOMP30. With the discoveries of such unique features of mitosomes of Entamoeba, there still remain a number of significant unanswered issues pertaining to this organelle. Particularly, the present understanding of the inner mitosomal membrane of Entamoeba is extremely limited. So far, only a few homologs for transporters of various substrates have been confirmed, while the components of the protein translocation complexes appear to be absent or are yet to be discovered. Employing a similar strategy as in our previous work, we collaborated to screen and discover mitosomal membrane proteins. Using a specialized prediction pipeline, we searched for proteins possessing α-helical transmembrane domains, which are unique to E. histolytica mitosomes. From the prediction algorithm, 25 proteins emerged as candidates, two of which were initially observed to be localized to the mitosomes. Further screening and analysis of the predicted proteins may provide clues to answer key questions on mitosomal evolution, biogenesis, dynamics, and biochemical processes.
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Affiliation(s)
- Herbert J Santos
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Kenichiro Imai
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Yuki Hanadate
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yoshinori Fukasawa
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Toshiyuki Oda
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Fumika Mi-Ichi
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Tomoyoshi Nozaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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22
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Kim H, Botelho SC, Park K, Kim H. Use of carbonate extraction in analyzing moderately hydrophobic transmembrane proteins in the mitochondrial inner membrane. Protein Sci 2015; 24:2063-9. [PMID: 26435163 DOI: 10.1002/pro.2817] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/30/2015] [Indexed: 11/10/2022]
Abstract
Resistance to sodium carbonate extraction is regarded as a canonical way to distinguish integral membrane proteins (MPs) from other membrane-associated proteins. However, it has been observed that carbonate extraction releases some mitochondrial integral MPs. Here, by analyzing both artificially designed and native mitochondrial inner MPs containing transmembrane domains (TMDs) of different hydrophobicities, we show that carbonate treatment can release moderately hydrophobic TMDs from the mitochondrial inner membrane. These results suggest that resistance and sensitivity to carbonate extraction may be interpreted with caution when analyzing the nature of mitochondrial inner MPs.
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Affiliation(s)
- Hayoung Kim
- Department of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Salomé Calado Botelho
- Department of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Kwangjin Park
- Department of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hyun Kim
- Department of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
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23
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Schulz C, Schendzielorz A, Rehling P. Unlocking the presequence import pathway. Trends Cell Biol 2015; 25:265-75. [DOI: 10.1016/j.tcb.2014.12.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 10/24/2022]
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24
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A Perspective on Transport of Proteins into Mitochondria: A Myriad of Open Questions. J Mol Biol 2015; 427:1135-58. [DOI: 10.1016/j.jmb.2015.02.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 11/22/2022]
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25
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Mgr2 functions as lateral gatekeeper for preprotein sorting in the mitochondrial inner membrane. Mol Cell 2014; 56:641-52. [PMID: 25454944 DOI: 10.1016/j.molcel.2014.10.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 08/14/2014] [Accepted: 10/09/2014] [Indexed: 11/21/2022]
Abstract
The majority of preproteins destined for mitochondria carry N-terminal presequences. The presequence translocase of the inner mitochondrial membrane (TIM23 complex) plays a central role in protein sorting. Preproteins are either translocated through the TIM23 complex into the matrix or are laterally released into the inner membrane. We report that the small hydrophobic protein Mgr2 controls the lateral release of preproteins. Mgr2 interacts with preproteins in transit through the TIM23 complex. Overexpression of Mgr2 delays preprotein release, whereas a lack of Mgr2 promotes preprotein sorting into the inner membrane. Preproteins with a defective inner membrane sorting signal are translocated into the matrix in wild-type mitochondria but are released into the inner membrane in Mgr2-deficient mitochondria. We conclude that Mgr2 functions as a lateral gatekeeper of the mitochondrial presequence translocase, providing quality control for the membrane sorting of preproteins.
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26
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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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27
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Park K, Jung SJ, Kim H, Kim H. Mode of membrane insertion of individual transmembrane segments in Mdl1 and Mdl2, multi-spanning mitochondrial ABC transporters. FEBS Lett 2014; 588:3445-53. [DOI: 10.1016/j.febslet.2014.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/25/2014] [Accepted: 08/03/2014] [Indexed: 10/24/2022]
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28
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Pogozheva ID, Mosberg HI, Lomize AL. Life at the border: adaptation of proteins to anisotropic membrane environment. Protein Sci 2014; 23:1165-96. [PMID: 24947665 DOI: 10.1002/pro.2508] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 12/25/2022]
Abstract
This review discusses main features of transmembrane (TM) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen-bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region-between double bonds and carbonyl groups of lipids. These "midpolar" regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side-chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein-lipid binding.
