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Warren JM, Salinas-Giegé T, Triant DA, Taylor DR, Drouard L, Sloan DB. Rapid shifts in mitochondrial tRNA import in a plant lineage with extensive mitochondrial tRNA gene loss. Mol Biol Evol 2021; 38:5735-5751. [PMID: 34436590 PMCID: PMC8662596 DOI: 10.1093/molbev/msab255] [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] [Indexed: 12/13/2022] Open
Abstract
In most eukaryotes, transfer RNAs (tRNAs) are one of the very few classes of genes remaining in the mitochondrial genome, but some mitochondria have lost these vestiges of their prokaryotic ancestry. Sequencing of mitogenomes from the flowering plant genus Silene previously revealed a large range in tRNA gene content, suggesting rapid and ongoing gene loss/replacement. Here, we use this system to test longstanding hypotheses about how mitochondrial tRNA genes are replaced by importing nuclear-encoded tRNAs. We traced the evolutionary history of these gene loss events by sequencing mitochondrial genomes from key outgroups (Agrostemma githago and Silene [=Lychnis] chalcedonica). We then performed the first global sequencing of purified plant mitochondrial tRNA populations to characterize the expression of mitochondrial-encoded tRNAs and the identity of imported nuclear-encoded tRNAs. We also confirmed the utility of high-throughput sequencing methods for the detection of tRNA import by sequencing mitochondrial tRNA populations in a species (Solanum tuberosum) with known tRNA trafficking patterns. Mitochondrial tRNA sequencing in Silene revealed substantial shifts in the abundance of some nuclear-encoded tRNAs in conjunction with their recent history of mt-tRNA gene loss and surprising cases where tRNAs with anticodons still encoded in the mitochondrial genome also appeared to be imported. These data suggest that nuclear-encoded counterparts are likely replacing mitochondrial tRNAs even in systems with recent mitochondrial tRNA gene loss, and the redundant import of a nuclear-encoded tRNA may provide a mechanism for functional replacement between translation systems separated by billions of years of evolutionary divergence.
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Affiliation(s)
- Jessica M Warren
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | - Thalia Salinas-Giegé
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, Strasbourg, F-67084, France
| | - Deborah A Triant
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Douglas R Taylor
- Department of Biology, University of Virginia, Charlottesville, VA, 22904-4328, USA
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, Strasbourg, F-67084, France
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
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2
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Huang J, Wu S, Wang P, Wang G. Non-coding RNA Regulated Cross-Talk Between Mitochondria and Other Cellular Compartments. Front Cell Dev Biol 2021; 9:688523. [PMID: 34414182 PMCID: PMC8369480 DOI: 10.3389/fcell.2021.688523] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/12/2021] [Indexed: 12/04/2022] Open
Abstract
Mitochondria are the main hubs for cellular energy production. Metabolites produced in mitochondria not only feed many important biosynthesis pathways but also function as signaling molecules. Mitochondrial biosynthesis requires collaboration of both nuclear and mitochondrial gene expression systems. In addition, mitochondria have to quickly respond to changes inside and outside the cells and have their own functional states reported to the nucleus and other cellular compartments. The underlying molecular mechanisms of these complex regulations have not been well understood. Recent evidence indicates that in addition to small molecules, non-coding RNAs may contribute to the communication between mitochondria and other cellular compartments and may even serve as signals. In this review, we summarize the current knowledge about mitochondrial non-coding RNAs (including nucleus-encoded non-coding RNAs that are imported into mitochondria and mitochondrion-encoded non-coding RNAs that are exported), their trafficking and their functions in co-regulation of mitochondrial and other cellular processes.
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Affiliation(s)
- Jinliang Huang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Sipeng Wu
- State Key laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Pengcheng Wang
- State Key laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Geng Wang
- State Key laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
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3
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Tarasenko TA, Klimenko ES, Tarasenko VI, Koulintchenko MV, Dietrich A, Weber-Lotfi F, Konstantinov YM. Plant mitochondria import DNA via alternative membrane complexes involving various VDAC isoforms. Mitochondrion 2021; 60:43-58. [PMID: 34303006 DOI: 10.1016/j.mito.2021.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/17/2021] [Accepted: 07/19/2021] [Indexed: 12/23/2022]
Abstract
Mitochondria possess transport mechanisms for import of RNA and DNA. Based on import into isolated Solanum tuberosum mitochondria in the presence of competitors, inhibitors or effectors, we show that DNA fragments of different size classes are taken up into plant organelles through distinct channels. Alternative channels can also be activated according to the amount of DNA substrate of a given size class. Analyses of Arabidopsis thaliana knockout lines pointed out a differential involvement of individual voltage-dependent anion channel (VDAC) isoforms in the formation of alternative channels. We propose several outer and inner membrane proteins as VDAC partners in these pathways.
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Affiliation(s)
- Tatiana A Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia
| | - Ekaterina S Klimenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia
| | - Vladislav I Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia
| | - Milana V Koulintchenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia.
| | - André Dietrich
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg, France
| | - Frédérique Weber-Lotfi
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg, France
| | - Yuri M Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia; Irkutsk State University, 1 Karl Marx St, Irkutsk 664003, Russia
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4
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tRNA-Dependent Import of a Transit Sequence-Less Aminoacyl-tRNA Synthetase (LeuRS2) into the Mitochondria of Arabidopsis. Int J Mol Sci 2021; 22:ijms22083808. [PMID: 33916944 PMCID: PMC8067559 DOI: 10.3390/ijms22083808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 11/17/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AaRS) charge tRNAs with amino acids for protein translation. In plants, cytoplasmic, mitochondrial, and chloroplast AaRS exist that are all coded for by nuclear genes and must be imported from the cytosol. In addition, only a few of the mitochondrial tRNAs needed for translation are encoded in mitochondrial DNA. Despite considerable progress made over the last few years, still little is known how the bulk of cytosolic AaRS and respective tRNAs are transported into mitochondria. Here, we report the identification of a protein complex that ties AaRS and tRNA import into the mitochondria of Arabidopsis thaliana. Using leucyl-tRNA synthetase 2 (LeuRS2) as a model for a mitochondrial signal peptide (MSP)-less precursor, a ≈30 kDa protein was identified that interacts with LeuRS2 during import. The protein identified is identical with a previously characterized mitochondrial protein designated HP30-2 (encoded by At3g49560) that contains a sterile alpha motif (SAM) similar to that found in RNA binding proteins. HP30-2 is part of a larger protein complex that contains with TIM22, TIM8, TIM9 and TIM10 four previously identified components of the translocase for MSP-less precursors. Lack of HP30-2 perturbed mitochondrial biogenesis and function and caused seedling lethality during greening, suggesting an essential role of HP30-2 in planta.
