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Kizmaz B, Nutz A, Egeler A, Herrmann JM. Protein insertion into the inner membrane of mitochondria: routes and mechanisms. FEBS Open Bio 2024; 14:1627-1639. [PMID: 38664330 PMCID: PMC11452304 DOI: 10.1002/2211-5463.13806] [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: 02/23/2024] [Revised: 03/28/2024] [Accepted: 04/11/2024] [Indexed: 10/06/2024] Open
Abstract
The inner membrane of mitochondria contains hundreds of different integral membrane proteins. These proteins transport molecules into and out of the matrix, they carry out multifold catalytic reactions and they promote the biogenesis or degradation of mitochondrial constituents. Most inner membrane proteins are encoded by nuclear genes and synthesized in the cytosol from where they are imported into mitochondria by translocases in the outer and inner membrane. Three different import routes direct proteins into the inner membrane and allow them to acquire their appropriate membrane topology. First, mitochondrial import intermediates can be arrested at the level of the TIM23 inner membrane translocase by a stop-transfer sequence to reach the inner membrane by lateral insertion. Second, proteins can be fully translocated through the TIM23 complex into the matrix from where they insert into the inner membrane in an export-like reaction. Carriers and other polytopic membrane proteins embark on a third insertion pathway: these hydrophobic proteins employ the specialized TIM22 translocase to insert from the intermembrane space (IMS) into the inner membrane. This review article describes these three targeting routes and provides an overview of the machinery that promotes the topogenesis of mitochondrial inner membrane proteins.
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Affiliation(s)
- Büsra Kizmaz
- Cell BiologyUniversity of Kaiserslautern, RPTUGermany
| | - Annika Nutz
- Cell BiologyUniversity of Kaiserslautern, RPTUGermany
| | - Annika Egeler
- Cell BiologyUniversity of Kaiserslautern, RPTUGermany
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2
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Moretti-Horten DN, Peselj C, Taskin AA, Myketin L, Schulte U, Einsle O, Drepper F, Luzarowski M, Vögtle FN. Synchronized assembly of the oxidative phosphorylation system controls mitochondrial respiration in yeast. Dev Cell 2024; 59:1043-1057.e8. [PMID: 38508182 DOI: 10.1016/j.devcel.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/19/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Control of protein stoichiometry is essential for cell function. Mitochondrial oxidative phosphorylation (OXPHOS) presents a complex stoichiometric challenge as the ratio of the electron transport chain (ETC) and ATP synthase must be tightly controlled, and assembly requires coordinated integration of proteins encoded in the nuclear and mitochondrial genome. How correct OXPHOS stoichiometry is achieved is unknown. We identify the Mitochondrial Regulatory hub for respiratory Assembly (MiRA) platform, which synchronizes ETC and ATP synthase biogenesis in yeast. Molecularly, this is achieved by a stop-and-go mechanism: the uncharacterized protein Mra1 stalls complex IV assembly. Two "Go" signals are required for assembly progression: binding of the complex IV assembly factor Rcf2 and Mra1 interaction with an Atp9-translating mitoribosome induce Mra1 degradation, allowing synchronized maturation of complex IV and the ATP synthase. Failure of the stop-and-go mechanism results in cell death. MiRA controls OXPHOS assembly, ensuring correct stoichiometry of protein machineries encoded by two different genomes.
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Affiliation(s)
- Daiana N Moretti-Horten
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Carlotta Peselj
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Asli Aras Taskin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Lisa Myketin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Friedel Drepper
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Biochemistry & Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Marcin Luzarowski
- Core Facility for Mass Spectrometry and Proteomics, Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - F-Nora Vögtle
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Network Aging Research, Heidelberg University, 69120 Heidelberg, Germany.
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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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Homberg B, Rehling P, Cruz-Zaragoza LD. The multifaceted mitochondrial OXA insertase. Trends Cell Biol 2023; 33:765-772. [PMID: 36863885 DOI: 10.1016/j.tcb.2023.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 03/04/2023]
Abstract
Most mitochondrial proteins are synthesized in the cytosol and transported into mitochondria by protein translocases. Yet, mitochondria contain their own genome and gene expression system, which generates proteins that are inserted in the inner membrane by the oxidase assembly (OXA) insertase. OXA contributes to targeting proteins from both genetic origins. Recent data provides insights into how OXA cooperates with the mitochondrial ribosome during synthesis of mitochondrial-encoded proteins. A picture of OXA emerges in which it coordinates insertion of OXPHOS core subunits and their assembly into protein complexes but also participates in the biogenesis of select imported proteins. These functions position the OXA as a multifunctional protein insertase that facilitates protein transport, assembly, and stability at the inner membrane.
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Affiliation(s)
- Bettina Homberg
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), 37073 University of Göttingen, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy TNM, 37075 Göttingen, Germany; Max Planck Institute for Multidisciplinary Science, 37077 Göttingen, Germany.
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5
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Wei Q, Chen B, Wang J, Huang M, Gui Y, Sayyed A, Tan BC. PHB3 Is Required for the Assembly and Activity of Mitochondrial ATP Synthase in Arabidopsis. Int J Mol Sci 2023; 24:ijms24108787. [PMID: 37240131 DOI: 10.3390/ijms24108787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Mitochondrial ATP synthase is a multiprotein complex, which consists of a matrix-localized F1 domain (F1-ATPase) and an inner membrane-embedded Fo domain (Fo-ATPase). The assembly process of mitochondrial ATP synthase is complex and requires the function of many assembly factors. Although extensive studies on mitochondrial ATP synthase assembly have been conducted on yeast, much less study has been performed on plants. Here, we revealed the function of Arabidopsis prohibitin 3 (PHB3) in mitochondrial ATP synthase assembly by characterizing the phb3 mutant. The blue native PAGE (BN-PAGE) and in-gel activity staining assays showed that the activities of ATP synthase and F1-ATPase were significantly decreased in the phb3 mutant. The absence of PHB3 resulted in the accumulation of the Fo-ATPase and F1-ATPase intermediates, whereas the abundance of the Fo-ATPase subunit a was decreased in the ATP synthase monomer. Furthermore, we showed that PHB3 could interact with the F1-ATPase subunits β and δ in the yeast two-hybrid system (Y2H) and luciferase complementation imaging (LCI) assay and with Fo-ATPase subunit c in the LCI assay. These results indicate that PHB3 acts as an assembly factor required for the assembly and activity of mitochondrial ATP synthase.
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Affiliation(s)
- Qingqing Wei
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Baoyin Chen
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Junjun Wang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Manna Huang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yuanye Gui
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Aqib Sayyed
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
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6
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Kabala AM, Binko K, Godard F, Charles C, Dautant A, Baranowska E, Skoczen N, Gombeau K, Bouhier M, Becker HD, Ackerman SH, Steinmetz LM, Tribouillard-Tanvier D, Kucharczyk R, di Rago JP. Assembly-dependent translation of subunits 6 (Atp6) and 9 (Atp9) of ATP synthase in yeast mitochondria. Genetics 2022; 220:iyac007. [PMID: 35100419 PMCID: PMC8893259 DOI: 10.1093/genetics/iyac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/30/2021] [Indexed: 12/04/2022] Open
Abstract
The yeast mitochondrial ATP synthase is an assembly of 28 subunits of 17 types of which 3 (subunits 6, 8, and 9) are encoded by mitochondrial genes, while the 14 others have a nuclear genetic origin. Within the membrane domain (FO) of this enzyme, the subunit 6 and a ring of 10 identical subunits 9 transport protons across the mitochondrial inner membrane coupled to ATP synthesis in the extra-membrane structure (F1) of ATP synthase. As a result of their dual genetic origin, the ATP synthase subunits are synthesized in the cytosol and inside the mitochondrion. How they are produced in the proper stoichiometry from two different cellular compartments is still poorly understood. The experiments herein reported show that the rate of translation of the subunits 9 and 6 is enhanced in strains with mutations leading to specific defects in the assembly of these proteins. These translation modifications involve assembly intermediates interacting with subunits 6 and 9 within the final enzyme and cis-regulatory sequences that control gene expression in the organelle. In addition to enabling a balanced output of the ATP synthase subunits, these assembly-dependent feedback loops are presumably important to limit the accumulation of harmful assembly intermediates that have the potential to dissipate the mitochondrial membrane electrical potential and the main source of chemical energy of the cell.