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Affiliation(s)
- Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, 48109-1065
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29
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Reithinger JH, Yim C, Park K, Björkholm P, von Heijne G, Kim H. A short C-terminal tail prevents mis-targeting of hydrophobic mitochondrial membrane proteins to the ER. FEBS Lett 2013; 587:3480-6. [PMID: 24055247 DOI: 10.1016/j.febslet.2013.08.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 08/28/2013] [Indexed: 10/26/2022]
Abstract
Sdh3/Shh3, a subunit of mitochondrial succinate dehydrogenase, contains transmembrane domains with a hydrophobicity comparable to that of endoplasmic reticulum (ER) proteins. Here, we show that a C-terminal reporter fusion to Sdh3/Shh3 results in partial mis-targeting of the protein to the ER. This mis-targeting is mediated by the signal recognition particle (SRP) and depends on the length of the C-terminal tail. These results imply that if nuclear-encoded mitochondrial proteins contain strongly hydrophobic transmembrane domains and a long C-terminal tail, they have the potential to be recognized by SRP and mis-targeted to the ER.
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Affiliation(s)
- Johannes H Reithinger
- School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea; Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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30
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Hewitt VL, Gabriel K, Traven A. The ins and outs of the intermembrane space: diverse mechanisms and evolutionary rewiring of mitochondrial protein import routes. Biochim Biophys Acta Gen Subj 2013; 1840:1246-53. [PMID: 23994494 DOI: 10.1016/j.bbagen.2013.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 08/09/2013] [Accepted: 08/20/2013] [Indexed: 11/24/2022]
Abstract
BACKGROUND Mitochondrial biogenesis is an essential process in all eukaryotes. Import of proteins from the cytosol into mitochondria is a key step in organelle biogenesis. Recent evidence suggests that a given mitochondrial protein does not take the same import route in all organisms, suggesting that pathways of mitochondrial protein import can be rewired through evolution. Examples of this process so far involve proteins destined to the mitochondrial intermembrane space (IMS). SCOPE OF REVIEW Here we review the components, substrates and energy sources of the known mechanisms of protein import into the IMS. We discuss evolutionary rewiring of the IMS import routes, focusing on the example of the lactate utilisation enzyme cytochrome b2 (Cyb2) in the model yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans. MAJOR CONCLUSIONS There are multiple import pathways used for protein entry into the IMS and they form a network capable of importing a diverse range of substrates. These pathways have been rewired, possibly in response to environmental pressures, such as those found in the niches in the human body inhabited by C. albicans. GENERAL SIGNIFICANCE We propose that evolutionary rewiring of mitochondrial import pathways can adjust the metabolic fitness of a given species to their environmental niche. This article is part of a Special Issue entitled Frontiers of Mitochondrial.
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Affiliation(s)
- Victoria L Hewitt
- Department of Biochemistry and Molecular Biology, Building 77, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne 3800, Australia.
| | - Kipros Gabriel
- Department of Biochemistry and Molecular Biology, Building 77, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne 3800, Australia.
| | - Ana Traven
- Department of Biochemistry and Molecular Biology, Building 77, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne 3800, Australia.
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31
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Malhotra K, Sathappa M, Landin JS, Johnson AE, Alder NN. Structural changes in the mitochondrial Tim23 channel are coupled to the proton-motive force. Nat Struct Mol Biol 2013; 20:965-72. [DOI: 10.1038/nsmb.2613] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 05/14/2013] [Indexed: 01/11/2023]
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32
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Ojemalm K, Botelho SC, Stüdle C, von Heijne G. Quantitative analysis of SecYEG-mediated insertion of transmembrane α-helices into the bacterial inner membrane. J Mol Biol 2013; 425:2813-22. [PMID: 23659793 DOI: 10.1016/j.jmb.2013.04.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/24/2013] [Accepted: 04/25/2013] [Indexed: 11/17/2022]
Abstract
Most integral membrane proteins, both in prokaryotic and eukaryotic cells, are co-translationally inserted into the membrane via Sec-type translocons: the SecYEG complex in prokaryotes and the Sec61 complex in eukaryotes. The contributions of individual amino acids to the overall free energy of membrane insertion of single transmembrane α-helices have been measured for Sec61-mediated insertion into the endoplasmic reticulum (ER) membrane (Nature 450:1026-1030) but have not been systematically determined for SecYEG-mediated insertion into the bacterial inner membrane. We now report such measurements, carried out in Escherichia coli. Overall, there is a good correlation between the results found for the mammalian ER and the E. coli inner membrane, but the hydrophobicity threshold for SecYEG-mediated insertion is distinctly lower than that for Sec61-mediated insertion.