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5
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Weaver RJ, Carrion G, Nix R, Maeda GP, Rabinowitz S, Iverson ENK, Thueson K, Havird JC. High mitochondrial mutation rates in Silene are associated with nuclear-mediated changes in mitochondrial physiology. Biol Lett 2020; 16:20200450. [PMID: 32933406 DOI: 10.1098/rsbl.2020.0450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial (mt) respiration depends on proteins encoded both by the mitochondrial and nuclear genomes. Variation in mt-DNA mutation rates exists across eukaryotes, although the functional consequences of elevated mt mutation rates in some lineages remain underexplored. In the angiosperm genus Silene, closely related, ecologically similar species have either 'fast' or 'slow' mt-DNA mutation rates. Here, we investigated the functional consequences of elevated mt-DNA mutation rates on mt respiration profiles of Silene mitochondria. Overall levels of respiration were similar among Species. Fast species had lower respiration efficiency than slow species and relied up to 48% more on nuclear-encoded respiratory enzymes alternative oxidase (AOX) and accessory dehydrogenases (DHex), which participate in stress responses in plants. However, not all fast species showed these trends. Respiratory profiles of some enzymes were correlated, most notably AOX and DHex. We conclude that subtle differences in mt physiology among Silene lineages with dramatically different mt mutation rates may underly similar phenotypes at higher levels of biological organization, betraying the consequences of mt mutations.
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Affiliation(s)
- Ryan J Weaver
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Gina Carrion
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Rachel Nix
- Hankamer School of Business, Baylor University, Waco, TX 76798, USA
| | - Gerald P Maeda
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Samantha Rabinowitz
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Erik N K Iverson
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Kiley Thueson
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
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6
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Jeandard D, Smirnova A, Tarassov I, Barrey E, Smirnov A, Entelis N. Import of Non-Coding RNAs into Human Mitochondria: A Critical Review and Emerging Approaches. Cells 2019; 8:E286. [PMID: 30917553 PMCID: PMC6468882 DOI: 10.3390/cells8030286] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/19/2019] [Accepted: 03/23/2019] [Indexed: 01/26/2023] Open
Abstract
Mitochondria harbor their own genetic system, yet critically depend on the import of a number of nuclear-encoded macromolecules to ensure their expression. In all eukaryotes, selected non-coding RNAs produced from the nuclear genome are partially redirected into the mitochondria, where they participate in gene expression. Therefore, the mitochondrial RNome represents an intricate mixture of the intrinsic transcriptome and the extrinsic RNA importome. In this review, we summarize and critically analyze data on the nuclear-encoded transcripts detected in human mitochondria and outline the proposed molecular mechanisms of their mitochondrial import. Special attention is given to the various experimental approaches used to study the mitochondrial RNome, including some recently developed genome-wide and in situ techniques.
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Affiliation(s)
- Damien Jeandard
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
| | - Anna Smirnova
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
| | - Ivan Tarassov
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
| | - Eric Barrey
- GABI-UMR1313, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | | | - Nina Entelis
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
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7
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Verechshagina NA, Konstantinov YM, Kamenski PA, Mazunin IO. Import of Proteins and Nucleic Acids into Mitochondria. BIOCHEMISTRY (MOSCOW) 2018; 83:643-661. [DOI: 10.1134/s0006297918060032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Rossig C, Gray J, Valdes O, Rustgi S, von Wettstein D, Reinbothe C, Reinbothe S. HP30-2, a mitochondrial PRAT protein for import of signal sequence-less precursor proteins in Arabidopsis thaliana. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:535-551. [PMID: 28544763 DOI: 10.1111/jipb.12555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/19/2017] [Indexed: 06/07/2023]
Abstract
Chloroplasts and mitochondria contain a family of putative preprotein and amino acid transporters designated PRAT. Here, we analyzed the role of two previously characterized PRAT protein family members, encoded by At3g49560 (HP30) and At5g24650 (HP30-2), in planta using a combination of genetic, cell biological and biochemical approaches. Expression studies and green fluorescent protein tagging identified HP30-2 both in chloroplasts and mitochondria, whereas HP30 was located exclusively in chloroplasts. Biochemical evidence was obtained for an association of mitochondrial HP30-2 with two distinct protein complexes, one containing the inner membrane translocase TIM22 and the other containing an alternative NAD(P)H dehydrogenase subunit (NDC1) implicated in a respiratory complex 1-like electron transport chain. Through its association with TIM22, HP30-2 is involved in the uptake of carrier proteins and other, hydrophobic membrane proteins lacking cleavable NH2 -terminal presequences, whereas HP30-2's interaction with NDC1 may permit controlling mitochondrial biogenesis and activity.
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Affiliation(s)
- Claudia Rossig
- Laboratory of Plant Molecular Genetics and Laboratory of Environmental and Systems Biology, Grenoble-Alpes-University, Grenoble, France
| | - John Gray
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Oscar Valdes
- Laboratory of Plant Molecular Genetics and Laboratory of Environmental and Systems Biology, Grenoble-Alpes-University, Grenoble, France
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, Florence, SC 29506, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman WA 99164-6420, USA
| | - Diter von Wettstein
- Department of Crop and Soil Sciences, Washington State University, Pullman WA 99164-6420, USA
| | - Christiane Reinbothe
- Laboratory of Plant Molecular Genetics and Laboratory of Environmental and Systems Biology, Grenoble-Alpes-University, Grenoble, France
| | - Steffen Reinbothe
- Laboratory of Plant Molecular Genetics and Laboratory of Environmental and Systems Biology, Grenoble-Alpes-University, Grenoble, France
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9
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Konstantinov YM, Dietrich A, Weber-Lotfi F, Ibrahim N, Klimenko ES, Tarasenko VI, Bolotova TA, Koulintchenko MV. DNA import into mitochondria. BIOCHEMISTRY (MOSCOW) 2016; 81:1044-1056. [DOI: 10.1134/s0006297916100035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Nucleic acid import into mitochondria: New insights into the translocation pathways. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:3165-81. [DOI: 10.1016/j.bbamcr.2015.09.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/16/2015] [Accepted: 09/10/2015] [Indexed: 11/18/2022]
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11
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Salinas-Giegé T, Giegé R, Giegé P. tRNA biology in mitochondria. Int J Mol Sci 2015; 16:4518-59. [PMID: 25734984 PMCID: PMC4394434 DOI: 10.3390/ijms16034518] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/23/2015] [Accepted: 01/29/2015] [Indexed: 01/23/2023] Open
Abstract
Mitochondria are the powerhouses of eukaryotic cells. They are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. These organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. Among them, mitochondria use many specific pathways to obtain complete and functional sets of tRNAs as required for translation. In some instances, tRNA genes have been partially or entirely transferred to the nucleus and mitochondria require precise import systems to attain their pool of tRNAs. Still, tRNA genes have also often been maintained in mitochondria. Their genetic arrangement is more diverse than previously envisaged. The expression and maturation of mitochondrial tRNAs often use specific enzymes that evolved during eukaryote history. For instance many mitochondria use a eukaryote-specific RNase P enzyme devoid of RNA. The structure itself of mitochondrial encoded tRNAs is also very diverse, as e.g., in Metazoan, where tRNAs often show non canonical or truncated structures. As a result, the translational machinery in mitochondria evolved adapted strategies to accommodate the peculiarities of these tRNAs, in particular simplified identity rules for their aminoacylation. Here, we review the specific features of tRNA biology in mitochondria from model species representing the major eukaryotic groups, with an emphasis on recent research on tRNA import, maturation and aminoacylation.