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Affiliation(s)
- Anna M Kabala
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Krystyna Binko
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - François Godard
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
| | - Camille Charles
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
| | - Alain Dautant
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
| | - Emilia Baranowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Natalia Skoczen
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Kewin Gombeau
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
| | - Marine Bouhier
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
| | - Hubert D Becker
- UPR ‘Architecture et Réactivité de l’ARN’, CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, F-67084 Strasbourg Cedex, France
| | - Sharon H Ackerman
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Genome Technology Center, Palo Alto, CA 94304, USA
| | | | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Jean-Paul di Rago
- CNRS, IBGC, University of Bordeaux, UMR 5095, F-33000 Bordeaux, France
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7
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Güngör B, Flohr T, Garg SG, Herrmann JM. The ER membrane complex (EMC) can functionally replace the Oxa1 insertase in mitochondria. PLoS Biol 2022; 20:e3001380. [PMID: 35231030 PMCID: PMC8887752 DOI: 10.1371/journal.pbio.3001380] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/17/2021] [Indexed: 12/18/2022] Open
Abstract
Two multisubunit protein complexes for membrane protein insertion were recently identified in the endoplasmic reticulum (ER): the guided entry of tail anchor proteins (GET) complex and ER membrane complex (EMC). The structures of both of their hydrophobic core subunits, which are required for the insertion reaction, revealed an overall similarity to the YidC/Oxa1/Alb3 family members found in bacteria, mitochondria, and chloroplasts. This suggests that these membrane insertion machineries all share a common ancestry. To test whether these ER proteins can functionally replace Oxa1 in yeast mitochondria, we generated strains that express mitochondria-targeted Get2-Get1 and Emc6-Emc3 fusion proteins in Oxa1 deletion mutants. Interestingly, the Emc6-Emc3 fusion was able to complement an Δoxa1 mutant and restored its respiratory competence. The Emc6-Emc3 fusion promoted the insertion of the mitochondrially encoded protein Cox2, as well as of nuclear encoded inner membrane proteins, although was not able to facilitate the assembly of the Atp9 ring. Our observations indicate that protein insertion into the ER is functionally conserved to the insertion mechanism in bacteria and mitochondria and adheres to similar topological principles.
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Affiliation(s)
- Büsra Güngör
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Tamara Flohr
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sriram G. Garg
- Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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8
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Anderson JM, Box JM, Stuart RA. The mitospecific domain of Mrp7 (bL27) supports mitochondrial translation during fermentation and is required for effective adaptation to respiration. Mol Biol Cell 2021; 33:ar7. [PMID: 34731012 PMCID: PMC8886811 DOI: 10.1091/mbc.e21-07-0370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We demonstrate here that mitoribosomal protein synthesis, responsible for the synthesis of oxidative phosphorylation (OXPHOS) subunits encoded by mitochondrial genome, occurs at high levels during glycolysis fermentation and in a manner uncoupled from OXPHOS complex assembly regulation. Furthermore, we provide evidence that the mitospecific domain of Mrp7 (bL27), a mitoribosomal component, is required to maintain mitochondrial protein synthesis during fermentation, but is not required under respiration growth conditions. Maintaining mitotranslation under high glucose fermentation conditions also involves Mam33 (p32/gC1qR homolog), a binding partner of Mrp7's mitospecific domain, and together they confer a competitive advantage for a cell's ability to adapt to respiration-based metabolism when glucose becomes limiting. Furthermore, our findings support that the mitoribosome, and specifically the central protuberance (CP) region, may be differentially regulated and/or assembled, under the different metabolic conditions of fermentation and respiration. Based on our findings, we propose the purpose of mitotranslation is not limited to the assembly of OXPHOS complexes, but also plays a role in mitochondrial signaling critical for switching cellular metabolism from a glycolysis- to a respiratory-based state.
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Affiliation(s)
| | - Jodie M Box
- Dept. of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Rosemary A Stuart
- Dept. of Biological Sciences, Marquette University, Milwaukee, WI, USA
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9
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Almendro-Vedia V, Natale P, Valdivieso González D, Lillo MP, Aragones JL, López-Montero I. How rotating ATP synthases can modulate membrane structure. Arch Biochem Biophys 2021; 708:108939. [PMID: 34052190 DOI: 10.1016/j.abb.2021.108939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 01/03/2023]
Abstract
F1Fo-ATP synthase (ATP synthase) is a central membrane protein that synthetizes most of the ATP in the cell through a rotational movement driven by a proton gradient across the hosting membrane. In mitochondria, ATP synthases can form dimers through specific interactions between some subunits of the protein. The dimeric form of ATP synthase provides the protein with a spontaneous curvature that sustain their arrangement at the rim of the high-curvature edges of mitochondrial membrane (cristae). Also, a direct interaction with cardiolipin, a lipid present in the inner mitochondrial membrane, induces the dimerization of ATP synthase molecules along cristae. The deletion of those biochemical interactions abolishes the protein dimerization producing an altered mitochondrial function and morphology. Mechanically, membrane bending is one of the key deformation modes by which mitochondrial membranes can be shaped. In particular, bending rigidity and spontaneous curvature are important physical factors for membrane remodelling. Here, we discuss a complementary mechanism whereby the rotatory movement of the ATP synthase might modify the mechanical properties of lipid bilayers and contribute to the formation and regulation of the membrane invaginations.
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Affiliation(s)
- Víctor Almendro-Vedia
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain
| | - Paolo Natale
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain
| | - David Valdivieso González
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain
| | - M Pilar Lillo
- Departamento Química Física Biológica, Instituto de Química-Física "Rocasolano" (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Juan L Aragones
- Departamento de Física Teórica de la Materia Condensada, Instituto Nicolás Cabrera and Condensed Matter Physics Centre (IFIMAC), Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Iván López-Montero
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain.
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10
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Franco LVR, Su CH, Tzagoloff A. Modular assembly of yeast mitochondrial ATP synthase and cytochrome oxidase. Biol Chem 2021; 401:835-853. [PMID: 32142477 DOI: 10.1515/hsz-2020-0112] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 02/24/2020] [Indexed: 12/27/2022]
Abstract
The respiratory pathway of mitochondria is composed of four electron transfer complexes and the ATP synthase. In this article, we review evidence from studies of Saccharomyces cerevisiae that both ATP synthase and cytochrome oxidase (COX) are assembled from independent modules that correspond to structurally and functionally identifiable components of each complex. Biogenesis of the respiratory chain requires a coordinate and balanced expression of gene products that become partner subunits of the same complex, but are encoded in the two physically separated genomes. Current evidence indicates that synthesis of two key mitochondrial encoded subunits of ATP synthase is regulated by the F1 module. Expression of COX1 that codes for a subunit of the COX catalytic core is also regulated by a mechanism that restricts synthesis of this subunit to the availability of a nuclear-encoded translational activator. The respiratory chain must maintain a fixed stoichiometry of the component enzyme complexes during cell growth. We propose that high-molecular-weight complexes composed of Cox6, a subunit of COX, and of the Atp9 subunit of ATP synthase play a key role in establishing the ratio of the two complexes during their assembly.
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Affiliation(s)
- Leticia Veloso Ribeiro Franco
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA.,Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, 05508-000, Brasil
| | - Chen Hsien Su
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Alexander Tzagoloff
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
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11
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Distinct Roles of Mitochondrial HIGD1A and HIGD2A in Respiratory Complex and Supercomplex Biogenesis. Cell Rep 2021; 31:107607. [PMID: 32375044 DOI: 10.1016/j.celrep.2020.107607] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/06/2020] [Accepted: 04/10/2020] [Indexed: 01/08/2023] Open
Abstract
The mitochondrial respiratory chain enzymes are organized as individual complexes and supercomplexes, whose biogenesis remains to be fully understood. To disclose the role of the human Hypoxia Inducible Gene Domain family proteins HIGD1A and HIGD2A in these processes, we generate and characterize HIGD-knockout (KO) cell lines. We show that HIGD2A controls and coordinates the modular assembly of isolated and supercomplexed complex IV (CIV) by acting on the COX3 assembly module. In contrast, HIGD1A regulates CIII and CIII-containing supercomplex biogenesis by supporting the incorporation of UQCRFS1. HIGD1A also clusters with COX4-1 and COX5A CIV subunits and, when overexpressed, suppresses the CIV biogenesis defect of HIGD2A-KO cells. We conclude that HIGD1A and HIGD2A have both independent and overlapping functions in the biogenesis of respiratory complexes and supercomplexes. Our data illuminate the existence of multiple pathways to assemble these structures by dynamic HIGD-mediated CIV biogenesis, potentially to adapt to changing environmental and nutritional conditions.
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12
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Bahri H, Buratto J, Rojo M, Dompierre JP, Salin B, Blancard C, Cuvellier S, Rose M, Ben Ammar Elgaaied A, Tetaud E, di Rago JP, Devin A, Duvezin-Caubet S. TMEM70 forms oligomeric scaffolds within mitochondrial cristae promoting in situ assembly of mammalian ATP synthase proton channel. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118942. [PMID: 33359711 DOI: 10.1016/j.bbamcr.2020.118942] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/28/2020] [Accepted: 12/18/2020] [Indexed: 01/14/2023]
Abstract
Mitochondrial ATP-synthesis is catalyzed by a F1Fo-ATP synthase, an enzyme of dual genetic origin enriched at the edge of cristae where it plays a key role in their structure/stability. The enzyme's biogenesis remains poorly understood, both from a mechanistic and a compartmentalization point of view. The present study provides novel molecular insights into this process through investigations on a human protein called TMEM70 with an unclear role in the assembly of ATP synthase. A recent study has revealed the existence of physical interactions between TMEM70 and the subunit c (Su.c), a protein present in 8 identical copies forming a transmembrane oligomeric ring (c-ring) within the ATP synthase proton translocating domain (Fo). Herein we analyzed the ATP-synthase assembly in cells lacking TMEM70, mitochondrial DNA or F1 subunits and observe a direct correlation between TMEM70 and Su.c levels, regardless of the status of other ATP synthase subunits or of mitochondrial bioenergetics. Immunoprecipitation, two-dimensional blue-native/SDS-PAGE, and pulse-chase experiments reveal that TMEM70 forms large oligomers that interact with Su.c not yet incorporated into ATP synthase complexes. Moreover, discrete TMEM70-Su.c complexes with increasing Su.c contents can be detected, suggesting a role for TMEM70 oligomers in the gradual assembly of the c-ring. Furthermore, we demonstrate using expansion super-resolution microscopy the specific localization of TMEM70 at the inner cristae membrane, distinct from the MICOS component MIC60. Taken together, our results show that TMEM70 oligomers provide a scaffold for c-ring assembly and that mammalian ATP synthase is assembled within inner cristae membranes.
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Affiliation(s)
- Hela Bahri
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France; Laboratoire de génétique, Immunologie et Pathologie Humaine, Faculté des sciences de Tunis, Université Tunis-El Manar FST, Tunis, Tunisie
| | - Jeremie Buratto
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France; Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Manuel Rojo
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Jim Paul Dompierre
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Bénédicte Salin
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Corinne Blancard
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Sylvain Cuvellier
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Marie Rose
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Amel Ben Ammar Elgaaied
- Laboratoire de génétique, Immunologie et Pathologie Humaine, Faculté des sciences de Tunis, Université Tunis-El Manar FST, Tunis, Tunisie
| | - Emmanuel Tetaud
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France; Laboratoire de Microbiologie Fondamentale et Pathogénicité UMR-CNRS 5234, 146 rue Léo Saignat, CEDEX F-33076 Bordeaux, France
| | - Jean-Paul di Rago
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Anne Devin
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Stéphane Duvezin-Caubet
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France.
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13
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Functions of Cytochrome c oxidase Assembly Factors. Int J Mol Sci 2020; 21:ijms21197254. [PMID: 33008142 PMCID: PMC7582755 DOI: 10.3390/ijms21197254] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 12/22/2022] Open
Abstract
Cytochrome c oxidase is the terminal complex of eukaryotic oxidative phosphorylation in mitochondria. This process couples the reduction of electron carriers during metabolism to the reduction of molecular oxygen to water and translocation of protons from the internal mitochondrial matrix to the inter-membrane space. The electrochemical gradient formed is used to generate chemical energy in the form of adenosine triphosphate to power vital cellular processes. Cytochrome c oxidase and most oxidative phosphorylation complexes are the product of the nuclear and mitochondrial genomes. This poses a series of topological and temporal steps that must be completed to ensure efficient assembly of the functional enzyme. Many assembly factors have evolved to perform these steps for insertion of protein into the inner mitochondrial membrane, maturation of the polypeptide, incorporation of co-factors and prosthetic groups and to regulate this process. Much of the information about each of these assembly factors has been gleaned from use of the single cell eukaryote Saccharomyces cerevisiae and also mutations responsible for human disease. This review will focus on the assembly factors of cytochrome c oxidase to highlight some of the outstanding questions in the assembly of this vital enzyme complex.
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14
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Mitochondrial OXPHOS Biogenesis: Co-Regulation of Protein Synthesis, Import, and Assembly Pathways. Int J Mol Sci 2020; 21:ijms21113820. [PMID: 32481479 PMCID: PMC7312649 DOI: 10.3390/ijms21113820] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 02/07/2023] Open
Abstract
The assembly of mitochondrial oxidative phosphorylation (OXPHOS) complexes is an intricate process, which—given their dual-genetic control—requires tight co-regulation of two evolutionarily distinct gene expression machineries. Moreover, fine-tuning protein synthesis to the nascent assembly of OXPHOS complexes requires regulatory mechanisms such as translational plasticity and translational activators that can coordinate mitochondrial translation with the import of nuclear-encoded mitochondrial proteins. The intricacy of OXPHOS complex biogenesis is further evidenced by the requirement of many tightly orchestrated steps and ancillary factors. Early-stage ancillary chaperones have essential roles in coordinating OXPHOS assembly, whilst late-stage assembly factors—also known as the LYRM (leucine–tyrosine–arginine motif) proteins—together with the mitochondrial acyl carrier protein (ACP)—regulate the incorporation and activation of late-incorporating OXPHOS subunits and/or co-factors. In this review, we describe recent discoveries providing insights into the mechanisms required for optimal OXPHOS biogenesis, including the coordination of mitochondrial gene expression with the availability of nuclear-encoded factors entering via mitochondrial protein import systems.
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15
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Franco LVR, Su CH, Burnett J, Teixeira LS, Tzagoloff A. Atco, a yeast mitochondrial complex of Atp9 and Cox6, is an assembly intermediate of the ATP synthase. PLoS One 2020; 15:e0233177. [PMID: 32413073 PMCID: PMC7228087 DOI: 10.1371/journal.pone.0233177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/29/2020] [Indexed: 02/05/2023] Open
Abstract
Mitochondrial oxidative phosphorylation (oxphos) is the process by which the ATP synthase conserves the energy released during the oxidation of different nutrients as ATP. The yeast ATP synthase consists of three assembly modules, one of which is a ring consisting of 10 copies of the Atp9 subunit. We previously reported the existence in yeast mitochondria of high molecular weight complexes composed of mitochondrially encoded Atp9 and of Cox6, an imported structural subunit of cytochrome oxidase (COX). Pulse-chase experiments indicated a correlation between the loss of newly translated Atp9 complexed to Cox6 and an increase of newly formed Atp9 ring, but did not exclude the possibility of an alternate source of Atp9 for ring formation. Here we have extended studies on the functions and structure of this complex, referred to as Atco. We show that Atco is the exclusive source of Atp9 for the ATP synthase assembly. Pulse-chase experiments show that newly translated Atp9, present in Atco, is converted to a ring, which is incorporated into the ATP synthase with kinetics characteristic of a precursor-product relationship. Even though Atco does not contain the ring form of Atp9, cross-linking experiments indicate that it is oligomeric and that the inter-subunit interactions are similar to those of the bona fide ring. We propose that, by providing Atp9 for biogenesis of ATP synthase, Atco complexes free Cox6 for assembly of COX. This suggests that Atco complexes may play a role in coordinating assembly and maintaining proper stoichiometry of the two oxphos enzymes
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Affiliation(s)
- Leticia Veloso Ribeiro Franco
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
- Department of Microbiology, University of São Paulo, São Paulo, SP, Brazil
| | - Chen-Hsien Su
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
| | - Julia Burnett
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
| | - Lorisa Simas Teixeira
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
| | - Alexander Tzagoloff
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
- * E-mail:
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16
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Kovalčíková J, Vrbacký M, Pecina P, Tauchmannová K, Nůsková H, Kaplanová V, Brázdová A, Alán L, Eliáš J, Čunátová K, Kořínek V, Sedlacek R, Mráček T, Houštěk J. TMEM70 facilitates biogenesis of mammalian ATP synthase by promoting subunit c incorporation into the rotor structure of the enzyme. FASEB J 2019; 33:14103-14117. [DOI: 10.1096/fj.201900685rr] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jana Kovalčíková
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Marek Vrbacký
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Pecina
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Kateřina Tauchmannová
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Nůsková
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Vilma Kaplanová
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Andrea Brázdová
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Lukáš Alán
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Eliáš
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Kristýna Čunátová
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Vladimír Kořínek
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics, The Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Institute of Molecular Genetics, The Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, The Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Mráček
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Josef Houštěk
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
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17
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Barros MH, McStay GP. Modular biogenesis of mitochondrial respiratory complexes. Mitochondrion 2019; 50:94-114. [PMID: 31669617 DOI: 10.1016/j.mito.2019.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/04/2019] [Accepted: 10/10/2019] [Indexed: 11/29/2022]
Abstract
Mitochondrial function relies on the activity of oxidative phosphorylation to synthesise ATP and generate an electrochemical gradient across the inner mitochondrial membrane. These coupled processes are mediated by five multi-subunit complexes that reside in this inner membrane. These complexes are the product of both nuclear and mitochondrial gene products. Defects in the function or assembly of these complexes can lead to mitochondrial diseases due to deficits in energy production and mitochondrial functions. Appropriate biogenesis and function are mediated by a complex number of assembly factors that promote maturation of specific complex subunits to form the active oxidative phosphorylation complex. The understanding of the biogenesis of each complex has been informed by studies in both simple eukaryotes such as Saccharomyces cerevisiae and human patients with mitochondrial diseases. These studies reveal each complex assembles through a pathway using specific subunits and assembly factors to form kinetically distinct but related assembly modules. The current understanding of these complexes has embraced the revolutions in genomics and proteomics to further our knowledge on the impact of mitochondrial biology in genetics, medicine, and evolution.
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Affiliation(s)
- Mario H Barros
- Departamento de Microbiologia - Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil.
| | - Gavin P McStay
- Department of Biological Sciences, Staffordshire University, Stoke-on-Trent, United Kingdom.
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18
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Singh S, Dey SS, Bhatia R, Kumar R, Behera TK. Current understanding of male sterility systems in vegetable Brassicas and their exploitation in hybrid breeding. PLANT REPRODUCTION 2019; 32:231-256. [PMID: 31053901 DOI: 10.1007/s00497-019-00371-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Overview of the current status of GMS and CMS systems available in Brassica vegetables, their molecular mechanism, wild sources of sterile cytoplasm and exploitation of male sterility in hybrid breeding. The predominantly herbaceous family Brassicaceae (crucifers or mustard family) encompasses over 3700 species, and many of them are scientifically and economically important. The genus Brassica is an economically important genus within the tribe Brassicaceae that comprises important vegetable, oilseed and fodder crops. Brassica vegetables display strong hybrid vigor, and heterosis breeding is the integral part in their improvement. Commercial production of F1 hybrid seeds in Brassica vegetables requires an effective male sterility system. Among the available male sterility systems, cytoplasmic male sterility (CMS) is the most widely exploited in Brassica vegetables. This system is maternally inherited and studied intensively. A limited number of reports about the genic male sterility (GMS) are available in Brassica vegetables. The GMS system is reported to be dominant, recessive and trirecessive in nature in different species. In this review, we discuss the available male sterility systems in Brassica vegetables and their potential use in hybrid breeding. The molecular mechanism of mt-CMS and causal mitochondrial genes of CMS has been discussed in detail. Finally, the exploitation of male sterility system in heterosis breeding of Brassica vegetables, future prospects and need for further understanding of these systems are highlighted.
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Affiliation(s)
- Saurabh Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - S S Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India.
| | - Reeta Bhatia
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Raj Kumar
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - T K Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
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19
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Carvalho HJF, Del Bondio A, Maltecca F, Colombo SF, Borgese N. The WRB Subunit of the Get3 Receptor is Required for the Correct Integration of its Partner CAML into the ER. Sci Rep 2019; 9:11887. [PMID: 31417168 PMCID: PMC6695381 DOI: 10.1038/s41598-019-48363-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/02/2019] [Indexed: 11/24/2022] Open
Abstract
Calcium-modulating cyclophilin ligand (CAML), together with Tryptophan rich basic protein (WRB, Get1 in yeast), constitutes the mammalian receptor for the Transmembrane Recognition Complex subunit of 40 kDa (TRC40, Get3 in yeast), a cytosolic ATPase with a central role in the post-translational targeting pathway of tail-anchored (TA) proteins to the endoplasmic reticulum (ER) membrane. CAML has also been implicated in other cell-specific processes, notably in immune cell survival, and has been found in molar excess over WRB in different cell types. Notwithstanding the stoichiometric imbalance, WRB and CAML depend strictly on each other for expression. Here, we investigated the mechanism by which WRB impacts CAML levels. We demonstrate that CAML, generated in the presence of sufficient WRB levels, is inserted into the ER membrane with three transmembrane segments (TMs) in its C-terminal region. By contrast, without sufficient levels of WRB, CAML fails to adopt this topology, and is instead incompletely integrated to generate two aberrant topoforms; these congregate in ER-associated clusters and are degraded by the proteasome. Our results suggest that WRB, a member of the recently proposed Oxa1 superfamily, acts catalytically to assist the topogenesis of CAML and may have wider functions in membrane biogenesis than previously appreciated.
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Affiliation(s)
- Hugo J F Carvalho
- Consiglio Nazionale delle Ricerche Institute of Neuroscience and BIOMETRA Department, Università degli Studi di Milano, I-20129, Milan, Italy.,Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Andrea Del Bondio
- Division of Neuroscience, Ospedale San Raffaele, I-20132, Milan, Italy
| | | | - Sara F Colombo
- Consiglio Nazionale delle Ricerche Institute of Neuroscience and BIOMETRA Department, Università degli Studi di Milano, I-20129, Milan, Italy.
| | - Nica Borgese
- Consiglio Nazionale delle Ricerche Institute of Neuroscience and BIOMETRA Department, Università degli Studi di Milano, I-20129, Milan, Italy.
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20
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Thompson K, Mai N, Oláhová M, Scialó F, Formosa LE, Stroud DA, Garrett M, Lax NZ, Robertson FM, Jou C, Nascimento A, Ortez C, Jimenez-Mallebrera C, Hardy SA, He L, Brown GK, Marttinen P, McFarland R, Sanz A, Battersby BJ, Bonnen PE, Ryan MT, Chrzanowska-Lightowlers ZM, Lightowlers RN, Taylor RW. OXA1L mutations cause mitochondrial encephalopathy and a combined oxidative phosphorylation defect. EMBO Mol Med 2019; 10:emmm.201809060. [PMID: 30201738 PMCID: PMC6220311 DOI: 10.15252/emmm.201809060] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
OXA1, the mitochondrial member of the YidC/Alb3/Oxa1 membrane protein insertase family, is required for the assembly of oxidative phosphorylation complexes IV and V in yeast. However, depletion of human OXA1 (OXA1L) was previously reported to impair assembly of complexes I and V only. We report a patient presenting with severe encephalopathy, hypotonia and developmental delay who died at 5 years showing complex IV deficiency in skeletal muscle. Whole exome sequencing identified biallelic OXA1L variants (c.500_507dup, p.(Ser170Glnfs*18) and c.620G>T, p.(Cys207Phe)) that segregated with disease. Patient muscle and fibroblasts showed decreased OXA1L and subunits of complexes IV and V. Crucially, expression of wild‐type human OXA1L in patient fibroblasts rescued the complex IV and V defects. Targeted depletion of OXA1L in human cells or Drosophila melanogaster caused defects in the assembly of complexes I, IV and V, consistent with patient data. Immunoprecipitation of OXA1L revealed the enrichment of mtDNA‐encoded subunits of complexes I, IV and V. Our data verify the pathogenicity of these OXA1L variants and demonstrate that OXA1L is required for the assembly of multiple respiratory chain complexes.
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Affiliation(s)
- Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Nicole Mai
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Filippo Scialó
- Institute for Cell and Molecular Biosciences, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Vic., Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Vic., Australia
| | - Madeleine Garrett
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Vic., Australia
| | - Nichola Z Lax
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Fiona M Robertson
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Cristina Jou
- Pathology Department, Hospital Sant Joan de Déu, CIBERER, Barcelona, Spain
| | - Andres Nascimento
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, CIBERER - ISCIII, Barcelona, Spain
| | - Carlos Ortez
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, CIBERER - ISCIII, Barcelona, Spain
| | - Cecilia Jimenez-Mallebrera
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, CIBERER - ISCIII, Barcelona, Spain
| | - Steven A Hardy
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Langping He
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Garry K Brown
- Oxford Medical Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paula Marttinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Alberto Sanz
- Institute for Cell and Molecular Biosciences, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | | | - Penelope E Bonnen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Vic., Australia
| | | | - Robert N Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
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21
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Reddemann A, Horn R. Recombination Events Involving the atp9 Gene Are Associated with Male Sterility of CMS PET2 in Sunflower. Int J Mol Sci 2018; 19:E806. [PMID: 29534485 PMCID: PMC5877667 DOI: 10.3390/ijms19030806] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022] Open
Abstract
Cytoplasmic male sterility (CMS) systems represent ideal mutants to study the role of mitochondria in pollen development. In sunflower, CMS PET2 also has the potential to become an alternative CMS source for commercial sunflower hybrid breeding. CMS PET2 originates from an interspecific cross of H. petiolaris and H. annuus as CMS PET1, but results in a different CMS mechanism. Southern analyses revealed differences for atp6, atp9 and cob between CMS PET2, CMS PET1 and the male-fertile line HA89. A second identical copy of atp6 was present on an additional CMS PET2-specific fragment. In addition, the atp9 gene was duplicated. However, this duplication was followed by an insertion of 271 bp of unknown origin in the 5' coding region of the atp9 gene in CMS PET2, which led to the creation of two unique open reading frames orf288 and orf231. The first 53 bp of orf288 are identical to the 5' end of atp9. Orf231 consists apart from the first 3 bp, being part of the 271-bp-insertion, of the last 228 bp of atp9. These CMS PET2-specific orfs are co-transcribed. All 11 editing sites of the atp9 gene present in orf231 are fully edited. The anther-specific reduction of the co-transcript in fertility-restored hybrids supports the involvement in male-sterility based on CMS PET2.
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Affiliation(s)
- Antje Reddemann
- Institut für Biowissenschaften, Abt. Pflanzengenetik, Universität Rostock, Albert-Einstein-Straße 3, D-18059 Rostock, Germany
| | - Renate Horn
- Institut für Biowissenschaften, Abt. Pflanzengenetik, Universität Rostock, Albert-Einstein-Straße 3, D-18059 Rostock, Germany.
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22
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Kolli R, Soll J, Carrie C. Plant Mitochondrial Inner Membrane Protein Insertion. Int J Mol Sci 2018; 19:E641. [PMID: 29495281 PMCID: PMC5855863 DOI: 10.3390/ijms19020641] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 02/20/2018] [Accepted: 02/22/2018] [Indexed: 02/06/2023] Open
Abstract
During the biogenesis of the mitochondrial inner membrane, most nuclear-encoded inner membrane proteins are laterally released into the membrane by the TIM23 and the TIM22 machinery during their import into mitochondria. A subset of nuclear-encoded mitochondrial inner membrane proteins and all the mitochondrial-encoded inner membrane proteins use the Oxa machinery-which is evolutionarily conserved from the endosymbiotic bacterial ancestor of mitochondria-for membrane insertion. Compared to the mitochondria from other eukaryotes, plant mitochondria have several unique features, such as a larger genome and a branched electron transport pathway, and are also involved in additional cellular functions such as photorespiration and stress perception. This review focuses on the unique aspects of plant mitochondrial inner membrane protein insertion machinery, which differs from that in yeast and humans, and includes a case study on the biogenesis of Cox2 in yeast, humans, two plant species, and an algal species to highlight lineage-specific similarities and differences. Interestingly, unlike mitochondria of other eukaryotes but similar to bacteria and chloroplasts, plant mitochondria appear to use the Tat machinery for membrane insertion of the Rieske Fe/S protein.
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Affiliation(s)
- Renuka Kolli
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, D-82152 Planegg-Martinsried, Germany.
| | - Jürgen Soll
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, D-82152 Planegg-Martinsried, Germany.
- Munich Center for Integrated Protein Science, CiPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany.
| | - Chris Carrie
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, D-82152 Planegg-Martinsried, Germany.
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Box JM, Kaur J, Stuart RA. MrpL35, a mitospecific component of mitoribosomes, plays a key role in cytochrome c oxidase assembly. Mol Biol Cell 2017; 28:3489-3499. [PMID: 28931599 PMCID: PMC5683760 DOI: 10.1091/mbc.e17-04-0239] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/28/2017] [Accepted: 09/11/2017] [Indexed: 01/03/2023] Open
Abstract
Mitoribosomes perform the synthesis of the core components of the oxidative phosphorylation (OXPHOS) system encoded by the mitochondrial genome. We provide evidence that MrpL35 (mL38), a mitospecific component of the yeast mitoribosomal central protuberance, assembles into a subcomplex with MrpL7 (uL5), Mrp7 (bL27), and MrpL36 (bL31) and mitospecific proteins MrpL17 (mL46) and MrpL28 (mL40). We isolated respiratory defective mrpL35 mutant yeast strains, which do not display an overall inhibition in mitochondrial protein synthesis but rather have a problem in cytochrome c oxidase complex (COX) assembly. Our findings indicate that MrpL35, with its partner Mrp7, play a key role in coordinating the synthesis of the Cox1 subunit with its assembly into the COX enzyme and in a manner that involves the Cox14 and Coa3 proteins. We propose that MrpL35 and Mrp7 are regulatory subunits of the mitoribosome acting to coordinate protein synthesis and OXPHOS assembly events and thus the bioenergetic capacity of the mitochondria.
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Affiliation(s)
- Jodie M Box
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Jasvinder Kaur
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Rosemary A Stuart
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
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Garlich J, Strecker V, Wittig I, Stuart RA. Mutational Analysis of the QRRQ Motif in the Yeast Hig1 Type 2 Protein Rcf1 Reveals a Regulatory Role for the Cytochrome c Oxidase Complex. J Biol Chem 2017; 292:5216-5226. [PMID: 28167530 DOI: 10.1074/jbc.m116.758045] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/12/2017] [Indexed: 01/01/2023] Open
Abstract
The yeast Rcf1 protein is a member of the conserved family of proteins termed the hypoxia-induced gene (domain) 1 (Hig1 or HIGD1) family. Rcf1 interacts with components of the mitochondrial oxidative phosphorylation system, in particular the cytochrome bc1 (complex III)-cytochrome c oxidase (complex IV) supercomplex (termed III-IV) and the ADP/ATP carrier proteins. Rcf1 plays a role in the assembly and modulation of the activity of complex IV; however, the molecular basis for how Rcf1 influences the activity of complex IV is currently unknown. Hig1 type 2 isoforms, which include the Rcf1 protein, are characterized in part by the presence of a conserved motif, (Q/I)X3(R/H)XRX3Q, termed here the QRRQ motif. We show that mutation of conserved residues within the Rcf1 QRRQ motif alters the interactions between Rcf1 and partner proteins and results in the destabilization of complex IV and alteration of its enzymatic properties. Our findings indicate that Rcf1 does not serve as a stoichiometric component, i.e. as a subunit of complex IV, to support its activity. Rather, we propose that Rcf1 serves to dynamically interact with complex IV during its assembly process and, in doing so, regulates a late maturation step of complex IV. We speculate that the Rcf1/Hig1 proteins play a role in the incorporation and/or remodeling of lipids, in particular cardiolipin, into complex IV and. possibly, other mitochondrial proteins such as ADP/ATP carrier proteins.
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Affiliation(s)
- Joshua Garlich
- From the Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53233 and
| | - Valentina Strecker
- Functional Proteomics, SFB 815 Core Unit, Goethe-Universität, 60590 Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Goethe-Universität, 60590 Frankfurt am Main, Germany
| | - Rosemary A Stuart
- From the Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53233 and
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25
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Chen CC, Fu SF, Norikazu M, Yang YW, Liu YJ, Ikeo K, Gojobori T, Huang HJ. Comparative miRNAs analysis of Two contrasting broccoli inbred lines with divergent head-forming capacity under temperature stress. BMC Genomics 2015; 16:1026. [PMID: 26625945 PMCID: PMC4667509 DOI: 10.1186/s12864-015-2201-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/11/2015] [Indexed: 11/10/2022] Open
Abstract
Background MicroRNAs (miRNAs) play a vital role in growth, development, and stress response at the post-transcriptional level. Broccoli (Brassica oleracea L. var italic) is an important vegetable crop, and the yield and quality of broccoli are decreased by heat stress. The broccoli inbred lines that are capable of producing head at high temperature in summer are unique varieties in Taiwan. However, knowledge of miRNAomes during the broccoli head formation under heat stress is limited. Methods In this study, molecular characterization of two nearly isogenic lines with contrasting head-forming capacity was investigated. Head-forming capacity was better for heat-tolerant (HT) than heat-sensitive (HS) broccoli under heat stress. Results By deep sequencing and computational analysis, 20 known miRNAs showed significant differential expression between HT and HS genotypes. According to the criteria for annotation of new miRNAs, 24 novel miRNA sequences with differential expression between the two genotypes were identified. To gain insight into functional significance, 213 unique potential targets of these 44 differentially expressed miRNAs were predicted. These targets were implicated in shoot apical development, phase change, response to temperature stimulus, hormone and energy metabolism. The head-forming capacity of the unique HT line was related to autonomous regulation of Bo-FT genes and less expression level of heat shock protein genes as compared to HS. For the genotypic comparison, a set of miRNAs and their targets had consistent expression patterns in various HT genotypes. Conclusions This large-scale characterization of broccoli miRNAs and their potential targets is to unravel the regulatory roles of miRNAs underlying heat-tolerant head-forming capacity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2201-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chi-Chien Chen
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, East Dist, Tainan, 701, Taiwan.
| | - Shih-Feng Fu
- Department of Biology, National Chunghua University of Education, No.1, Jin-De Road, Changhua, 500, Taiwan.
| | - Monma Norikazu
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan.
| | - Yau-Wen Yang
- Kale Biotech. Co, No.68-1, Chongde 16th St., East Dist, Tainan, 701, Taiwan.
| | - Yu-Ju Liu
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, East Dist, Tainan, 701, Taiwan.
| | - Kazuho Ikeo
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan.
| | - Takashi Gojobori
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan.
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, East Dist, Tainan, 701, Taiwan.
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26
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Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, Keenan RJ. A YidC-like Protein in the Archaeal Plasma Membrane. Structure 2015; 23:1715-1724. [PMID: 26256539 PMCID: PMC4558205 DOI: 10.1016/j.str.2015.06.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 05/29/2015] [Accepted: 06/21/2015] [Indexed: 01/08/2023]
Abstract
Cells possess specialized machinery to direct the insertion of membrane proteins into the lipid bilayer. In bacteria, the essential protein YidC inserts certain proteins into the plasma membrane, and eukaryotic orthologs are present in the mitochondrial inner membrane and the chloroplast thylakoid membrane. The existence of homologous insertases in archaea has been proposed based on phylogenetic analysis. However, limited sequence identity, distinct architecture, and the absence of experimental data have made this assignment ambiguous. Here we describe the 3.5-Å crystal structure of an archaeal DUF106 protein from Methanocaldococcus jannaschii (Mj0480), revealing a lipid-exposed hydrophilic surface presented by a conserved YidC-like fold. Functional analysis reveals selective binding of Mj0480 to ribosomes displaying a stalled YidC substrate, and a direct interaction between the buried hydrophilic surface of Mj0480 and the nascent chain. These data provide direct experimental evidence that the archaeal DUF106 proteins are YidC/Oxa1/Alb3-like insertases of the archaeal plasma membrane.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - S Andrei Anghel
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
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27
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Wesołowski W, Szklarczyk M, Szalonek M, Słowińska J. Analysis of the mitochondrial proteome in cytoplasmic male-sterile and male-fertile beets. J Proteomics 2015; 119:61-74. [DOI: 10.1016/j.jprot.2014.12.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/10/2014] [Accepted: 12/10/2014] [Indexed: 11/29/2022]
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28
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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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29
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Rühle T, Leister D. Assembly of F1F0-ATP synthases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:849-60. [PMID: 25667968 DOI: 10.1016/j.bbabio.2015.02.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 12/31/2022]
Abstract
F1F0-ATP synthases are multimeric protein complexes and common prerequisites for their correct assembly are (i) provision of subunits in appropriate relative amounts, (ii) coordination of membrane insertion and (iii) avoidance of assembly intermediates that uncouple the proton gradient or wastefully hydrolyse ATP. Accessory factors facilitate these goals and assembly occurs in a modular fashion. Subcomplexes common to bacteria and mitochondria, but in part still elusive in chloroplasts, include a soluble F1 intermediate, a membrane-intrinsic, oligomeric c-ring, and a membrane-embedded subcomplex composed of stator subunits and subunit a. The final assembly step is thought to involve association of the preformed F1-c10-14 with the ab2 module (or the ab8-stator module in mitochondria)--mediated by binding of subunit δ in bacteria or OSCP in mitochondria, respectively. Despite the common evolutionary origin of F1F0-ATP synthases, the set of auxiliary factors required for their assembly in bacteria, mitochondria and chloroplasts shows clear signs of evolutionary divergence. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
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Affiliation(s)
- Thilo Rühle
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München (LMU), Großhaderner Straße 2, 82152 Planegg-Martinsried, Germany.
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München (LMU), Großhaderner Straße 2, 82152 Planegg-Martinsried, Germany.
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30
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Rühle T, Razeghi JA, Vamvaka E, Viola S, Gandini C, Kleine T, Schünemann D, Barbato R, Jahns P, Leister D. The Arabidopsis protein CONSERVED ONLY IN THE GREEN LINEAGE160 promotes the assembly of the membranous part of the chloroplast ATP synthase. PLANT PHYSIOLOGY 2014; 165:207-26. [PMID: 24664203 PMCID: PMC4012581 DOI: 10.1104/pp.114.237883] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 03/23/2014] [Indexed: 05/18/2023]
Abstract
The chloroplast F1Fo-ATP synthase/ATPase (cpATPase) couples ATP synthesis to the light-driven electrochemical proton gradient. The cpATPase is a multiprotein complex and consists of a membrane-spanning protein channel (comprising subunit types a, b, b', and c) and a peripheral domain (subunits α, β, γ, δ, and ε). We report the characterization of the Arabidopsis (Arabidopsis thaliana) CONSERVED ONLY IN THE GREEN LINEAGE160 (AtCGL160) protein (AtCGL160), conserved in green algae and plants. AtCGL160 is an integral thylakoid protein, and its carboxyl-terminal portion is distantly related to prokaryotic ATP SYNTHASE PROTEIN1 (Atp1/UncI) proteins that are thought to function in ATP synthase assembly. Plants without AtCGL160 display an increase in xanthophyll cycle activity and energy-dependent nonphotochemical quenching. These photosynthetic perturbations can be attributed to a severe reduction in cpATPase levels that result in increased acidification of the thylakoid lumen. AtCGL160 is not an integral cpATPase component but is specifically required for the efficient incorporation of the c-subunit into the cpATPase. AtCGL160, as well as a chimeric protein containing the amino-terminal part of AtCGL160 and Synechocystis sp. PCC6803 Atp1, physically interact with the c-subunit. We conclude that AtCGL160 and Atp1 facilitate the assembly of the membranous part of the cpATPase in their hosts, but loss of their functions provokes a unique compensatory response in each organism.
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31
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Mitochondrion role in molecular basis of cytoplasmic male sterility. Mitochondrion 2014; 19 Pt B:198-205. [PMID: 24732436 DOI: 10.1016/j.mito.2014.04.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/31/2014] [Accepted: 04/04/2014] [Indexed: 11/24/2022]
Abstract
Cytoplasmic male sterility and its fertility restoration via nuclear genes offer the possibility to understand the role of mitochondria during microsporogenesis. In most cases rearrangements in the mitochondrial DNA involving known mitochondrial genes as well as unknown sequences result in the creation of new chimeric open reading frames, which encode proteins containing transmembrane domains. So far, most of the CMS systems have been characterized via restriction fragment polymorphisms followed by transcript analysis. However, whole mitochondrial genome sequence analyses comparing male sterile and fertile cytoplasm open options for deeper insights into mitochondrial genome rearrangements. We more and more start to unravel how mitochondria are involved in triggering death of the male reproductive organs. Reduced levels of ATP accompanied by increased concentrations of reactive oxygen species, which are produced more under conditions of mitochondrial dysfunction, seem to play a major role in the fate of pollen production. Nuclear genes, so called restorer-of-fertility are able to restore the male fertility. Fertility restoration can occur via pentatricopeptide repeat (PPR) proteins or via different mechanisms involving non-PPR proteins.
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32
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Dalbey RE, Kuhn A, Zhu L, Kiefer D. The membrane insertase YidC. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1489-96. [PMID: 24418623 DOI: 10.1016/j.bbamcr.2013.12.022] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/19/2013] [Accepted: 12/31/2013] [Indexed: 12/28/2022]
Abstract
The membrane insertases YidC-Oxa1-Alb3 provide a simple cellular system that catalyzes the transmembrane topology of newly synthesized membrane proteins. The insertases are composed of a single protein with 5 to 6 transmembrane (TM) helices that contact hydrophobic segments of the substrate proteins. Since YidC also cooperates with the Sec translocase it is widely involved in the assembly of many different membrane proteins including proteins that obtain complex membrane topologies. Homologues found in mitochondria (Oxa1) and thylakoids (Alb3) point to a common evolutionary origin and also demonstrate the general importance of this cellular process. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Ross E Dalbey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
| | - Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Garbenstr 30, 70599 Stuttgart, Germany.
| | - Lu Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Doro Kiefer
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Garbenstr 30, 70599 Stuttgart, Germany
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33
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Post-translational membrane insertion of an endogenous YidC substrate. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2781-2788. [DOI: 10.1016/j.bbamcr.2013.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 06/27/2013] [Accepted: 07/08/2013] [Indexed: 11/18/2022]
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34
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Ostojić J, Glatigny A, Herbert CJ, Dujardin G, Bonnefoy N. Does the study of genetic interactions help predict the function of mitochondrial proteins in Saccharomyces cerevisiae? Biochimie 2013; 100:27-37. [PMID: 24262604 DOI: 10.1016/j.biochi.2013.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/06/2013] [Indexed: 10/26/2022]
Abstract
Mitochondria are complex organelles of eukaryotic cells that contain their own genome, encoding key subunits of the respiratory complexes. The successive steps of mitochondrial gene expression are intimately linked, and are under the control of a large number of nuclear genes encoding factors that are imported into mitochondria. Investigating the relationships between these genes and their interaction networks, and whether they reveal direct or indirect partners, can shed light on their role in mitochondrial biogenesis, as well as identify new actors in this process. These studies, mainly developed in yeasts, are significant because mammalian equivalents of such yeast genes are candidate genes in mitochondrial pathologies. In practice, studies of physical, chemical and genetic interactions can be undertaken. The search for genetic interactions, either aggravating or alleviating the phenotype of the starting mutants, has proved to be particularly powerful in yeast since even subtle changes in respiratory phenotypes can be screened in a very efficient way. In addition, several high throughput genetic approaches have recently been developed. In this review we analyze the genetic network of three genes involved in different steps of mitochondrial gene expression, from the transcription and translation of mitochondrial RNAs to the insertion of newly synthesized proteins into the inner mitochondrial membrane, and we examine their relevance to our understanding of mitochondrial biogenesis. We find that these genetic interactions are seldom redundant with physical interactions, and thus bring a considerable amount of original and significant information as well as open new areas of research.
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Affiliation(s)
- Jelena Ostojić
- Centre de Génétique Moléculaire, CNRS UPR3404 Associated to the University Paris XI-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Annie Glatigny
- Centre de Génétique Moléculaire, CNRS UPR3404 Associated to the University Paris XI-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Christopher J Herbert
- Centre de Génétique Moléculaire, CNRS UPR3404 Associated to the University Paris XI-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Geneviève Dujardin
- Centre de Génétique Moléculaire, CNRS UPR3404 Associated to the University Paris XI-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Nathalie Bonnefoy
- Centre de Génétique Moléculaire, CNRS UPR3404 Associated to the University Paris XI-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France.
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35
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Zhang C, Marcia M, Langer JD, Peng G, Michel H. Role of the N-terminal signal peptide in the membrane insertion ofAquifex aeolicusF1F0ATP synthase c-subunit. FEBS J 2013; 280:3425-35. [DOI: 10.1111/febs.12336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 05/03/2013] [Accepted: 05/07/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Chunli Zhang
- Max Planck Institute of Biophysics; Department of Molecular Membrane Biology; Frankfurt am Main Germany
| | - Marco Marcia
- Department of Molecular, Cellular and Developmental Biology; Yale University; New Haven CT USA
| | - Julian D. Langer
- Max Planck Institute of Biophysics; Department of Molecular Membrane Biology; Frankfurt am Main Germany
| | - Guohong Peng
- Max Planck Institute of Biophysics; Department of Molecular Membrane Biology; Frankfurt am Main Germany
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
| | - Hartmut Michel
- Max Planck Institute of Biophysics; Department of Molecular Membrane Biology; Frankfurt am Main Germany
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36
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Abstract
The mitochondrion is arguably the most complex organelle in the budding yeast cell cytoplasm. It is essential for viability as well as respiratory growth. Its innermost aqueous compartment, the matrix, is bounded by the highly structured inner membrane, which in turn is bounded by the intermembrane space and the outer membrane. Approximately 1000 proteins are present in these organelles, of which eight major constituents are coded and synthesized in the matrix. The import of mitochondrial proteins synthesized in the cytoplasm, and their direction to the correct soluble compartments, correct membranes, and correct membrane surfaces/topologies, involves multiple pathways and macromolecular machines. The targeting of some, but not all, cytoplasmically synthesized mitochondrial proteins begins with translation of messenger RNAs localized to the organelle. Most proteins then pass through the translocase of the outer membrane to the intermembrane space, where divergent pathways sort them to the outer membrane, inner membrane, and matrix or trap them in the intermembrane space. Roughly 25% of mitochondrial proteins participate in maintenance or expression of the organellar genome at the inner surface of the inner membrane, providing 7 membrane proteins whose synthesis nucleates the assembly of three respiratory complexes.
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37
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Michalak de Jimenez MK, Bassi FM, Ghavami F, Simons K, Dizon R, Seetan RI, Alnemer LM, Denton AM, Doğramacı M, Šimková H, Doležel J, Seth K, Luo MC, Dvorak J, Gu YQ, Kianian SF. A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus. Funct Integr Genomics 2013. [PMID: 23479086 DOI: 10.1007/s10142‐013‐0318‐3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The species cytoplasm specific (scs) genes affect nuclear-cytoplasmic interactions in interspecific hybrids. A radiation hybrid (RH) mapping population of 188 individuals was employed to refine the location of the scs (ae) locus on Triticum aestivum chromosome 1D. "Wheat Zapper," a comparative genomics tool, was used to predict synteny between wheat chromosome 1D, Oryza sativa, Brachypodium distachyon, and Sorghum bicolor. A total of 57 markers were developed based on synteny or literature and genotyped to produce a RH map spanning 205.2 cR. A test-cross methodology was devised for phenotyping of RH progenies, and through forward genetic, the scs (ae) locus was pinpointed to a 1.1 Mb-segment containing eight genes. Further, the high resolution provided by RH mapping, combined with chromosome-wise synteny analysis, located the ancestral point of fusion between the telomeric and centromeric repeats of two paleochromosomes that originated chromosome 1D. Also, it indicated that the centromere of this chromosome is likely the result of a neocentromerization event, rather than the conservation of an ancestral centromere as previously believed. Interestingly, location of scs locus in the vicinity of paleofusion is not associated with the expected disruption of synteny, but rather with a good degree of conservation across grass species. Indeed, these observations advocate the evolutionary importance of this locus as suggested by "Maan's scs hypothesis."
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Michalak de Jimenez MK, Bassi FM, Ghavami F, Simons K, Dizon R, Seetan RI, Alnemer LM, Denton AM, Doğramacı M, Šimková H, Doležel J, Seth K, Luo MC, Dvorak J, Gu YQ, Kianian SF. A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus. Funct Integr Genomics 2013; 13:19-32. [PMID: 23479086 DOI: 10.1007/s10142-013-0318-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 10/27/2022]
Abstract
The species cytoplasm specific (scs) genes affect nuclear-cytoplasmic interactions in interspecific hybrids. A radiation hybrid (RH) mapping population of 188 individuals was employed to refine the location of the scs (ae) locus on Triticum aestivum chromosome 1D. "Wheat Zapper," a comparative genomics tool, was used to predict synteny between wheat chromosome 1D, Oryza sativa, Brachypodium distachyon, and Sorghum bicolor. A total of 57 markers were developed based on synteny or literature and genotyped to produce a RH map spanning 205.2 cR. A test-cross methodology was devised for phenotyping of RH progenies, and through forward genetic, the scs (ae) locus was pinpointed to a 1.1 Mb-segment containing eight genes. Further, the high resolution provided by RH mapping, combined with chromosome-wise synteny analysis, located the ancestral point of fusion between the telomeric and centromeric repeats of two paleochromosomes that originated chromosome 1D. Also, it indicated that the centromere of this chromosome is likely the result of a neocentromerization event, rather than the conservation of an ancestral centromere as previously believed. Interestingly, location of scs locus in the vicinity of paleofusion is not associated with the expected disruption of synteny, but rather with a good degree of conservation across grass species. Indeed, these observations advocate the evolutionary importance of this locus as suggested by "Maan's scs hypothesis."
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39
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Benz M, Soll J, Ankele E. Arabidopsis thaliana Oxa proteins locate to mitochondria and fulfill essential roles during embryo development. PLANTA 2013; 237:573-88. [PMID: 23179441 DOI: 10.1007/s00425-012-1793-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/19/2012] [Indexed: 05/12/2023]
Abstract
Members of the Alb3/Oxa1/YidC protein family function as insertases in chloroplasts, mitochondria, and bacteria. Due to independent gene duplications, all organisms possess two isoforms, Oxa1 and Oxa2 except gram-negative bacteria, which encode only for one YidC-like protein. The genome of Arabidopsis thaliana however, encodes for eight different isoforms. The localization of three of these isoforms has been identified earlier: Alb3 and Alb4 located in thylakoid membranes of chloroplasts while AtOxa1 was found in the inner membrane of mitochondria. Here, we show that the second Oxa1 protein, Oxa1b as well as two Oxa2 proteins are also localized in mitochondria. The last two isoforms most likely encode truncated versions of Oxa-like proteins, which might be inoperable pseudogenes. Homozygous mutant lines were only obtained for Oxa1b, which did not reveal any significant phenotypes, while T-DNA insertion lines of Oxa1a, Oxa2a and Oxa2b resulted only in heterozygous plants indicating that these genes are indispensable for plant development. Phenotyping heterozygous lines showed that embryos are either retarded in growth, display an albino phenotype or embryo formation was entirely abolished suggesting that Oxa1a and both Oxa2 proteins function in embryo formation although at different developmental stages as indicated by the various phenotypes observed.
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Affiliation(s)
- Monique Benz
- Energy Biosciences Institute, University of California, 2151 Berkeley Way, Berkeley, CA 94720-5230, USA.
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Stoldt S, Wenzel D, Hildenbeutel M, Wurm CA, Herrmann JM, Jakobs S. The inner-mitochondrial distribution of Oxa1 depends on the growth conditions and on the availability of substrates. Mol Biol Cell 2012; 23:2292-301. [PMID: 22513091 PMCID: PMC3374748 DOI: 10.1091/mbc.e11-06-0538] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 04/12/2012] [Accepted: 04/13/2012] [Indexed: 11/16/2022] Open
Abstract
The Oxa1 protein is a well-conserved integral protein of the inner membrane of mitochondria. It mediates the insertion of both mitochondrial- and nuclear-encoded proteins from the matrix into the inner membrane. We investigated the distribution of budding yeast Oxa1 between the two subdomains of the contiguous inner membrane--the cristae membrane (CM) and the inner boundary membrane (IBM)--under different physiological conditions. We found that under fermentable growth conditions, Oxa1 is enriched in the IBM, whereas under nonfermentable (respiratory) growth conditions, it is predominantly localized in the CM. The enrichment of Oxa1 in the CM requires mitochondrial translation; similarly, deletion of the ribosome-binding domain of Oxa1 prevents an enrichment of Oxa1 in the CM. The predominant localization in the IBM under fermentable growth conditions is prevented by inhibiting mitochondrial protein import. Furthermore, overexpression of the nuclear-encoded Oxa1 substrate Mdl1 shifts the distribution of Oxa1 toward the IBM. Apparently, the availability of nuclear- and mitochondrial-encoded substrates influences the inner-membrane distribution of Oxa1. Our findings show that the distribution of Oxa1 within the inner membrane is dynamic and adapts to different physiological needs.
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Affiliation(s)
- Stefan Stoldt
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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Rcf1 and Rcf2, members of the hypoxia-induced gene 1 protein family, are critical components of the mitochondrial cytochrome bc1-cytochrome c oxidase supercomplex. Mol Cell Biol 2012; 32:1363-73. [PMID: 22310663 DOI: 10.1128/mcb.06369-11] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We report that Rcf1 (formerly Aim31), a member of the conserved hypoxia-induced gene 1 (Hig1) protein family, represents a novel component of the yeast cytochrome bc(1)-cytochrome c oxidase (COX) supercomplex. Rcf1 (respiratory supercomplex factor 1) partitions with the COX complex, and evidence that it may act as a bridge to the cytochrome bc(1) complex is presented. Rcf1 interacts with the Cox3 subunit and can do so prior to their assembly into the COX complex. A close proximity of Rcf1 and members of the ADP/ATP carrier (AAC) family was also established. Rcf1 displays overlapping function with another Hig1-related protein, Rcf2 (formerly Aim38), and their joint presence is required for optimal COX enzyme activity and the correct assembly of the cytochrome bc(1)-COX supercomplex. Rcf1 and Rcf2 can independently associate with the cytochrome bc(1)-COX supercomplex, indicating that at least two forms of this supercomplex exist within mitochondria. We provide evidence that the association with the cytochrome bc(1)-COX supercomplex and regulation of the COX complex are a conserved feature of Hig1 family members. Based on our findings, we propose a model where the Hig1 proteins regulate the COX enzyme activity through Cox3 and associated Cox12 protein, in a manner that may be influenced by the neighboring AAC proteins.
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Luirink J, Yu Z, Wagner S, de Gier JW. Biogenesis of inner membrane proteins in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:965-76. [PMID: 22201544 DOI: 10.1016/j.bbabio.2011.12.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 12/05/2011] [Accepted: 12/12/2011] [Indexed: 11/26/2022]
Abstract
The inner membrane proteome of the model organism Escherichia coli is composed of inner membrane proteins, lipoproteins and peripherally attached soluble proteins. Our knowledge of the biogenesis of inner membrane proteins is rapidly increasing. This is in particular true for the early steps of biogenesis - protein targeting to and insertion into the membrane. However, our knowledge of inner membrane protein folding and quality control is still fragmentary. Furthering our knowledge in these areas will bring us closer to understand the biogenesis of individual inner membrane proteins in the context of the biogenesis of the inner membrane proteome of Escherichia coli as a whole. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes.
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Affiliation(s)
- Joen Luirink
- Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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43
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Mitochondria and fungal pathogenesis: drug tolerance, virulence, and potential for antifungal therapy. EUKARYOTIC CELL 2011; 10:1376-83. [PMID: 21926328 DOI: 10.1128/ec.05184-11] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, mitochondria have been identified as important contributors to the virulence and drug tolerance of human fungal pathogens. In different scenarios, either hypo- or hypervirulence can result from changes in mitochondrial function. Similarly, specific mitochondrial mutations lead to either sensitivity or resistance to antifungal drugs. Here, we provide a synthesis of this emerging field, proposing that mitochondrial function in membrane lipid homeostasis is the common denominator underlying the observed effects of mitochondria in drug tolerance (both sensitivity and resistance). We discuss how the contrasting effects of mitochondrial dysfunction on fungal drug tolerance and virulence could be explained and the potential for targeting mitochondrial factors for future antifungal drug development.
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Freitas JS, Silva EM, Leal J, Gras DE, Martinez-Rossi NM, dos Santos LD, Palma MS, Rossi A. Transcription of the Hsp30, Hsp70, and Hsp90 heat shock protein genes is modulated by the PalA protein in response to acid pH-sensing in the fungus Aspergillus nidulans. Cell Stress Chaperones 2011; 16:565-72. [PMID: 21553327 PMCID: PMC3156257 DOI: 10.1007/s12192-011-0267-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 03/30/2011] [Accepted: 04/22/2011] [Indexed: 01/09/2023] Open
Abstract
Heat shock proteins are molecular chaperones linked to a myriad of physiological functions in both prokaryotes and eukaryotes. In this study, we show that the Aspergillus nidulans hsp30 (ANID_03555.1), hsp70 (ANID_05129.1), and hsp90 (ANID_08269.1) genes are preferentially expressed in an acidic milieu, whose expression is dependent on the palA (+) background under optimal temperature for fungal growth. Heat shock induction of these three hsp genes showed different patterns in response to extracellular pH changes in the palA(+) background. However, their accumulation upon heating for 2 h was almost unaffected by ambient pH changes in the palA (-) background. The PalA protein is a member of a conserved signaling cascade that is involved in the pH-mediated regulation of gene expression. Moreover, we identified several genes whose expression at pH 5.0 is also dependent on the palA (+) background. These results reveal novel aspects of the heat- and pH-sensing networks of A. nidulans.
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Affiliation(s)
- Janaína S. Freitas
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049–900 Ribeirão Preto, São Paulo Brazil
| | - Emiliana M. Silva
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049–900 Ribeirão Preto, São Paulo Brazil
| | - Juliana Leal
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049–900 Ribeirão Preto, São Paulo Brazil
| | - Diana E. Gras
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049–900 Ribeirão Preto, São Paulo Brazil
| | - Nilce M. Martinez-Rossi
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049–900 Ribeirão Preto, São Paulo Brazil
| | - Lucilene Delazari dos Santos
- Centro de Estudos de Insetos Sociais, Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista, 13506–900 Rio Claro, São Paulo Brazil
| | - Mario S. Palma
- Centro de Estudos de Insetos Sociais, Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista, 13506–900 Rio Claro, São Paulo Brazil
| | - Antonio Rossi
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049–900 Ribeirão Preto, São Paulo Brazil
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Dimmer KS, Rapaport D. Unresolved mysteries in the biogenesis of mitochondrial membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1085-90. [PMID: 21889926 DOI: 10.1016/j.bbamem.2011.08.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 08/10/2011] [Accepted: 08/15/2011] [Indexed: 10/17/2022]
Abstract
Mitochondria are essential eukaryotic organelles that are surrounded by two membranes. Both membranes contain a variety of different integral membrane proteins. After three decades of research on mitochondrial biogenesis five major import complexes with more than 40 subunits altogether were identified and characterized. In the current contribution we want to draw attention to some unexplored issues regarding the integration of mitochondrial membrane proteins and to formulate crucial questions that remain unanswered. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Affiliation(s)
- Kai Stefan Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany.
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Affiliation(s)
- Ross E. Dalbey
- The Ohio State University, Department of Chemistry, Columbus, Ohio 43210;
| | - Peng Wang
- The Ohio State University, Department of Chemistry, Columbus, Ohio 43210;
| | - Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, 70599 Stuttgart, Germany;
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Funes S, Kauff F, van der Sluis EO, Ott M, Herrmann JM. Evolution of YidC/Oxa1/Alb3 insertases: three independent gene duplications followed by functional specialization in bacteria, mitochondria and chloroplasts. Biol Chem 2011; 392:13-9. [PMID: 21194367 DOI: 10.1515/bc.2011.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Members of the YidC/Oxa1/Alb3 protein family facilitate the insertion, folding and assembly of proteins of the inner membranes of bacteria and mitochondria and the thylakoid membrane of plastids. All homologs share a conserved hydrophobic core region comprising five transmembrane domains. On the basis of phylogenetic analyses, six subgroups of the family can be distinguished which presumably arose from three independent gene duplications followed by functional specialization. During evolution of bacteria, mitochondria and chloroplasts, subgroup-specific regions were added to the core domain to facilitate the association with ribosomes or other components contributing to the substrate spectrum of YidC/Oxa1/Alb3 proteins.
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Affiliation(s)
- Soledad Funes
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Circuito Exterior s/n, Ciudad Universitaria, Universidad Nacional Autónoma de México, Mexico D.F. 04510, Mexico
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Francis BR, Thorsness PE. Hsp90 and mitochondrial proteases Yme1 and Yta10/12 participate in ATP synthase assembly in Saccharomyces cerevisiae. Mitochondrion 2011; 11:587-600. [PMID: 21439406 DOI: 10.1016/j.mito.2011.03.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 02/22/2011] [Accepted: 03/15/2011] [Indexed: 10/18/2022]
Abstract
Hsc82 and Hsp82, the Hsp90 family proteins of yeast, are both required for fermentative growth at 37°C. Inactivation of either of the mitochondrial AAA proteases, Yme1 or Yta10/12, allows fermentative growth of hsc82∆ or hsp82∆ strains at 37°C. Genetic evidence indicates interaction of Hsc82/Hsp82 with the Yme1 and Yta10/Yta12 complexes in promoting F(1)F(o)-ATPase activity, with Hsc82 specifically required for F(1)-ATPase assembly. A previously reported mutation in Rpt3, one of the six ATPases of the proteasome, suppresses yme1∆ phenotypes and increases transcription of HSC82 but not HSP82. These genetic interactions describe a functional role for Hsp90 proteins in mitochondrial biogenesis.
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Affiliation(s)
- Brian R Francis
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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Price CE, Otto A, Fusetti F, Becher D, Hecker M, Driessen AJM. Differential effect of YidC depletion on the membrane proteome of Escherichia coli under aerobic and anaerobic growth conditions. Proteomics 2011; 10:3235-47. [PMID: 20706981 DOI: 10.1002/pmic.201000284] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
YidC of Escherichia coli belongs to the evolutionarily conserved Oxa1/Alb3/YidC family. Members of the family have all been implicated in membrane protein biogenesis of respiratory and energy transducing proteins. The number of proteins identified thus far to require YidC for their membrane biogenesis remains limited and the identification of new substrates may allow the elucidation of properties that define the YidC specificity. To this end we investigated changes in the membrane proteome of E. coli upon YidC depletion using metabolic labeling of proteins with 15N/14N combined with a MS-centered proteomics approach and compared the effects of YidC depletion under aerobic and anaerobic growth conditions. We found that YidC depletion resulted in protein aggregation/misfolding in the cytoplasm as well as in the inner membrane of E. coli. A dramatic increase was observed in the chaperone-mediated stress response upon YidC depletion and this response was limited to aerobically grown cells. A number of transporter proteins were identified as possible candidates for the YidC-dependent insertion and/or folding pathway. These included the small metal ion transporter CorA, numerous ABC transporters, as well as the MFS transporters KgtP and ProP, providing a new subset of proteins potentially requiring YidC for membrane biogenesis.
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Affiliation(s)
- Claire E Price
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Kluyver Centre for the Genomics of Industrial Fermentations and the Zernike Institute of Advanced Materials, University of Groningen, NN Haren, The Netherlands
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50
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Modular assembly of yeast mitochondrial ATP synthase. EMBO J 2011; 30:920-30. [PMID: 21266956 DOI: 10.1038/emboj.2010.364] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 12/16/2010] [Indexed: 11/08/2022] Open
Abstract
The mitochondrial ATP synthase (F(1)-F(0) complex) of Saccharomces cerevisiae is a composite of different structural and functional units that jointly couple ATP synthesis and hydrolysis to proton transfer across the inner membrane. In organello, pulse labelling and pulse-chase experiments have enabled us to track the mitochondrially encoded Atp6p, Atp8p and Atp9p subunits of F(0) and to identify different assembly intermediates into which they are assimilated. Surprisingly, these core subunits of F(0) segregated into two different assembly intermediates one of which is composed of Atp6p, Atp8p, at least two stator subunits, and the Atp10p chaperone while the second consists of the F(1) ATPase and Atp9p ring. These studies show that assembly of the ATP synthase is not a single linear process, as previously thought, but rather involves two separate but coordinately regulated pathways that converge at the end stage.
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