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Affiliation(s)
- Karin Ojemalm
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
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33
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Gumbart JC, Teo I, Roux B, Schulten K. Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion. J Am Chem Soc 2013; 135:2291-7. [PMID: 23298280 PMCID: PMC3573731 DOI: 10.1021/ja310777k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
For the vast majority of membrane proteins, insertion
into a membrane
is not direct, but rather is catalyzed by a protein-conducting channel,
the translocon. This channel provides a lateral exit into the bilayer
while simultaneously offering a pathway into the aqueous lumen. The
determinants of a nascent protein’s choice between these two
pathways are not comprehensively understood, although both energetic
and kinetic factors have been observed. To elucidate the specific
roles of some of these factors, we have carried out extensive all-atom
molecular dynamics simulations of different nascent transmembrane
segments embedded in a ribosome-bound bacterial translocon, SecY.
Simulations on the μs time scale reveal a spontaneous motion
of the substrate segment into the membrane or back into the channel,
depending on its hydrophobicity. Potential of mean force (PMF) calculations
confirm that the observed motion is the result of local free-energy
differences between channel and membrane. Based on these and other
PMFs, the time-dependent probability of membrane insertion is determined
and is shown to mimic a two-state partition scheme with an apparent
free energy that is compressed relative to the molecular-level PMFs.
It is concluded that insertion kinetics underlies the experimentally
observed thermodynamic partitioning process.
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Affiliation(s)
- James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30363, USA
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34
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Botelho SC, Tatsuta T, von Heijne G, Kim H. Dislocation by the m-AAA protease increases the threshold hydrophobicity for retention of transmembrane helices in the inner membrane of yeast mitochondria. J Biol Chem 2013; 288:4792-8. [PMID: 23283966 DOI: 10.1074/jbc.m112.430892] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sorting of mitochondrial inner membrane proteins is a complex process in which translocons and proteases function in a concerted way. Many inner membrane proteins insert into the membrane via the TIM23 translocon, and some are then further acted upon by the mitochondrial m-AAA protease, a molecular motor capable of dislocating proteins from the inner membrane. This raises the possibility that the threshold hydrophobicity for the retention of transmembrane segments in the inner membrane is different depending on whether they belong to membrane proteins that are m-AAA protease substrates or not. Here, using model transmembrane segments engineered into m-AAA protease-dependent proteins, we show that the threshold hydrophobicity for membrane retention measured in yeast cells in the absence of a functional m-AAA protease is markedly lower than that measured in its presence. Whether a given hydrophobic segment in a mitochondrial inner membrane protein will ultimately form a transmembrane helix may therefore depend on whether or not it will be exposed to the pulling force exerted by the m-AAA protease during biogenesis.
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Affiliation(s)
- Salomé Calado Botelho
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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35
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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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36
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Duncan MR, Fullerton M, Chaudhuri M. Tim50 in Trypanosoma brucei possesses a dual specificity phosphatase activity and is critical for mitochondrial protein import. J Biol Chem 2012; 288:3184-97. [PMID: 23212919 DOI: 10.1074/jbc.m112.436378] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In eukaryotes, proteins are imported into mitochondria via multiprotein translocases of the mitochondrial outer and inner membranes, TOM and TIM, respectively. Trypanosoma brucei, a hemoflagellated parasitic protozoan and the causative agent of African trypanosomiasis, imports about a thousand proteins into the mitochondrion; however, the mitochondrial protein import machinery in this organism is largely unidentified. Here, we characterized a homolog of Tim50 that is localized in the mitochondrial membrane in T. brucei. Similar to Tim50 proteins from fungi and mammals, Tim50 in T. brucei (TbTim50) possesses a mitochondrial targeting signal at its N terminus and a C-terminal domain phosphatase motif at its C terminus. Knockdown of TbTim50 reduced cell growth and inhibited import of proteins that contain N-terminal targeting signals. Co-immunoprecipitation analysis revealed that TbTim50 interacts with TbTim17. Unlike its fungal counterpart but similar to the human homolog of Tim50, recombinant TbTim50 possesses a dual specificity phosphatase activity with a greater affinity for protein tyrosine phosphate than for protein serine/threonine phosphate. Mutation of the aspartic acid residues to alanine in the C-terminal domain phosphatase motif (242)DXDX(V/T)(246) abolished activity for both type of substrates. TbTim50 knockdown increased and its overexpression decreased the level of voltage-dependent anion channel (VDAC). However, the VDAC level was unaltered when the phosphatase-inactive mutant of TbTim50 was overexpressed, suggesting that the phosphatase activity of TbTim50 plays a role in regulation of VDAC expression. In contrast, phosphatase activity of the TbTim50 is required neither for mitochondrial protein import nor for its interaction with TbTim17. Overall, our results show that TbTim50 plays additional roles in mitochondrial activities besides preprotein translocation.