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Affiliation(s)
- Thalia Salinas-Giegé
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France.
| | - Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France.
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France.
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12
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Kubiszewski-Jakubiak S, Megel C, Ubrig E, Salinas T, Duchêne AM, Maréchal-Drouard L. In vitro RNA uptake studies in plant mitochondria. Methods Mol Biol 2015; 1305:45-60. [PMID: 25910726 DOI: 10.1007/978-1-4939-2639-8_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
During evolution, most of the ancestral genes from the endosymbiotic α-proteobacteria at the origin of mitochondria have been either lost or transferred to the nuclear genome. To allow the comeback of proteins and RNAs [in particular transfer RNA (tRNAs)] into the organelle, macromolecule import systems were universally established. While protein import processes have been studied into details, much less is known about tRNA mitochondrial import. In plants, part of the knowledge on the tRNA import process into mitochondria has been acquired thanks to in vitro import assays. Furthermore, the development of in vitro RNA import strategies allowed the study of plant mitochondrial gene expression. The purpose of this chapter is to provide detailed protocols to perform in vitro RNA uptake into potato (Solanum tuberosum) or Arabidopsis (Arabidopsis thaliana) mitochondria as well as approaches to analyze them.
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Affiliation(s)
- Szymon Kubiszewski-Jakubiak
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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13
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Michaud M, Maréchal-Drouard L, Duchêne AM. Targeting of cytosolic mRNA to mitochondria: naked RNA can bind to the mitochondrial surface. Biochimie 2013; 100:159-66. [PMID: 24252184 DOI: 10.1016/j.biochi.2013.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 11/08/2013] [Indexed: 01/06/2023]
Abstract
Mitochondria contain hundreds of proteins but only a few are encoded by the mitochondrial genome. The other proteins are nuclear-encoded and imported into mitochondria. These proteins can be translated on free cytosolic polysomes, then targeted and imported into mitochondria. Nonetheless, numerous cytosolic mRNAs encoding mitochondrial proteins are detected at the surface of mitochondria in yeast, plants and animals. The localization of mRNAs to the vicinity of mitochondria would be a way for mitochondrial protein sorting. The mechanisms responsible for mRNA targeting to mitochondria are not clearly identified. Sequences within the mRNA molecules (cis-elements), as well as a few trans-acting factors, have been shown to be essential for targeting of some mRNAs. In order to identify receptors involved in mRNA docking to the mitochondrial surface, we have developed an in vitro mRNA binding assay with isolated plant mitochondria. We show that naked mRNAs are able to bind to isolated mitochondria, and our results strongly suggest that mRNA docking to the plant mitochondrial outer membrane requires at least one component of TOM complex.
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Affiliation(s)
- Morgane Michaud
- Institut de Biologie Moléculaire des Plantes, UPR 2357 du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Laurence Maréchal-Drouard
- Institut de Biologie Moléculaire des Plantes, UPR 2357 du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Anne-Marie Duchêne
- Institut de Biologie Moléculaire des Plantes, UPR 2357 du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
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14
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Zhou W, Karcher D, Bock R. Importance of adenosine-to-inosine editing adjacent to the anticodon in an Arabidopsis alanine tRNA under environmental stress. Nucleic Acids Res 2013; 41:3362-72. [PMID: 23355609 PMCID: PMC3597679 DOI: 10.1093/nar/gkt013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In all organisms, transfer RNAs (tRNAs) undergo extensive post-transcriptional modifications. Although base modifications in the anticodon are known to alter decoding specificity or improve decoding accuracy, much less is known about the functional relevance of modifications in other positions of tRNAs. Here, we report the identification of an A-to-I tRNA editing enzyme that modifies the tRNA-Ala(AGC) in the model plant Arabidopsis thaliana. The enzyme is homologous to Tad1p, a yeast tRNA-specific adenosine deaminase, and it selectively deaminates the adenosine in the position 3'-adjacent to the anticodon (A37) to inosine. We show that the AtTAD1 protein is exclusively localized in the nucleus. The tad1 loss-of-function mutants isolated in Arabidopsis show normal accumulation of the tRNA-Ala(AGC), suggesting that the loss of the I37 modification does not affect tRNA stability. The tad1 knockout mutants display no discernible phenotype under standard growth conditions, but produce less biomass under environmental stress conditions. Our results provide the first evidence in support of a physiological relevance of the A37-to-I modification in eukaryotes.
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Affiliation(s)
| | | | - Ralph Bock
- *To whom correspondence should be addressed. Tel: +49 3315 67 8700; Fax: +49 3315 67 8701;
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15
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Tammineni P, Anugula C, Mohammed F, Anjaneyulu M, Larner AC, Sepuri NBV. The import of the transcription factor STAT3 into mitochondria depends on GRIM-19, a component of the electron transport chain. J Biol Chem 2012; 288:4723-32. [PMID: 23271731 DOI: 10.1074/jbc.m112.378984] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The signal transducer and activator of transcription 3 (STAT3), a nuclear transcription factor, is also present in mitochondria and regulates cellular respiration in a transcriptional-independent manner. The mechanism of STAT3 import into mitochondria remains obscure. In this report we show that mitochondrial-localized STAT3 resides in the inner mitochondrial membrane. In vitro import studies show that the gene associated with retinoid interferon induced cell mortality 19 (GRIM-19), a complex I subunit that acts as a chaperone to recruit STAT3 into mitochondria. In addition, GRIM-19 enhances the integration of STAT3 into complex I. A S727A mutation in STAT3 reduces its import and assembly even in the presence of GRIM-19. Together, our studies unveil a novel chaperone function for GRIM-19 in the recruitment of STAT3 into mitochondria.
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Affiliation(s)
- Prasad Tammineni
- Department of Biochemistry, University of Hyderabad, Hyderabad 500046, India
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16
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Seed Plant Mitochondrial Genomes: Complexity Evolving. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2012. [DOI: 10.1007/978-94-007-2920-9_8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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17
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Homblé F, Krammer EM, Prévost M. Plant VDAC: facts and speculations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1486-501. [PMID: 22155681 DOI: 10.1016/j.bbamem.2011.11.028] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/12/2011] [Accepted: 11/22/2011] [Indexed: 01/01/2023]
Abstract
The voltage-dependent anion-selective channel (VDAC) is the most abundant protein in the mitochondrial outer membrane and the major transport pathway for a large variety of compounds ranging from ions to large polymeric molecules such as DNA and tRNA. Plant VDACs feature a secondary structure content and electrophysiological properties akin to those of VDACs from other organisms. They however undergo a specific regulation. The general importance of VDAC in plant physiology has only recently emerged. Besides their role in metabolite transport, plant VDACs are also involved in the programmed cell death triggered in response to biotic and abiotic stresses. Moreover, their colocalization in non-mitochondrial membranes suggests a diversity of function. This review summarizes our current understanding of the structure and function of plant VDACs. This article is part of a Special Issue entitled: VDAC structure, function, and regulation of mitochondrial metabolism.
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Affiliation(s)
- Fabrice Homblé
- Structure et Fontion des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles, Boulevard du Triomphe CP, Brussels, Belgium.
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18
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Val R, Wyszko E, Valentin C, Szymanski M, Cosset A, Alioua M, Dreher TW, Barciszewski J, Dietrich A. Organelle trafficking of chimeric ribozymes and genetic manipulation of mitochondria. Nucleic Acids Res 2011; 39:9262-74. [PMID: 21768127 PMCID: PMC3241634 DOI: 10.1093/nar/gkr580] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 06/28/2011] [Accepted: 06/29/2011] [Indexed: 01/15/2023] Open
Abstract
With the expansion of the RNA world, antisense strategies have become widespread to manipulate nuclear gene expression but organelle genetic systems have remained aside. The present work opens the field to mitochondria. We demonstrate that customized RNAs expressed from a nuclear transgene and driven by a transfer RNA-like (tRNA-like) moiety are taken up by mitochondria in plant cells. The process appears to follow the natural tRNA import specificity, suggesting that translocation indeed occurs through the regular tRNA uptake pathway. Upon validation of the strategy with a reporter sequence, we developed a chimeric catalytic RNA composed of a specially designed trans-cleaving hammerhead ribozyme and a tRNA mimic. Organelle import of the chimeric ribozyme and specific target cleavage within mitochondria were demonstrated in transgenic tobacco cell cultures and Arabidopsis thaliana plants, providing the first directed knockdown of a mitochondrial RNA in a multicellular eukaryote. Further observations point to mitochondrial messenger RNA control mechanisms related to the plant developmental stage and culture conditions. Transformation of mitochondria is only accessible in yeast and in the unicellular alga Chlamydomonas. Based on the widespread tRNA import pathway, our data thus make a breakthrough for direct investigation and manipulation of mitochondrial genetics.
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Affiliation(s)
- Romain Val
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland and Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
| | - Eliza Wyszko
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland and Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
| | - Clarisse Valentin
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland and Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
| | - Maciej Szymanski
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland and Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
| | - Anne Cosset
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland and Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
| | - Malek Alioua
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland and Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
| | - Theo W. Dreher
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland and Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
| | - Jan Barciszewski
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland and Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
| | - André Dietrich
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland and Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
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19
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Abstract
The mitochondrial genomes of most eukaryotes lack a variable number of tRNA genes. This lack is compensated for by import of a small fraction of the corresponding cytosolic tRNAs. There are two broad mechanisms for the import of tRNAs into mitochondria. In the first one, the tRNA is coimported together with a mitochondrial precursor protein along the protein import pathway. It applies to the yeast tRNA(Lys) and has been elucidated in great detail. In the second more vaguely defined mechanism, which is mainly found in plants and protozoa, tRNAs are directly imported independent of cytosolic factors. However, results in plants indicate that direct import of tRNAs may nevertheless require some components of the protein import machinery. All imported tRNAs in all systems are of the eukaryotic type but need to be functionally integrated into the mitochondrial translation system of bacterial descent. For some tRNAs, this is not trivial and requires unique evolutionary adaptations.
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Affiliation(s)
- André Schneider
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.
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20
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Rubio MAT, Hopper AK. Transfer RNA travels from the cytoplasm to organelles. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:802-17. [PMID: 21976284 DOI: 10.1002/wrna.93] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Transfer RNAs (tRNAs) encoded by the nuclear genome are surprisingly dynamic. Although tRNAs function in protein synthesis occurring on cytoplasmic ribosomes, tRNAs can transit from the cytoplasm to the nucleus and then again return to the cytoplasm by a process known as the tRNA retrograde process. Subsets of the cytoplasmic tRNAs are also imported into mitochondria and function in mitochondrial protein synthesis. The numbers of tRNA species that are imported into mitochondria differ among organisms, ranging from just a few to the entire set needed to decode mitochondrially encoded mRNAs. For some tRNAs, import is dependent on the mitochondrial protein import machinery, whereas the majority of tRNA mitochondrial import is independent of this machinery. Although cytoplasmic proteins and proteins located on the mitochondrial surface participating in the tRNA import process have been described for several organisms, the identity of these proteins differ among organisms. Likewise, the tRNA determinants required for mitochondrial import differ among tRNA species and organisms. Here, we present an overview and discuss the current state of knowledge regarding the mechanisms involved in the tRNA retrograde process and continue with an overview of tRNA import into mitochondria. Finally, we highlight areas of future research to understand the function and regulation of movement of tRNAs between the cytoplasm and organelles.
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Affiliation(s)
- Mary Anne T Rubio
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
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21
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In vivo study in Trypanosoma brucei links mitochondrial transfer RNA import to mitochondrial protein import. EMBO Rep 2011; 12:825-32. [PMID: 21720389 DOI: 10.1038/embor.2011.111] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 04/21/2011] [Accepted: 05/16/2011] [Indexed: 11/08/2022] Open
Abstract
Trypanosoma brucei imports all mitochondrial transfer RNAs (tRNAs) from the cytosol. By using cell lines that allow independent tetracycline-inducible RNA interference and isopropyl-β-D-thiogalactopyranoside-inducible expression of a tagged tRNA, we show that ablation of Tim17 and mitochondrial heat-shock protein 70, components of the inner-membrane protein translocation machinery, strongly inhibits import of newly synthesized tRNAs. These findings, together with previous results in yeast and plants, suggest that the requirement for mitochondrial protein-import factors might be a conserved feature of mitochondrial tRNA import in all systems.
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22
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Sieber F, Placido A, El Farouk-Ameqrane S, Duchêne AM, Maréchal-Drouard L. A protein shuttle system to target RNA into mitochondria. Nucleic Acids Res 2011; 39:e96. [PMID: 21596779 PMCID: PMC3152368 DOI: 10.1093/nar/gkr380] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Mitochondria play a key role in essential cellular functions. A deeper understanding of mitochondrial molecular processes is hampered by the difficulty of incorporating foreign nucleic acids into organelles. Mitochondria of most eukaryotic species import cytosolic tRNAs. Based on this natural process, we describe here a powerful shuttle system to internalize several types of RNAs into isolated mitochondria. We demonstrate that this tool is useful to investigate tRNA processing or mRNA editing in plant mitochondria. Furthermore, we show that the same strategy can be used to address both tRNA and mRNA to isolated mammalian mitochondria. We anticipate our novel approach to be the starting point for various studies on mitochondrial processes. Finally, our study provides new insights into the mechanism of RNA import into mitochondria.
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Affiliation(s)
- François Sieber
- Institut de Biologie Moléculaire des Plantes, UPR 2357-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France
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23
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RNA-mediated restoration of mitochondrial function in cells harboring a Kearns Sayre Syndrome mutation. Mitochondrion 2011; 11:564-74. [PMID: 21406250 DOI: 10.1016/j.mito.2011.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 03/03/2011] [Indexed: 11/20/2022]
Abstract
Mutations in mitochondrial DNA (mtDNA) generate multi-system disorders due to failure of ATP production. A cybrid containing a 1.9-kb mtDNA deletion from a patient with Kearns Sayre Syndrome is respiration-defective and grows glycolytically. When treated with a ribonucleoprotein (RNP) complex of polycistronic RNA 1 (pcRNA1) containing mtDNA-encoded genes and a multi-subunit carrier complex R8, full-length pcRNA1 was transported to mitochondria. Translation of the pcRNA1-encoded mRNAs was observed in mitochondria from RNP-treated cells. Respiration of the cybrid was rescued to approximately 90% of normal within hours, switching the cells to aerobic growth. These findings have implications for the development of effective mitochondrial gene therapy.
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24
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Mitochondrial RNA import: from diversity of natural mechanisms to potential applications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2011; 287:145-90. [PMID: 21414588 DOI: 10.1016/b978-0-12-386043-9.00004-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondria, owing to their bacterial origin, still contain their own DNA. However, the majority of bacterial genes were lost or transferred to the nuclear genome and the biogenesis of the "present-day" mitochondria mainly depends on the expression of the nuclear genome. Thus, most mitochondrial proteins and a small number of mitochondrial RNAs (mostly tRNAs) expressed from nuclear genes need to be imported into the organelle. During evolution, macromolecule import systems were universally established. The processes of protein mitochondrial import are very well described in the literature. By contrast, deciphering the mitochondrial RNA import phenomenon is still a real challenge. The purpose of this review is to present a general survey of our present knowledge in this field in different model organisms, protozoa, plants, yeast, and mammals. Questions still under debate and major challenges are discussed. Mitochondria are involved in numerous human diseases. The targeting of macromolecule to mitochondria represents a promising way to fight mitochondrial disorders and recent developments in this area of research are presented.
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25
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Miyamoto H, Machida RJ, Nishida S. Complete mitochondrial genome sequences of the three pelagic chaetognaths Sagitta nagae, Sagitta decipiens and Sagitta enflata. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2009; 5:65-72. [PMID: 20374943 DOI: 10.1016/j.cbd.2009.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 11/13/2009] [Accepted: 11/16/2009] [Indexed: 11/25/2022]
Abstract
The complete nucleotide sequences of the mitochondrial genomes were determined for the three pelagic chaetognaths, Sagitta nagae, Sagitta decipiens, and Sagitta enflata. The mitochondrial genomes of these species which were 11,459, 11,121, and 12,631bp in length, respectively, contained 14 genes (11 protein-coding genes, one transfer RNA gene, and two ribosomal RNA genes), and were found to have lost 23 genes that are present in the typical metazoan mitochondrial genome. The same mitochondrial genome contents have been reported from the benthic chaetognaths belonging to the family Spadellidae, Paraspadella gotoi and Spadella cephaloptera. Within the phylum Chaetognatha, Sagitta and Spadellidae are distantly related, suggesting that the gene loss occurred in the ancestral species of the phylum. The gene orders of the three Sagitta species are markedly different from those of the other non-Chaetognatha metazoans. In contrast to the region with frequent gene rearrangements, no gene rearrangements were observed in the gene cluster encoding COII-III, ND1-3, srRNA, and tRNA(met). Within this conserved gene cluster, gene rearrangements were not observed in the three Sagitta species or between the Sagitta and Spadellidae species. The gene order of this cluster was also assumed to be the ancestral state of the phylum.
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Affiliation(s)
- Hiroomi Miyamoto
- Ocean Research Institute, University of Tokyo, Tokyo, 164-8639, Japan.
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26
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Duchêne AM, Pujol C, Maréchal-Drouard L. Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria. Curr Genet 2008; 55:1-18. [PMID: 19083240 DOI: 10.1007/s00294-008-0223-9] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/21/2008] [Accepted: 11/24/2008] [Indexed: 12/13/2022]
Abstract
During evolution, most of the bacterial genes from the ancestral endosymbiotic alpha-proteobacteria at the origin of mitochondria have been either lost or transferred to the nuclear genome. A crucial evolutionary step was the establishment of macromolecule import systems to allow the come back of proteins and RNAs into the organelle. Paradoxically, the few mitochondria-encoded protein genes remain essential and must be translated by a mitochondrial translation machinery mainly constituted by nucleus-encoded components. Two crucial partners of the mitochondrial translation machinery are the aminoacyl-tRNA synthetases and the tRNAs. All mitochondrial aminoacyl-tRNA synthetases and many tRNAs are imported from the cytosol into the mitochondria in eukaryotic cells. During the last few years, their origin and their import into the organelle have been studied in evolutionary distinct organisms and we review here what is known in this field.
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Affiliation(s)
- Anne-Marie Duchêne
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche du CNRS, Associated with Louis Pasteur University, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France.
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27
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Millar AH, Small ID, Day DA, Whelan J. Mitochondrial biogenesis and function in Arabidopsis. THE ARABIDOPSIS BOOK 2008; 6:e0111. [PMID: 22303236 DOI: 10.1199/tab.0105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Mitochondria represent the powerhouse of cells through their synthesis of ATP. However, understanding the role of mitochondria in the growth and development of plants will rely on a much deeper appreciation of the complexity of this organelle. Arabidopsis research has provided clear identification of mitochondrial components, allowed wide-scale analysis of gene expression, and has aided reverse genetic manipulation to test the impact of mitochondrial component loss on plant function. Forward genetics in Arabidopsis has identified mitochondrial involvement in mutations with notable impacts on plant metabolism, growth and development. Here we consider the evidence for components involved in mitochondria biogenesis, metabolism and signalling to the nucleus.
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28
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Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import. Proc Natl Acad Sci U S A 2008; 105:9186-91. [PMID: 18587046 DOI: 10.1073/pnas.0804283105] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial genomes generally encode a minimal set of tRNAs necessary for protein synthesis. However, a number of eukaryotes import tRNAs from the cytoplasm into their mitochondria. For instance, Saccharomyces cerevisiae imports cytoplasmic tRNA(Gln) into the mitochondrion without any added protein factors. Here, we examine the existence of a similar active tRNA import system in mammalian mitochondria. We have used subcellular RNA fractions from rat liver and human cells to perform RT-PCR with oligonucleotide primers specific for nucleus-encoded tRNA(CUG)(Gln) and tRNA(UUG)(Gln) species, and we show that these tRNAs are present in rat and human mitochondria in vivo. Import of in vitro transcribed tRNAs, but not of heterologous RNAs, into isolated mitochondria also demonstrates that this process is tRNA-specific and does not require the addition of cytosolic factors. Although this in vitro system requires ATP, it is resistant to inhibitors of the mitochondrial electrochemical gradient, a key component of protein import. tRNA(Gln) import into mammalian mitochondria proceeds by a mechanism distinct from protein import. We also show that both tRNA(Gln) species and a bacterial pre-tRNA(Asp) can be imported in vitro into mitochondria isolated from myoclonic epilepsy with ragged-red fiber cells if provided with sufficient ATP (2 mM). This work suggests that tRNA import is more widespread than previously thought and may be a universal trait of mitochondria. Mutations in mitochondrial tRNA genes have been associated with human disease; the tRNA import system described here could possibly be exploited for the manipulation of defective mitochondria.
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29
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Dinoflagellates: a mitochondrial genome all at sea. Trends Genet 2008; 24:328-35. [PMID: 18514360 DOI: 10.1016/j.tig.2008.04.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 04/25/2008] [Accepted: 04/28/2008] [Indexed: 11/23/2022]
Abstract
Dinoflagellate algae are notorious for their highly unusual organization of nuclear and chloroplast genomes. Early studies on the dinoflagellate mitochondrial genome indicated that it encodes the same three protein-coding genes found in Plasmodium spp., but with a complex organization and transcript editing. Recent work has extended this view, showing that the dinoflagellate mitochondrial genome contains a wide array of gene fragments and genes interspersed with noncoding inverted repeats. The genome seems to require noncanonical start and stop codons, as well as high levels of editing, trans-splicing and the addition of oligonucleotide caps at the 5' and 3' ends of transcripts. Despite its small coding content, the dinoflagellate mitochondrial genome is one of the most complex known.
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30
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Basu S, Mukherjee S, Adhya S. Proton-guided movements of tRNA within the Leishmania mitochondrial RNA import complex. Nucleic Acids Res 2008; 36:1599-609. [PMID: 18250088 PMCID: PMC2275131 DOI: 10.1093/nar/gkn010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The RNA import complex (RIC) from the mitochondrion of the kinetoplastid protozoan Leishmania tropica contains two subunits that directly bind to import signals on two distinct subsets of tRNA and interact with each other allosterically. What happens to the tRNA subsequent to its loading on the complex is unknown. A third subunit-RIC9-has intrinsic affinity for both types of tRNA and is essential for import in vivo. Here we show that antibody against RIC9 inhibited the import of both types of tRNA into mitoplasts in vitro, but failed to inhibit the binding of these tRNAs to their respective receptors, indicating that RIC9 acts in a subsequent step. Using photoaffinity crosslinking-immunoprecipitation to detect translocation intermediates, it was observed that tRNA was transferred from its cognate receptor to RIC9, followed by translocation across the membrane and release as free tRNA in the inner compartment. Transfer required elevated temperatures and ATP, but ATP was substituted by acid pH. These tRNA movements were sensitive to uncouplers and inhibitors, suggesting distinct roles of the electrical and chemical components of the proton motive force generated by vectorial proton translocation accompanying ATP hydrolysis. By analysis of partially assembled complexes in L. tropica depleted of various subunits, and in vitro assembly assays, RIC9 was shown to make stable contacts with RIC8A, a tRNA receptor and RIC6, a membrane-embedded component. The results have implications for the mechanism of tRNA import.
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Affiliation(s)
- Sudarshana Basu
- Genetic Engineering Laboratory, Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Calcutta 700 032, India
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31
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Mukhopadhyay A, Weiner H. Delivery of drugs and macromolecules to mitochondria. Adv Drug Deliv Rev 2007; 59:729-38. [PMID: 17659805 PMCID: PMC2267434 DOI: 10.1016/j.addr.2007.06.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Accepted: 06/12/2007] [Indexed: 01/24/2023]
Abstract
Mitochondria is where the bulk of the cell's ATP is produced. Mutations occur to genes coding for members of the complexes involved in energy production. Some are a result of damages to nuclear coded genes and others to mitochondrial coded genes. This review describes approaches to bring small molecules, proteins and RNA/DNA into mitochondria. The purpose is to repair damaged genes as well as to interrupt mitochondrial function including energy production, oxygen radical formation and the apoptotic pathway.
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Affiliation(s)
- Abhijit Mukhopadhyay
- Address correspondence to: Abhijit Mukhopadhyay () or Henry Weiner (), Purdue University, Department of Biochemistry, 175 S. University Street, West Lafayette, Indiana 47907-2063, Phone: (765) 494-1650, Fax: (765) 494-7897
| | - Henry Weiner
- Address correspondence to: Abhijit Mukhopadhyay () or Henry Weiner (), Purdue University, Department of Biochemistry, 175 S. University Street, West Lafayette, Indiana 47907-2063, Phone: (765) 494-1650, Fax: (765) 494-7897
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32
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Hammargren J, Salinas T, Maréchal-Drouard L, Knorpp C. The pea mitochondrial nucleoside diphosphate kinase cleaves DNA and RNA. FEBS Lett 2007; 581:3507-11. [PMID: 17624336 DOI: 10.1016/j.febslet.2007.06.062] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Accepted: 06/22/2007] [Indexed: 01/17/2023]
Abstract
Here, we present the characterization of a plant NDPK exhibiting nuclease activity. This is the first identification of a nuclease localised in the intermembrane space of plant mitochondria. The recombinant pea NDPK3 protein cleaves not only supercoiled plasmid DNA, but also highly structured RNA molecules such as tRNAs or the 3'UTR of the atp9 mRNA suggesting that the NDPK3 nuclease activity has a structural requirement. ATP inhibits this nuclease activity, while ADP has no effect. Furthermore, studies on NDPK mutant proteins indicate that the nuclease- and the kinase-mechanisms are separate.
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Affiliation(s)
- Jenni Hammargren
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, Box 7080, S-750 07 Uppsala, Sweden
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33
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Nicolaï M, Duprat A, Sormani R, Rodriguez C, Roncato MA, Rolland N, Robaglia C. Higher plant chloroplasts import the mRNA coding for the eucaryotic translation initiation factor 4E. FEBS Lett 2007; 581:3921-6. [PMID: 17662723 DOI: 10.1016/j.febslet.2007.07.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Revised: 06/25/2007] [Accepted: 07/08/2007] [Indexed: 11/20/2022]
Abstract
Plant chloroplasts probably originate from an endosymbiosis event between a photosynthetic bacteria and a eucaryotic cell. The proper functioning of this association requires a high level of integration between the chloroplastic genome and the plant cell genome. Many chloroplastic genes have been transferred to the nucleus of the host cell and the proteins coded by these genes are imported into the chloroplast. Chloroplastic activity also regulates the expression of these genes at the transcriptional and post-transcriptional levels. The importation of nucleic acids from the host cell into the chloroplast has never been observed. This work show that the mRNA coding for the eucaryotic translation factor 4E, an essential regulator of translation, enters the chloroplast in four different plant species, and is located in the stroma. Furthermore, the localization in the chloroplast of an heterologous GFP mRNA fused to the eIF4E RNA was also observed.
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Affiliation(s)
- Maryse Nicolaï
- Laboratoire de Génétique et Biophysique des Plantes, SBVME, IBEB, DSV, CEA, CNRS, Aix Marseille Université, Faculté des Sciences de Luminy, Marseille, F-13009 Marseille, France
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34
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Kamenski PA, Vinogradova EN, Krasheninnikov IA, Tarassov IA. Directed import of macromolecules into mitochondria. Mol Biol 2007. [DOI: 10.1134/s0026893307020021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Salinas T, Duchêne AM, Delage L, Nilsson S, Glaser E, Zaepfel M, Maréchal-Drouard L. The voltage-dependent anion channel, a major component of the tRNA import machinery in plant mitochondria. Proc Natl Acad Sci U S A 2006; 103:18362-7. [PMID: 17105808 PMCID: PMC1838756 DOI: 10.1073/pnas.0606449103] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In plants, as in most eukaryotic cells, import of nuclear-encoded cytosolic tRNAs is an essential process for mitochondrial biogenesis. Despite its broad occurrence, the mechanisms governing RNA transport into mitochondria are far less understood than protein import. This article demonstrates by Northwestern and gel-shift experiments that the plant mitochondrial voltage-dependent anion channel (VDAC) protein interacts with tRNA in vitro. It shows also that this porin, known to play a key role in metabolite transport, is a major component of the channel involved in the tRNA translocation step through the plant mitochondrial outer membrane, as supported by inhibition of tRNA import into isolated mitochondria by VDAC antibodies and Ruthenium red. However VDAC is not a tRNA receptor on the outer membrane. Rather, two major components from the TOM (translocase of the outer mitochondrial membrane) complex, namely TOM20 and TOM40, are important for tRNA binding at the surface of mitochondria, suggesting that they are also involved in tRNA import. Finally, we show that proteins and tRNAs are translocated into plant mitochondria by different pathways. Together, these findings identify unexpected components of the tRNA import machinery and suggest that the plant tRNA import pathway has evolved by recruiting multifunctional proteins.
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Affiliation(s)
- Thalia Salinas
- *Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357, Conventionné avec l'Université Louis Pasteur (Strasbourg1), Centre National de la Recherche Scientifique, 12 Rue du Général Zimmer, 67084 Strasbourg Cedex, France; and
| | - Anne-Marie Duchêne
- *Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357, Conventionné avec l'Université Louis Pasteur (Strasbourg1), Centre National de la Recherche Scientifique, 12 Rue du Général Zimmer, 67084 Strasbourg Cedex, France; and
| | - Ludovic Delage
- *Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357, Conventionné avec l'Université Louis Pasteur (Strasbourg1), Centre National de la Recherche Scientifique, 12 Rue du Général Zimmer, 67084 Strasbourg Cedex, France; and
| | - Stefan Nilsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Elzbieta Glaser
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Marlyse Zaepfel
- *Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357, Conventionné avec l'Université Louis Pasteur (Strasbourg1), Centre National de la Recherche Scientifique, 12 Rue du Général Zimmer, 67084 Strasbourg Cedex, France; and
| | - Laurence Maréchal-Drouard
- *Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357, Conventionné avec l'Université Louis Pasteur (Strasbourg1), Centre National de la Recherche Scientifique, 12 Rue du Général Zimmer, 67084 Strasbourg Cedex, France; and
- To whom correspondence should be addressed. E-mail:
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36
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Entelis N, Brandina I, Kamenski P, Krasheninnikov IA, Martin RP, Tarassov I. A glycolytic enzyme, enolase, is recruited as a cofactor of tRNA targeting toward mitochondria in Saccharomyces cerevisiae. Genes Dev 2006; 20:1609-20. [PMID: 16738406 PMCID: PMC1482481 DOI: 10.1101/gad.385706] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Accepted: 04/11/2006] [Indexed: 11/24/2022]
Abstract
In many organisms, mitochondria import nuclear DNA-encoded small RNAs. In yeast Saccharomyces cerevisiae, one out of two cytoplasmic isoacceptor tRNAs(Lys) is partially addressed into the organelle. Mitochondrial targeting of this tRNA was shown to depend on interaction with the precursor of mitochondrial lysyl-tRNA synthetase, preMsk1p. However, preMsk1p alone was unable to direct tRNA targeting, suggesting the existence of additional protein factor(s). Here, we identify the glycolytic enzyme, enolase, as such a factor. We demonstrate that recombinant enolase and preMSK1p are sufficient to direct tRNA import in vitro and that depletion of enolase inhibits tRNA import in vivo. Enzymatic and tRNA targeting functions of enolase appear to be independent. Three newly characterized properties of the enolase can be related to its novel function: (1) specific affinity to the imported tRNA, (2) the ability to facilitate formation of the complex between preMsk1p and the imported tRNA, and (3) partial targeting toward the mitochondrial outer membrane. We propose a model suggesting that the cell exploits mitochondrial targeting of the enolase in order to address the tRNA toward peri-mitochondrially synthesized preMsk1p. Our results indicate an alternative molecular chaperone function of glycolytic enzyme enolase in tRNA mitochondrial targeting.
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Affiliation(s)
- Nina Entelis
- Department of "Molecular and Cellular Genetics," UMR 7156, CNRS-Université Louis Pasteur, Strasbourg 67084, France
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37
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Goswami S, Adhya S. The alpha-subunit of Leishmania F1 ATP synthase hydrolyzes ATP in presence of tRNA. J Biol Chem 2006; 281:18914-7. [PMID: 16735512 DOI: 10.1074/jbc.c600089200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Import of tRNAs into the mitochondria of the kinetoplastid protozoon Leishmania requires the tRNA-dependent hydrolysis of ATP leading to the generation of membrane potential through the pumping of protons. Subunit RIC1 of the inner membrane RNA import complex is a bi-functional protein that is identical to the alpha-subunit of F1F0 ATP synthase and specifically binds to a subset (Type I) of importable tRNAs. We show that recombinant, purified RIC1 is a Type I tRNA-dependent ATP hydrolase. The activity was insensitive to oligomycin, sensitive to mutations within the import signal of the tRNA, and required the cooperative interaction between the ATP-binding and C-terminal domains of RIC1. The ATPase activity of the intact complex was inhibited by anti-RIC1 antibody, while knockdown of RIC1 in Leishmania tropica resulted in deficiency of the tRNA-dependent ATPase activity of the mitochondrial inner membrane. Moreover, RIC1 knockdown extracts failed to generate a membrane potential across reconstituted proteoliposomes, as shown by a rhodamine 123 uptake assay, but activity was restored by adding back purified RIC1. These observations identify RIC1 as a novel form of the F1 ATP synthase alpha-subunit that acts as the major energy transducer for tRNA import.
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Affiliation(s)
- Srikanta Goswami
- Genetic Engineering Laboratory, Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Calcutta 700032, India
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38
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Salinas T, Schaeffer C, Maréchal-Drouard L, Duchêne AM. Sequence dependence of tRNA(Gly) import into tobacco mitochondria. Biochimie 2005; 87:863-72. [PMID: 15927343 DOI: 10.1016/j.biochi.2005.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2004] [Revised: 03/29/2005] [Accepted: 04/01/2005] [Indexed: 11/16/2022]
Abstract
Plant mitochondrial genomes lack a number of tRNA genes and the corresponding tRNAs, which are nuclear-encoded, are imported from the cytosol. We show that specific import of tRNA(Gly) isoacceptors occurs in tobacco mitochondria: tRNA(Gly)(UCC) and tRNA(Gly)(CCC) are cytosolic and mitochondrial, while tRNA(Gly)(GCC) is found only in the cytosol. Exchange of sequences between tRNA(Gly)(UCC) and tRNA(Gly)(GCC) shows that the anticodon and D-domain are essential for tRNA(Gly)(UCC) import. However the reverse mutations in tRNA(Gly)(GCC) are not sufficient to promote its import into tobacco mitochondria.
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Affiliation(s)
- Thalia Salinas
- Institut de Biologie Moléculaire des Plantes, UPR du CNRS no. 2357, Université Louis Pasteur, 12, rue du Général Zimmer, 67000 Strasbourg, France
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39
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Duroc Y, Gaillard C, Hiard S, Defrance MC, Pelletier G, Budar F. Biochemical and functional characterization of ORF138, a mitochondrial protein responsible for Ogura cytoplasmic male sterility in Brassiceae. Biochimie 2005; 87:1089-100. [PMID: 15979231 DOI: 10.1016/j.biochi.2005.05.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Revised: 05/20/2005] [Accepted: 05/20/2005] [Indexed: 11/24/2022]
Abstract
In cytoplasmic male sterility (CMS), original mitochondrial genes contribute to sex determinism by provoking pollen abortion. The function of the encoded proteins remains unclear. We studied the ORF138 protein, responsible for the 'Ogura' CMS, which is both used in hybrid seed production and present in natural populations. We analyzed the biochemical and structural properties of this protein in male-sterile plants and in E. coli. We showed that this protein spontaneously forms dimers in vitro. Truncated variants of the protein, containing either the hydrophobic or the hydrophilic moiety, also spontaneously dimerize. By fractionating mitochondria, we showed that ORF138 was strongly associated with the inner mitochondrial membrane of male-sterile plants. Our results also strongly suggest that ORF138 forms oligomers in male-sterile plant mitochondria. In E. coli, ORF138 was associated with the plasma membrane, as shown by membrane fractionation, and formed oligomers. The production of this protein strongly inhibited bacterial growth, but not by inhibiting respiration. The observed toxic effects required both the hydrophilic and hydrophobic moieties of the protein.
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Affiliation(s)
- Yann Duroc
- Station de Génétique et d'Amélioration des Plantes, Institut Jean-Pierre Bourgin, INRA, Route de Saint-Cyr, 78026 Versailles cedex, France
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40
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Abstract
Despite recent epidemiological studies confirming that mitochondrial respiratory chain disorders due to mutations in either the mitochondrial or nuclear genome are amongst the most common inherited human diseases, realistic therapeutic strategies for these patients remain limited. The disappointing response to various vitamins, cofactors and electron acceptors that have been administered to patients in an attempt to bypass the underlying respiratory chain defect, coupled with the complexities of human mitochondrial genetics, means that novel and innovative means are required to offer realistic treatments. Several 'gene therapy' strategies have therefore been proposed to treat patients with pathogenic mitochondrial DNA mutations, and although these are not without their own inherent problems, several exciting approaches promise much in the near future. This review will provide a basic background to mitochondrial genetics and mitochondrial DNA disorders before introducing the various strategies being tested in vitro at present, in cell culture and animal models, and, in the example of therapeutic exercise, in patients themselves.
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Affiliation(s)
- Robert W Taylor
- University of Newcastle upon Tyne, Mitochondrial Research Group, School of Neurology, Neurobiology and Psychiatry, Newcastle upon Tyne, NE2 4HH, UK.
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Rinehart J, Krett B, Rubio MAT, Alfonzo JD, Söll D. Saccharomyces cerevisiae imports the cytosolic pathway for Gln-tRNA synthesis into the mitochondrion. Genes Dev 2005; 19:583-92. [PMID: 15706032 PMCID: PMC551578 DOI: 10.1101/gad.1269305] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2004] [Accepted: 01/06/2005] [Indexed: 11/25/2022]
Abstract
Aminoacyl-tRNA (aa-tRNA) formation, an essential process in protein biosynthesis, is generally achieved by direct attachment of an amino acid to tRNA by the aa-tRNA synthetases. An exception is Gln-tRNA synthesis, which in eukaryotes is catalyzed by glutaminyl-tRNA synthetase (GlnRS), while most bacteria, archaea, and chloroplasts employ the transamidation pathway, in which a tRNA-dependent glutamate modification generates Gln-tRNA. Mitochondrial protein synthesis is carried out normally by mitochondrial enzymes and organelle-encoded tRNAs that are different from their cytoplasmic counterparts. Early work suggested that mitochondria use the transamidation pathway for Gln-tRNA formation. We found no biochemical support for this in Saccharomyces cerevisiae mitochondria, but demonstrated the presence of the cytoplasmic GlnRS in the organelle and its involvement in mitochondrial Gln-tRNA synthesis. In addition, we showed in vivo localization of cytoplasmic tRNAGln in mitochondria and demonstrated its role in mitochondrial translation. We furthermore reconstituted in vitro cytoplasmic tRNAGln import into mitochondria by a novel mechanism. This tRNA import mechanism expands our knowledge of RNA trafficking in the eukaryotic cell. These findings change our view of the evolution of organellar protein synthesis.
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MESH Headings
- Amino Acyl-tRNA Synthetases/genetics
- Amino Acyl-tRNA Synthetases/metabolism
- Biological Transport, Active/genetics
- Biological Transport, Active/physiology
- Gene Expression Regulation, Fungal/genetics
- Gene Expression Regulation, Fungal/physiology
- Mitochondria/genetics
- Mitochondria/physiology
- Protein Biosynthesis/genetics
- Protein Biosynthesis/physiology
- Protein Transport/genetics
- Protein Transport/physiology
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Gln/genetics
- RNA, Transfer, Gln/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/physiology
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
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Affiliation(s)
- Jesse Rinehart
- