1
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Herbert CJ, Labarre-Mariotte S, Cornu D, Sophie C, Panozzo C, Michel T, Dujardin G, Bonnefoy N. Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria. Nucleic Acids Res 2021; 49:11145-11166. [PMID: 34634819 PMCID: PMC8565316 DOI: 10.1093/nar/gkab789] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/24/2021] [Accepted: 10/05/2021] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial mRNAs encode key subunits of the oxidative phosphorylation complexes that produce energy for the cell. In Saccharomyces cerevisiae, mitochondrial translation is under the control of translational activators, specific to each mRNA. In Schizosaccharomyces pombe, which more closely resembles the human system by its mitochondrial DNA structure and physiology, most translational activators appear to be either lacking, or recruited for post-translational functions. By combining bioinformatics, genetic and biochemical approaches we identified two interacting factors, Cbp7 and Cbp8, controlling Cytb production in S. pombe. We show that their absence affects cytb mRNA stability and impairs the detection of the Cytb protein. We further identified two classes of Cbp7/Cbp8 partners and showed that they modulated Cytb or Cox1 synthesis. First, two isoforms of bS1m, a protein of the small mitoribosomal subunit, that appear mutually exclusive and confer translational specificity. Second, a complex of four proteins dedicated to Cox1 synthesis, which includes an RNA helicase that interacts with the mitochondrial ribosome. Our results suggest that S. pombe contains, in addition to complexes of translational activators, a heterogeneous population of mitochondrial ribosomes that could specifically modulate translation depending on the mRNA translated, in order to optimally balance the production of different respiratory complex subunits.
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Affiliation(s)
- Christopher J Herbert
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Sylvie Labarre-Mariotte
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - David Cornu
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cyrielle Sophie
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cristina Panozzo
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Thomas Michel
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Geneviève Dujardin
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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2
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Mechanisms and regulation of protein synthesis in mitochondria. Nat Rev Mol Cell Biol 2021; 22:307-325. [PMID: 33594280 DOI: 10.1038/s41580-021-00332-2] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 02/06/2023]
Abstract
Mitochondria are cellular organelles responsible for generation of chemical energy in the process called oxidative phosphorylation. They originate from a bacterial ancestor and maintain their own genome, which is expressed by designated, mitochondrial transcription and translation machineries that differ from those operating for nuclear gene expression. In particular, the mitochondrial protein synthesis machinery is structurally and functionally very different from that governing eukaryotic, cytosolic translation. Despite harbouring their own genetic information, mitochondria are far from being independent of the rest of the cell and, conversely, cellular fitness is closely linked to mitochondrial function. Mitochondria depend heavily on the import of nuclear-encoded proteins for gene expression and function, and hence engage in extensive inter-compartmental crosstalk to regulate their proteome. This connectivity allows mitochondria to adapt to changes in cellular conditions and also mediates responses to stress and mitochondrial dysfunction. With a focus on mammals and yeast, we review fundamental insights that have been made into the biogenesis, architecture and mechanisms of the mitochondrial translation apparatus in the past years owing to the emergence of numerous near-atomic structures and a considerable amount of biochemical work. Moreover, we discuss how cellular mitochondrial protein expression is regulated, including aspects of mRNA and tRNA maturation and stability, roles of auxiliary factors, such as translation regulators, that adapt mitochondrial translation rates, and the importance of inter-compartmental crosstalk with nuclear gene expression and cytosolic translation and how it enables integration of mitochondrial translation into the cellular context.
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3
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Levitskii SA, Baleva MV, Chicherin IV, Krasheninnikov IA, Kamenski PA. Protein Biosynthesis in Mitochondria: Past Simple, Present Perfect, Future Indefinite. BIOCHEMISTRY (MOSCOW) 2021; 85:257-263. [PMID: 32564730 DOI: 10.1134/s0006297920030013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mitochondria are obligate organelles of most eukaryotic cells that perform many different functions important for cellular homeostasis. The main role of mitochondria is supplying cells with energy in a form of ATP, which is synthesized in a chain of oxidative phosphorylation reactions on the organelle inner membrane. It is commonly believed now that mitochondria have the endosymbiotic origin. In the course of evolution, they have lost most of their genetic material as a result of genome reduction and gene transfer to the nucleus. The majority of mitochondrial proteins are synthesized in the cytosol and then imported to the mitochondria. However, almost all known mitochondria still contain genomes that are maintained and expressed. The processes of protein biosynthesis in the mitochondria - mitochondrial translation - substantially differs from the analogous processes in bacteria and the cytosol of eukaryotic cells. Mitochondrial translation is characterized by a high degree of specialization and specific regulatory mechanisms. In this review, we analyze available information on the common principles of mitochondrial translation with emphasis on the molecular mechanisms of translation initiation in the mitochondria of yeast and mammalian cells.
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Affiliation(s)
- S A Levitskii
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - M V Baleva
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - I V Chicherin
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - I A Krasheninnikov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - P A Kamenski
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia.
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4
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Ferrari A, Del'Olio S, Barrientos A. The Diseased Mitoribosome. FEBS Lett 2020; 595:1025-1061. [PMID: 33314036 DOI: 10.1002/1873-3468.14024] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 12/17/2022]
Abstract
Mitochondria control life and death in eukaryotic cells. Harboring a unique circular genome, a by-product of an ancient endosymbiotic event, mitochondria maintains a specialized and evolutionary divergent protein synthesis machinery, the mitoribosome. Mitoribosome biogenesis depends on elements encoded in both the mitochondrial genome (the RNA components) and the nuclear genome (all ribosomal proteins and assembly factors). Recent cryo-EM structures of mammalian mitoribosomes have illuminated their composition and provided hints regarding their assembly and elusive mitochondrial translation mechanisms. A growing body of literature involves the mitoribosome in inherited primary mitochondrial disorders. Mutations in genes encoding mitoribosomal RNAs, proteins, and assembly factors impede mitoribosome biogenesis, causing protein synthesis defects that lead to respiratory chain failure and mitochondrial disorders such as encephalo- and cardiomyopathy, deafness, neuropathy, and developmental delays. In this article, we review the current fundamental understanding of mitoribosome assembly and function, and the clinical landscape of mitochondrial disorders driven by mutations in mitoribosome components and assembly factors, to portray how basic and clinical studies combined help us better understand both mitochondrial biology and medicine.
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Affiliation(s)
- Alberto Ferrari
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA
| | - Samuel Del'Olio
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Molecular and Cellular Pharmacology Graduate Program, University of Miami Miller School of Medicine, FL, USA
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, FL, USA
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5
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Rudler DL, Hughes LA, Viola HM, Hool LC, Rackham O, Filipovska A. Fidelity and coordination of mitochondrial protein synthesis in health and disease. J Physiol 2020; 599:3449-3462. [PMID: 32710561 DOI: 10.1113/jp280359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
The evolutionary acquisition of mitochondria has given rise to the diversity of eukaryotic life. Mitochondria have retained their ancestral α-proteobacterial traits through the maintenance of double membranes and their own circular genome. Their genome varies in size from very large in plants to the smallest in animals and their parasites. The mitochondrial genome encodes essential genes for protein synthesis and has to coordinate its expression with the nuclear genome from which it sources most of the proteins required for mitochondrial biogenesis and function. The mitochondrial protein synthesis machinery is unique because it is encoded by both the nuclear and mitochondrial genomes thereby requiring tight regulation to produce the respiratory complexes that drive oxidative phosphorylation for energy production. The fidelity and coordination of mitochondrial protein synthesis are essential for ATP production. Here we compare and contrast the mitochondrial translation mechanisms in mammals and fungi to bacteria and reveal that their diverse regulation can have unusual impacts on the health and disease of these organisms. We highlight that in mammals the rate of protein synthesis is more important than the fidelity of translation, enabling coordinated biogenesis of the mitochondrial respiratory chain with respiratory chain proteins synthesised by cytoplasmic ribosomes. Changes in mitochondrial protein fidelity can trigger the activation of the diverse cellular signalling networks in fungi and mammals to combat dysfunction in energy conservation. The physiological consequences of altered fidelity of protein synthesis can range from liver regeneration to the onset and development of cardiomyopathy.
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Affiliation(s)
- Danielle L Rudler
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia
| | - Laetitia A Hughes
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia
| | - Helena M Viola
- School of Human Sciences, University of Western Australia, 35 Stirling Highway, Nedlands, Western Australia, 6009, Australia
| | - Livia C Hool
- School of Human Sciences, University of Western Australia, 35 Stirling Highway, Nedlands, Western Australia, 6009, Australia.,Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Western Australia, 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, 6102, Australia.,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia, Australia.,School of Molecular Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
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6
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Yeast Mitochondrial Translation Initiation Factor 3 Interacts with Pet111p to Promote COX2 mRNA Translation. Int J Mol Sci 2020; 21:ijms21103414. [PMID: 32408541 PMCID: PMC7279496 DOI: 10.3390/ijms21103414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genomes code for several core components of respiratory chain complexes. Thus, mitochondrial translation is of great importance for the organelle as well as for the whole cell. In yeast, mitochondrial translation initiation factor 3, Aim23p, is not essential for the organellar protein synthesis; however, its absence leads to a significant quantitative imbalance of the mitochondrial translation products. This fact points to a possible specific action of Aim23p on the biosynthesis of some mitochondrial protein species. In this work, we examined such peculiar effects of Aim23p in relation to yeast mitochondrial COX2 mRNA translation. We show that Aim23p is indispensable to this process. According to our data, this is mediated by Aimp23p interaction with the known specific factor of the COX2 mRNA translation, Pet111p. If there is no Aim23p in the yeast cells, an increased amount of Pet111p ensures proper COX2 mRNA translation. Our results demonstrate the additional non-canonical function of initiation factor 3 in yeast mitochondrial translation.
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7
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Waltz F, Giegé P. Striking Diversity of Mitochondria-Specific Translation Processes across Eukaryotes. Trends Biochem Sci 2019; 45:149-162. [PMID: 31780199 DOI: 10.1016/j.tibs.2019.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022]
Abstract
Mitochondria are essential organelles that act as energy conversion powerhouses and metabolic hubs. Their gene expression machineries combine traits inherited from prokaryote ancestors and specific features acquired during eukaryote evolution. Mitochondrial research has wide implications ranging from human health to agronomy. We highlight recent advances in mitochondrial translation. Functional, biochemical, and structural data have revealed an unexpected diversity of mitochondrial translation systems, particularly of their key players, the mitochondrial ribosomes (mitoribosomes). Ribosome assembly and translation mechanisms, such as initiation, are discussed and put in perspective with the prevalence of eukaryote-specific families of mitochondrial translation factors such as pentatricopeptide repeat (PPR) proteins.
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Affiliation(s)
- Florent Waltz
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France; Institut Européen de Chimie et de Biologie, l'Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Bordeaux, 2 rue Robert Escarpit, 33607 Pessac, France.
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
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8
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Ayyub SA, Varshney U. Translation initiation in mammalian mitochondria- a prokaryotic perspective. RNA Biol 2019; 17:165-175. [PMID: 31696767 DOI: 10.1080/15476286.2019.1690099] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
ATP is generated in mitochondria of eukaryotic cells by oxidative phosphorylation (OXPHOS). The OXPHOS complex, which is crucial for cellular metabolism, comprises of both nuclear and mitochondrially encoded subunits. Also, the occurrence of several pathologies because of mutations in the mitochondrial translation apparatus indicates the importance of mitochondrial translation and its regulation. The mitochondrial translation apparatus is similar to its prokaryotic counterpart due to a common origin of evolution. However, mitochondrial translation has diverged from prokaryotic translation in many ways by reductive evolution. In this review, we focus on mammalian mitochondrial translation initiation, a highly regulated step of translation, and present a comparison with prokaryotic translation.
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Affiliation(s)
- Shreya Ahana Ayyub
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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9
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Luo Y, Su R, Wang Y, Xie W, Liu Z, Huang Y. Schizosaccharomyces pombe Mti2 and Mti3 act in conjunction during mitochondrial translation initiation. FEBS J 2019; 286:4542-4553. [PMID: 31350787 DOI: 10.1111/febs.15021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/23/2019] [Accepted: 07/24/2019] [Indexed: 01/15/2023]
Abstract
Mitochondrial DNA encodes key subunits of the oxidative phosphorylation complexes essential for ATP production. Translation initiation in mitochondria requires two general factors, mtIF2 and mtIF3, whose counterparts in bacteria are essential for protein synthesis. In this study, we report the characterization of the fission yeast Schizosaccharomyces pombe mtIF2 (Mti2) and mtIF3 (Mti3). Deletion of mti2 impairs cell growth on the respiratory medium. The growth defect of the mti2 deletion mutant can be suppressed by expressing IFM1, the Saccharomyces cerevisiae homolog of Mti2, demonstrating functional conservation between the two proteins. Deletion of mti2 also impairs mitochondrial protein synthesis. Unlike mti2, deletion of mti3 does not affect cell growth on respiratory media and mitochondrial translation. However, deletion of mti3 exacerbates the growth defect of the Δmti2 mutant, suggesting that the two proteins have distinct, but partially overlapping functions during the process of mitochondrial translation initiation in S. pombe. Both Mti2 and Mti3 are associated with the small subunit of the mitochondrial ribosome (mitoribosome). Disruption of mti2, but not mti3, causes dissociation of the mitoribosome and also abolishes Mti3 binding to the small subunit of the mitoribosome. Our results suggest that Mti2 and Mti3 bind in a sequential manner to the small subunit of the mitoribosome and that Mti3 facilitates the function of Mti2 in mitochondrial translation initiation. Our findings also support the view that the importance of the mitochondrial translation initiation factors varies among the organisms.
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Affiliation(s)
- Ying Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, China
| | - Ruyue Su
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, China
| | - Yirong Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, China
| | - Wanqiu Xie
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, China
| | - Zecheng Liu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, China
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10
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Levitskii S, Baleva MV, Chicherin I, Krasheninnikov IA, Kamenski P. S. cerevisiae Strain Lacking Mitochondrial IF3 Shows Increased Levels of Tma19p during Adaptation to Respiratory Growth. Cells 2019; 8:cells8070645. [PMID: 31248014 PMCID: PMC6678281 DOI: 10.3390/cells8070645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 11/16/2022] Open
Abstract
After billions of years of evolution, mitochondrion retains its own genome, which gets expressed in mitochondrial matrix. Mitochondrial translation machinery rather differs from modern bacterial and eukaryotic cytosolic systems. Any disturbance in mitochondrial translation drastically impairs mitochondrial function. In budding yeast Saccharomyces cerevisiae, deletion of the gene coding for mitochondrial translation initiation factor 3 - AIM23, leads to an imbalance in mitochondrial protein synthesis and significantly delays growth after shifting from fermentable to non-fermentable carbon sources. Molecular mechanism underlying this adaptation to respiratory growth was unknown. Here, we demonstrate that slow adaptation from glycolysis to respiration in the absence of Aim23p is accompanied by a gradual increase of cytochrome c oxidase activity and by increased levels of Tma19p protein, which protects mitochondria from oxidative stress.
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Affiliation(s)
- Sergey Levitskii
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119234 Moscow, Russia.
| | - Maria V Baleva
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119234 Moscow, Russia.
| | - Ivan Chicherin
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119234 Moscow, Russia.
- M.V. Lomonosov Moscow State University, Institute of Functional Genomics, 119234 Moscow, Russia.
| | | | - Piotr Kamenski
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119234 Moscow, Russia.
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11
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Franco LVR, Moda BS, Soares MAKM, Barros MH. Msc6p is required for mitochondrial translation initiation in the absence of formylated Met-tRNA fMet. FEBS J 2019; 286:1407-1419. [PMID: 30767393 DOI: 10.1111/febs.14785] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/27/2018] [Accepted: 02/13/2019] [Indexed: 01/04/2023]
Abstract
Mitochondrial translation normally requires formylation of the initiator tRNA-met, a reaction catalyzed by the enzyme formyltransferase, Fmt1p and MTFMT in Saccharomyces cerevisiae and human mitochondria, respectively. Yeast fmt1 mutants devoid of Fmt1p, however, can synthesize all mitochondrial gene products by initiating translation with a non-formylated methionyl-tRNA. Yeast synthetic respiratory-deficient fmt1 mutants have uncovered several factors suggested to play a role in translation initiation with non-formylated methionyl-tRNA. Here, we present evidence that Msc6p, a member of the pentatricopeptide repeat (PPR) motif family, is another essential factor for mitochondrial translation in fmt1 mutants. The PPR motif is characteristic of RNA-binding proteins found in chloroplasts and plant and fungal mitochondria, and is generally involved in RNA stability and transport. Moreover, in the present study, we show that the respiratory deficiency of fmt1msc6 double mutants can be rescued by overexpression of the yeast mitochondrial initiation factor mIF-2, encoded by IFM1. The role of Msc6p in translational initiation is further supported by pull-down assays showing that it transiently interacts with mIF-2. Altogether, our data indicate that Msc6p is an important factor in mitochondrial translation with an auxiliary function related to the mIF-2-dependent formation of the initiation complex.
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Affiliation(s)
| | - Bruno S Moda
- Departamento de Microbiologia - Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
| | - Maria A K M Soares
- Departamento de Microbiologia - Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
| | - Mario H Barros
- Departamento de Microbiologia - Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
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12
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Chicherin IV, Zinina VV, Levitskiy SA, Serebryakova MV, Kamenski PA. Aim23p Interacts with the Yeast Mitochondrial Ribosomal Small Subunit. BIOCHEMISTRY (MOSCOW) 2019; 84:40-46. [DOI: 10.1134/s000629791901005x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Ogunbona OB, Claypool SM. Emerging Roles in the Biogenesis of Cytochrome c Oxidase for Members of the Mitochondrial Carrier Family. Front Cell Dev Biol 2019; 7:3. [PMID: 30766870 PMCID: PMC6365663 DOI: 10.3389/fcell.2019.00003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/10/2019] [Indexed: 12/11/2022] Open
Abstract
The mitochondrial carrier family (MCF) is a group of transport proteins that are mostly localized to the inner mitochondrial membrane where they facilitate the movement of various solutes across the membrane. Although these carriers represent potential targets for therapeutic application and are repeatedly associated with human disease, research on the MCF has not progressed commensurate to their physiologic and pathophysiologic importance. Many of the 53 MCF members in humans are orphans and lack known transport substrates. Even for the relatively well-studied members of this family, such as the ADP/ATP carrier and the uncoupling protein, there exist fundamental gaps in our understanding of their biological roles including a clear rationale for the existence of multiple isoforms. Here, we briefly review this important family of mitochondrial carriers, provide a few salient examples of their diverse metabolic roles and disease associations, and then focus on an emerging link between several distinct MCF members, including the ADP/ATP carrier, and cytochrome c oxidase biogenesis. As the ADP/ATP carrier is regarded as the paradigm of the entire MCF, its newly established role in regulating translation of the mitochondrial genome highlights that we still have a lot to learn about these metabolite transporters.
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Affiliation(s)
- Oluwaseun B. Ogunbona
- Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
- Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - Steven M. Claypool
- Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
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14
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Zhao J, Qin B, Nikolay R, Spahn CMT, Zhang G. Translatomics: The Global View of Translation. Int J Mol Sci 2019; 20:ijms20010212. [PMID: 30626072 PMCID: PMC6337585 DOI: 10.3390/ijms20010212] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 01/01/2023] Open
Abstract
In all kingdoms of life, proteins are synthesized by ribosomes in a process referred to as translation. The amplitude of translational regulation exceeds the sum of transcription, mRNA degradation and protein degradation. Therefore, it is essential to investigate translation in a global scale. Like the other “omics”-methods, translatomics investigates the totality of the components in the translation process, including but not limited to translating mRNAs, ribosomes, tRNAs, regulatory RNAs and nascent polypeptide chains. Technical advances in recent years have brought breakthroughs in the investigation of these components at global scale, both for their composition and dynamics. These methods have been applied in a rapidly increasing number of studies to reveal multifaceted aspects of translation control. The process of translation is not restricted to the conversion of mRNA coding sequences into polypeptide chains, it also controls the composition of the proteome in a delicate and responsive way. Therefore, translatomics has extended its unique and innovative power to many fields including proteomics, cancer research, bacterial stress response, biological rhythmicity and plant biology. Rational design in translation can enhance recombinant protein production for thousands of times. This brief review summarizes the main state-of-the-art methods of translatomics, highlights recent discoveries made in this field and introduces applications of translatomics on basic biological and biomedical research.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Bo Qin
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Rainer Nikolay
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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15
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Derbikova K, Kuzmenko A, Levitskii S, Klimontova M, Chicherin I, Baleva MV, Krasheninnikov IA, Kamenski P. Biological and Evolutionary Significance of Terminal Extensions of Mitochondrial Translation Initiation Factor 3. Int J Mol Sci 2018; 19:ijms19123861. [PMID: 30518034 PMCID: PMC6321546 DOI: 10.3390/ijms19123861] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 01/14/2023] Open
Abstract
Protein biosynthesis in mitochondria is organized in a bacterial manner. However, during evolution, mitochondrial translation mechanisms underwent many organelle-specific changes. In particular, almost all mitochondrial translation factors, being orthologous to bacterial proteins, are characterized by some unique elements of primary or secondary structure. In the case of the organellar initiation factor 3 (IF3), these elements are several dozen amino acids long N- and C-terminal extensions. This study focused on the terminal extensions of baker's yeast mitochondrial IF3, Aim23p. By in vivo deletion and complementation analysis, we show that at least one extension is necessary for Aim23p function. At the same time, human mitochondrial IF3 is fully functional in yeast mitochondria even without both terminal extensions. While Escherichia coli IF3 itself is poorly active in yeast mitochondria, adding Aim23p terminal extensions makes the resulting chimeric protein as functional as the cognate factor. Our results show that the terminal extensions of IF3 have evolved as the "adaptors" that accommodate the translation factor of bacterial origin to the evolutionary changed protein biosynthesis system in mitochondria.
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Affiliation(s)
- Ksenia Derbikova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
| | - Anton Kuzmenko
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
- Institute of Molecular Genetics, Russian Academy of Science, 119991 Moskva, Russia.
| | - Sergey Levitskii
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
| | - Maria Klimontova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
- Faculty of Biosciences, Heidelberg University, 69117 Heidelberg, Germany.
| | - Ivan Chicherin
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
| | - Maria V Baleva
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
| | | | - Piotr Kamenski
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
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16
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Levitskii S, Derbikova K, Baleva MV, Kuzmenko A, Golovin AV, Chicherin I, Krasheninnikov IA, Kamenski P. 60S dynamic state of bacterial ribosome is fixed by yeast mitochondrial initiation factor 3. PeerJ 2018; 6:e5620. [PMID: 30245939 PMCID: PMC6147165 DOI: 10.7717/peerj.5620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/21/2018] [Indexed: 11/24/2022] Open
Abstract
The processes of association and dissociation of ribosomal subunits are of great importance for the protein biosynthesis. The mechanistic details of these processes, however, are not well known. In bacteria, upon translation termination, the ribosome dissociates into subunits which is necessary for its further involvement into new initiation step. The dissociated state of the ribosome is maintained by initiation factor 3 (IF3) which binds to free small subunits and prevents their premature association with large subunits. In this work, we have exchanged IF3 in Escherichia coli cells by its ortholog from Saccharomyces cerevisiae mitochondria (Aim23p) and showed that yeast protein cannot functionally substitute the bacterial one and is even slightly toxic for bacterial cells. Our in vitro experiments have demonstrated that Aim23p does not split E. coli ribosomes into subunits. Instead, it fixes a state of ribosomes characterized by sedimentation coefficient about 60S which is not a stable structure but rather reflects a shift of dynamic equilibrium between associated and dissociated states of the ribosome. Mitochondria-specific terminal extensions of Aim23p are necessary for “60S state” formation, and molecular modeling results point out that these extensions might stabilize the position of the protein on the bacterial ribosome.
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Affiliation(s)
| | | | - Maria V Baleva
- Faculty of Biology, Moscow State University, Moscow, Russia
| | - Anton Kuzmenko
- Faculty of Biology, Moscow State University, Moscow, Russia
| | - Andrey V Golovin
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia.,Faculty of Computer Science, Higher School of Economics, Moscow, Russia
| | - Ivan Chicherin
- Faculty of Biology, Moscow State University, Moscow, Russia
| | | | - Piotr Kamenski
- Faculty of Biology, Moscow State University, Moscow, Russia
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17
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Ramrath DJF, Niemann M, Leibundgut M, Bieri P, Prange C, Horn EK, Leitner A, Boehringer D, Schneider A, Ban N. Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes. Science 2018; 362:science.aau7735. [PMID: 30213880 DOI: 10.1126/science.aau7735] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/03/2018] [Indexed: 01/19/2023]
Abstract
Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of Trypanosoma brucei, a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the "minimal" set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements.
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Affiliation(s)
- David J F Ramrath
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Moritz Niemann
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Philipp Bieri
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Céline Prange
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Elke K Horn
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland.
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18
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Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. Nature 2018; 560:263-267. [PMID: 30089917 DOI: 10.1038/s41586-018-0373-y] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/17/2018] [Indexed: 11/09/2022]
Abstract
Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation1,2. The initiation of protein synthesis in mitochondria differs substantially from bacterial or cytosolic translation systems. Mitochondrial translation initiation lacks initiation factor 1, which is essential in all other translation systems from bacteria to mammals3,4. Furthermore, only one type of methionyl transfer RNA (tRNAMet) is used for both initiation and elongation4,5, necessitating that the initiation factor specifically recognizes the formylated version of tRNAMet (fMet-tRNAMet). Lastly, most mitochondrial mRNAs do not possess 5' leader sequences to promote mRNA binding to the ribosome2. There is currently little mechanistic insight into mammalian mitochondrial translation initiation, and it is not clear how mRNA engagement, initiator-tRNA recruitment and start-codon selection occur. Here we determine the cryo-EM structure of the complete translation initiation complex from mammalian mitochondria at 3.2 Å. We describe the function of an additional domain insertion that is present in the mammalian mitochondrial initiation factor 2 (mtIF2). By closing the decoding centre, this insertion stabilizes the binding of leaderless mRNAs and induces conformational changes in the rRNA nucleotides involved in decoding. We identify unique features of mtIF2 that are required for specific recognition of fMet-tRNAMet and regulation of its GTPase activity. Finally, we observe that the ribosomal tunnel in the initiating ribosome is blocked by insertion of the N-terminal portion of mitochondrial protein mL45, which becomes exposed as the ribosome switches to elongation mode and may have an additional role in targeting of mitochondrial ribosomes to the protein-conducting pore in the inner mitochondrial membrane.
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19
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Ogunbona OB, Baile MG, Claypool SM. Cardiomyopathy-associated mutation in the ADP/ATP carrier reveals translation-dependent regulation of cytochrome c oxidase activity. Mol Biol Cell 2018; 29:1449-1464. [PMID: 29688796 PMCID: PMC6014099 DOI: 10.1091/mbc.e17-12-0700] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/16/2018] [Accepted: 04/18/2018] [Indexed: 01/07/2023] Open
Abstract
How the absence of the major mitochondrial ADP/ATP carrier in yeast, Aac2p, results in a specific defect in cytochrome c oxidase (COX; complex IV) activity is a long-standing mystery. Aac2p physically associates with respiratory supercomplexes, which include complex IV, raising the possibility that its activity is dependent on its association with Aac2p. Here, we have leveraged a transport-dead pathogenic AAC2 point mutant to determine the basis for the reduced COX activity in the absence of Aac2p. The steady-state levels of complex IV subunits encoded by the mitochondrial genome are significantly reduced in the absence of Aac2p function, whether its association with respiratory supercomplexes is preserved or not. This diminution in COX amounts is not caused by a reduction in the mitochondrial genome copy number or the steady-state level of its transcripts, and does not reflect a defect in complex IV assembly. Instead, the absence of Aac2p activity, genetically or pharmacologically, results in an aberrant pattern of mitochondrial translation. Interestingly, compared with the complete absence of Aac2p, the complex IV-related defects are greater in mitochondria expressing the transport-inactive Aac2p mutant. Our results highlight a critical role for Aac2p transport in mitochondrial translation whose disturbance uniquely impacts cytochrome c oxidase.
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Affiliation(s)
- Oluwaseun B. Ogunbona
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | | | - Steven M. Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
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20
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Derbikova KS, Levitsky SA, Chicherin IV, Vinogradova EN, Kamenski PA. Activation of Yeast Mitochondrial Translation: Who Is in Charge? BIOCHEMISTRY (MOSCOW) 2018; 83:87-97. [DOI: 10.1134/s0006297918020013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Abstract
Mitochondria play fundamental roles in the regulation of life and death of eukaryotic cells. They mediate aerobic energy conversion through the oxidative phosphorylation (OXPHOS) system, and harbor and control the intrinsic pathway of apoptosis. As a descendant of a bacterial endosymbiont, mitochondria retain a vestige of their original genome (mtDNA), and its corresponding full gene expression machinery. Proteins encoded in the mtDNA, all components of the multimeric OXPHOS enzymes, are synthesized in specialized mitochondrial ribosomes (mitoribosomes). Mitoribosomes are therefore essential in the regulation of cellular respiration. Additionally, an increasing body of literature has been reporting an alternative role for several mitochondrial ribosomal proteins as apoptosis-inducing factors. No surprisingly, the expression of genes encoding for mitoribosomal proteins, mitoribosome assembly factors and mitochondrial translation factors is modified in numerous cancers, a trait that has been linked to tumorigenesis and metastasis. In this article, we will review the current knowledge regarding the dual function of mitoribosome components in protein synthesis and apoptosis and their association with cancer susceptibility and development. We will also highlight recent developments in targeting mitochondrial ribosomes for the treatment of cancer.
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22
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Habib S, Vaishya S, Gupta K. Translation in Organelles of Apicomplexan Parasites. Trends Parasitol 2016; 32:939-952. [DOI: 10.1016/j.pt.2016.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/19/2016] [Accepted: 07/25/2016] [Indexed: 01/27/2023]
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23
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Affiliation(s)
- Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
| | - Alexey Amunts
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden;
| | - Alan Brown
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, United Kingdom;
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24
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Ostojić J, Panozzo C, Bourand-Plantefol A, Herbert CJ, Dujardin G, Bonnefoy N. Ribosome recycling defects modify the balance between the synthesis and assembly of specific subunits of the oxidative phosphorylation complexes in yeast mitochondria. Nucleic Acids Res 2016; 44:5785-97. [PMID: 27257059 PMCID: PMC4937339 DOI: 10.1093/nar/gkw490] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/20/2016] [Indexed: 01/07/2023] Open
Abstract
Mitochondria have their own translation machinery that produces key subunits of the OXPHOS complexes. This machinery relies on the coordinated action of nuclear-encoded factors of bacterial origin that are well conserved between humans and yeast. In humans, mutations in these factors can cause diseases; in yeast, mutations abolishing mitochondrial translation destabilize the mitochondrial DNA. We show that when the mitochondrial genome contains no introns, the loss of the yeast factors Mif3 and Rrf1 involved in ribosome recycling neither blocks translation nor destabilizes mitochondrial DNA. Rather, the absence of these factors increases the synthesis of the mitochondrially-encoded subunits Cox1, Cytb and Atp9, while strongly impairing the assembly of OXPHOS complexes IV and V. We further show that in the absence of Rrf1, the COX1 specific translation activator Mss51 accumulates in low molecular weight forms, thought to be the source of the translationally-active form, explaining the increased synthesis of Cox1. We propose that Rrf1 takes part in the coordination between translation and OXPHOS assembly in yeast mitochondria. These interactions between general and specific translation factors might reveal an evolutionary adaptation of the bacterial translation machinery to the set of integral membrane proteins that are translated within mitochondria.
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Affiliation(s)
- Jelena Ostojić
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Cristina Panozzo
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Alexa Bourand-Plantefol
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Christopher J Herbert
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Geneviève Dujardin
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
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25
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70S-scanning initiation is a novel and frequent initiation mode of ribosomal translation in bacteria. Proc Natl Acad Sci U S A 2016; 113:E1180-9. [PMID: 26888283 DOI: 10.1073/pnas.1524554113] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
According to the standard model of bacterial translation initiation, the small ribosomal 30S subunit binds to the initiation site of an mRNA with the help of three initiation factors (IF1-IF3). Here, we describe a novel type of initiation termed "70S-scanning initiation," where the 70S ribosome does not necessarily dissociate after translation of a cistron, but rather scans to the initiation site of the downstream cistron. We detailed the mechanism of 70S-scanning initiation by designing unique monocistronic and polycistronic mRNAs harboring translation reporters, and by reconstituting systems to characterize each distinct mode of initiation. Results show that 70S scanning is triggered by fMet-tRNA and does not require energy; the Shine-Dalgarno sequence is an essential recognition element of the initiation site. IF1 and IF3 requirements for the various initiation modes were assessed by the formation of productive initiation complexes leading to synthesis of active proteins. IF3 is essential and IF1 is highly stimulating for the 70S-scanning mode. The task of IF1 appears to be the prevention of untimely interference by ternary aminoacyl (aa)-tRNA•elongation factor thermo unstable (EF-Tu)•GTP complexes. Evidence indicates that at least 50% of bacterial initiation events use the 70S-scanning mode, underscoring the relative importance of this translation initiation mechanism.
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26
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Nag JK, Chahar D, Shrivastava N, Gupta CL, Bajpai P, Chandra D, Misra-Bhattacharya S. Functional attributes of evolutionary conserved Arg45 of Wolbachia (Brugia malayi) translation initiation factor-1. Future Microbiol 2016; 11:195-214. [PMID: 26855259 DOI: 10.2217/fmb.15.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Wolbachia is a promising antifilarial chemotherapeutic target. Translation initiation factor-1 (Tl IF-1) is an essential factor in prokaryotes. Functional characterization of Wolbachia's novel proteins/enzymes is necessary for the development of adulticidal drugs. MATERIALS & METHODS Mutant, Wol Tl IF-1 R45D was constructed by site directed mutagenesis. Fluorimetry and size exclusion chromatography were used to determine the biophysical characteristics. Mobility shift assay and fluorescence resonance energy transfer were used to investigate the functional aspect of Wol Tl IF-1 with its mutant. RESULTS Both wild and mutant were in monomeric native conformations. Wild exhibits nonspecific binding with ssRNA/ssDNA fragments under electrostatic conditions and showed annealing and displacement of RNA strands in comparison to mutant. CONCLUSION Point mutation impaired RNA chaperone activity of the mutant and its interaction with nucleotides.
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Affiliation(s)
- Jeetendra Kumar Nag
- Division of Parasitology, CSIR-Central Drug Research Institute, BS 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow (UP) 226031, India.,Department of Biochemistry, Lucknow University, Lucknow (UP) 226007, India
| | - Dhanvantri Chahar
- Division of Parasitology, CSIR-Central Drug Research Institute, BS 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow (UP) 226031, India.,Academy of Scientific & Innovative Research, Coordination Office, Mathura Road, CRRI, Jasola, New Delhi 110020, India
| | - Nidhi Shrivastava
- Division of Parasitology, CSIR-Central Drug Research Institute, BS 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow (UP) 226031, India
| | - Chhedi Lal Gupta
- Department of Biosciences, Integral University, Lucknow (UP) 226026, India
| | - Preeti Bajpai
- Department of Biosciences, Integral University, Lucknow (UP) 226026, India
| | - Deepak Chandra
- Department of Biochemistry, Lucknow University, Lucknow (UP) 226007, India
| | - Shailja Misra-Bhattacharya
- Division of Parasitology, CSIR-Central Drug Research Institute, BS 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow (UP) 226031, India.,Academy of Scientific & Innovative Research, Coordination Office, Mathura Road, CRRI, Jasola, New Delhi 110020, India
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27
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Kuzmenko A, Derbikova K, Salvatori R, Tankov S, Atkinson GC, Tenson T, Ott M, Kamenski P, Hauryliuk V. Aim-less translation: loss of Saccharomyces cerevisiae mitochondrial translation initiation factor mIF3/Aim23 leads to unbalanced protein synthesis. Sci Rep 2016; 6:18749. [PMID: 26728900 PMCID: PMC4700529 DOI: 10.1038/srep18749] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/09/2015] [Indexed: 12/22/2022] Open
Abstract
The mitochondrial genome almost exclusively encodes a handful of transmembrane constituents of the oxidative phosphorylation (OXPHOS) system. Coordinated expression of these genes ensures the correct stoichiometry of the system’s components. Translation initiation in mitochondria is assisted by two general initiation factors mIF2 and mIF3, orthologues of which in bacteria are indispensible for protein synthesis and viability. mIF3 was thought to be absent in Saccharomyces cerevisiae until we recently identified mitochondrial protein Aim23 as the missing orthologue. Here we show that, surprisingly, loss of mIF3/Aim23 in S. cerevisiae does not indiscriminately abrogate mitochondrial translation but rather causes an imbalance in protein production: the rate of synthesis of the Atp9 subunit of F1F0 ATP synthase (complex V) is increased, while expression of Cox1, Cox2 and Cox3 subunits of cytochrome c oxidase (complex IV) is repressed. Our results provide one more example of deviation of mitochondrial translation from its bacterial origins.
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Affiliation(s)
- Anton Kuzmenko
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia.,Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Ksenia Derbikova
- Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Roger Salvatori
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Stoyan Tankov
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Gemma C Atkinson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia.,Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, SE-901 87 Umeå, Sweden
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Martin Ott
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Piotr Kamenski
- Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Vasili Hauryliuk
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia.,Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, SE-901 87 Umeå, Sweden
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28
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Two novel mitogenomes of Dipodidae species and phylogeny of Rodentia inferred from the complete mitogenomes. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.04.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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Haider A, Allen SM, Jackson KE, Ralph SA, Habib S. Targeting and function of proteins mediating translation initiation in organelles of Plasmodium falciparum. Mol Microbiol 2015; 96:796-814. [PMID: 25689481 DOI: 10.1111/mmi.12972] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2015] [Indexed: 01/13/2023]
Abstract
The malaria parasite Plasmodium falciparum has two translationally active organelles - the apicoplast and mitochondrion, which import nuclear-encoded translation factors to mediate protein synthesis. Initiation of translation is a complex step wherein initiation factors (IFs) act in a regulated manner to form an initiation complex. We identified putative organellar IFs and investigated the targeting, structure and function of IF1, IF2 and IF3 homologues encoded by the parasite nuclear genome. A single PfIF1 is targeted to the apicoplast. Apart from its critical ribosomal interactions, PfIF1 also exhibited nucleic-acid binding and melting activities and mediated transcription anti-termination. This suggests a prominent ancillary function for PfIF1 in destabilisation of DNA and RNA hairpin loops encountered during transcription and translation of the A+T rich apicoplast genome. Of the three putative IF2 homologues, only one (PfIF2a) was an organellar protein with mitochondrial localisation. We additionally identified an IF3 (PfIF3a) that localised exclusively to the mitochondrion and another protein, PfIF3b, that was apicoplast targeted. PfIF3a exhibited ribosome anti-association activity, and monosome splitting by PfIF3a was enhanced by ribosome recycling factor (PfRRF2) and PfEF-G(Mit). These results fill a gap in our understanding of organellar translation in Plasmodium, which is the site of action of several anti-malarial compounds.
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Affiliation(s)
- Afreen Haider
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Stacey M Allen
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Vic., 3010, Australia
| | - Katherine E Jackson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Vic., 3010, Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Vic., 3010, Australia
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
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30
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Atkinson GC. The evolutionary and functional diversity of classical and lesser-known cytoplasmic and organellar translational GTPases across the tree of life. BMC Genomics 2015; 16:78. [PMID: 25756599 PMCID: PMC4342817 DOI: 10.1186/s12864-015-1289-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/27/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The ribosome translates mRNA to protein with the aid of a number of accessory protein factors. Translational GTPases (trGTPases) are an integral part of the 'core set' of essential translational factors, and are some of the most conserved proteins across life. This study takes advantage of the wealth of available genomic data, along with novel functional information that has come to light for a number of trGTPases to address the full evolutionary and functional diversity of this superfamily across all domains of life. RESULTS Through sensitive sequence searching combined with phylogenetic analysis, 57 distinct subfamilies of trGTPases are identified: 14 bacterial, 7 archaeal and 35 eukaryotic (of which 21 are known or predicted to be organellar). The results uncover the functional evolution of trGTPases from before the last common ancestor of life on earth to the current day. CONCLUSIONS While some trGTPases are universal, others are limited to certain taxa, suggesting lineage-specific translational control mechanisms that exist on a base of core factors. These lineage-specific features may give organisms the ability to tune their translation machinery to respond to their environment. Only a fraction of the diversity of the trGTPase superfamily has been subjected to experimental analyses; this comprehensive classification brings to light novel and overlooked translation factors that are worthy of further investigation.
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Kuzmenko AV, Levitskii SA, Vinogradova EN, Atkinson GC, Hauryliuk V, Zenkin N, Kamenski PA. Protein biosynthesis in mitochondria. BIOCHEMISTRY (MOSCOW) 2014; 78:855-66. [PMID: 24228873 DOI: 10.1134/s0006297913080014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Translation, that is biosynthesis of polypeptides in accordance with information encoded in the genome, is one of the most important processes in the living cell, and it has been in the spotlight of international research for many years. The mechanisms of protein biosynthesis in bacteria and in the eukaryotic cytoplasm are now understood in great detail. However, significantly less is known about translation in eukaryotic mitochondria, which is characterized by a number of unusual features. In this review, we summarize current knowledge about mitochondrial translation in different organisms while paying special attention to the aspects of this process that differ from cytoplasmic protein biosynthesis.
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Affiliation(s)
- A V Kuzmenko
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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Das Roy R, Dash D. Selection of relevant features from amino acids enables development of robust classifiers. Amino Acids 2014; 46:1343-51. [PMID: 24604165 DOI: 10.1007/s00726-014-1697-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 02/14/2014] [Indexed: 12/30/2022]
Abstract
Machine learning (ML) has been extensively applied to develop models and to understand high-throughput data of biological processes. However, new ML models, trained with novel experimental results, are required to build regularly for more precise predictions. ML methods can build models from numeric data, whereas biological data are generally textual (DNA, protein sequences) or images and needs feature calculation algorithms to generate quantitative features. Programming skills along with domain knowledge are required to develop these algorithms. Therefore, the process of knowledge discovery through ML is decelerated due to lack of generic tools to construct features and to build models directly from the data. Hence, we developed a schema that calculates about 5,000 features, selects relevant features and develops protein classifiers from the training data. To demonstrate the general applicability and robustness of our method, fungal adhesins and nuclear receptor proteins were used for building classifiers which outperformed existing classifiers when tested on independent data. Next, we built a classifier for mitochondrial proteins of Plasmodium falciparum which causes human malaria because the latest corresponding classifiers are not publically accessible. Our classifier attained 98.18 % accuracy and 0.95 Matthews correlation coefficient by fivefold cross-validation and outperformed existing classifiers on independent test set. We implemented this schema as user-friendly and open source application Pro-Gyan ( http://code.google.com/p/pro-gyan/ ), to build and share executable classifiers without programming knowledge.
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Affiliation(s)
- Rishi Das Roy
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India,
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Abstract
SIGNIFICANCE The mitochondrial genetic system is responsible for the production of a few core-subunits of the respiratory chain and ATP synthase, the membrane protein complexes driving oxidative phosphorylation (OXPHOS). Efficiency and accuracy of mitochondrial protein synthesis determines how efficiently new OXPHOS complexes can be made. RECENT ADVANCES The system responsible for expression of the mitochondrial-encoded subunits developed from that of the bacterial ancestor of mitochondria. Importantly, many aspects of genome organization, transcription, and translation have diverged during evolution. Recent research has provided new insights into the architecture, regulation, and organelle-specific features of mitochondrial translation. Mitochondrial ribosomes contain a number of proteins absent from prokaryotic ribosomes, implying that in mitochondria, ribosomes were tailored to fit the requirements of the organelle. In addition, mitochondrial gene expression is regulated post-transcriptionally by a number of mRNA-specific translational activators. At least in yeast, these factors can regulate translation in respect to OXPHOS complex assembly to adjust the level of newly synthesized proteins to amounts that can be successfully assembled into respiratory chain complexes. CRITICAL ISSUES Mitochondrial gene expression is determining aging in eukaryotes, and a number of recent reports indicate that efficiency of translation directly influences this process. FUTURE DIRECTIONS Here we will summarize recent advances in our understanding of mitochondrial protein synthesis by comparing the knowledge acquired in the systems most commonly used to study mitochondrial biogenesis. However, many steps have not been understood mechanistically. Innovative biochemical and genetic approaches have to be elaborated to shed light on these important processes.
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Affiliation(s)
- Kirsten Kehrein
- 1 Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
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Kuzmenko A, Atkinson GC, Levitskii S, Zenkin N, Tenson T, Hauryliuk V, Kamenski P. Mitochondrial translation initiation machinery: conservation and diversification. Biochimie 2013; 100:132-40. [PMID: 23954798 PMCID: PMC3978653 DOI: 10.1016/j.biochi.2013.07.024] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 07/29/2013] [Indexed: 11/29/2022]
Abstract
The highly streamlined mitochondrial genome encodes almost exclusively a handful of transmembrane components of the respiratory chain complex. In order to ensure the correct assembly of the respiratory chain, the products of these genes must be produced in the correct stoichiometry and inserted into the membrane, posing a unique challenge to the mitochondrial translational system. In this review we describe the proteins orchestrating mitochondrial translation initiation: bacterial-like general initiation factors mIF2 and mIF3, as well as mitochondria-specific components – mRNA-specific translational activators and mRNA-nonspecific accessory initiation factors. We consider how the fast rate of evolution in these organelles has not only created a system that is divergent from that of its bacterial ancestors, but has led to a huge diversity in lineage specific mechanistic features of mitochondrial translation initiation among eukaryotes. Mitochondrially-encoded proteins are mostly respiratory chain components. The mitochondrial translation system is thus organized in a very specific way. Initiation involves mRNA-specific activators and bacteria-like initiation factors. We show that Saccharomyces cerevisiae Aim23p is a functional ortholog of bacterial IF3. We review the lineage specific features of mitochondrial translation initiation.
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Affiliation(s)
- Anton Kuzmenko
- University of Tartu, Institute of Technology, Nooruse 1, Tartu, Estonia; Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Gemma C Atkinson
- University of Tartu, Institute of Technology, Nooruse 1, Tartu, Estonia
| | - Sergey Levitskii
- Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, Tartu, Estonia
| | - Vasili Hauryliuk
- University of Tartu, Institute of Technology, Nooruse 1, Tartu, Estonia; Department of Molecular Biology, Umeå University, Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
| | - Piotr Kamenski
- Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia.
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