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Affiliation(s)
- Melanie R Duncan
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, Tennessee 37208, USA
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37
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Park K, Botelho SC, Hong J, Österberg M, Kim H. Dissecting stop transfer versus conservative sorting pathways for mitochondrial inner membrane proteins in vivo. J Biol Chem 2012. [PMID: 23184936 DOI: 10.1074/jbc.m112.409748] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial inner membrane proteins that carry an N-terminal presequence are sorted by one of two pathways: stop transfer or conservative sorting. However, the sorting pathway is known for only a small number of proteins, in part due to the lack of robust experimental tools with which to study. Here we present an approach that facilitates determination of inner membrane protein sorting pathways in vivo by fusing a mitochondrial inner membrane protein to the C-terminal part of Mgm1p containing the rhomboid cleavage region. We validated the Mgm1 fusion approach using a set of proteins for which the sorting pathway is known, and determined sorting pathways of inner membrane proteins for which the sorting mode was previously uncharacterized. For Sdh4p, a multispanning membrane protein, our results suggest that both conservative sorting and stop transfer mechanisms are required for insertion. Furthermore, the sorting process of Mgm1 fusion proteins was analyzed under different growth conditions and yeast mutant strains that were defective in the import motor or the m-AAA protease function. Our results show that the sorting of mitochondrial proteins carrying moderately hydrophobic transmembrane segments is sensitive to cellular conditions, implying that mitochondrial import and membrane sorting in the physiological environment may be dynamically tuned.
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Affiliation(s)
- Kwangjin Park
- School of Biological Sciences, Seoul National University, Building 504-421, Seoul 151-747, South Korea
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38
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Gilmore R, Mandon EC. Understanding integration of α-helical membrane proteins: the next steps. Trends Biochem Sci 2012; 37:303-8. [PMID: 22748693 DOI: 10.1016/j.tibs.2012.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/16/2012] [Accepted: 05/23/2012] [Indexed: 11/19/2022]
Abstract
Integration of a protein into the endoplasmic reticulum (ER) membrane occurs through a series of multistep reactions that include targeting of ribosome-nascent polypeptide complexes to the ER, attachment of the ribosome to the protein translocation channel, lateral partitioning of α-helical transmembrane spans into the lipid bilayer, and folding of the lumenal, cytosolic and membrane-embedded domains of the protein. However, the molecular mechanisms and kinetics of these steps are still not entirely clear. To obtain a better understanding of the mechanism of membrane protein integration, we propose that it will be important to utilize in vivo experiments to examine the kinetics of membrane protein integration and in vitro experiments to characterize interactions between nascent membrane proteins, protein translocation factors and molecular chaperones.
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Affiliation(s)
- Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-2324, USA.
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39
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Abstract
Depending on the organism, mitochondria consist approximately of 500-1,400 different proteins. By far most of these proteins are encoded by nuclear genes and synthesized on cytosolic ribosomes. Targeting signals direct these proteins into mitochondria and there to their respective subcompartment: the outer membrane, the intermembrane space (IMS), the inner membrane, and the matrix. Membrane-embedded translocation complexes allow the translocation of proteins across and, in the case of membrane proteins, the insertion into mitochondrial membranes. A small number of proteins are encoded by the mitochondrial genome: Most mitochondrial translation products represent hydrophobic proteins of the inner membrane which-together with many nuclear-encoded proteins-form the respiratory chain complexes. This chapter gives an overview on the mitochondrial protein translocases and the mechanisms by which they drive the transport and assembly of mitochondrial proteins.
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40
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Charged flanking residues control the efficiency of membrane insertion of the first transmembrane segment in yeast mitochondrial Mgm1p. FEBS Lett 2011; 585:1238-42. [PMID: 21457713 DOI: 10.1016/j.febslet.2011.03.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Revised: 03/24/2011] [Accepted: 03/24/2011] [Indexed: 11/20/2022]
Abstract
Mgm1p is a nuclearly encoded GTPase important for mitochondrial fusion. Long and short isoforms of the protein are generated in a unique "alternative topogenesis" process in which the most N-terminal of two hydrophobic segments in the protein is inserted into the inner mitochondrial membrane in about half of the molecules and translocated across the inner membrane in the other half. In the latter population, the second hydrophobic segment is cleaved by the inner membrane protease Pcp1p, generating the short isoform. Here, we show that charged residues in the regions flanking the first segment critically affect the ratio between the two isoforms, providing new insight into the importance of charged residues in the insertion of proteins into the mitochondrial inner membrane.
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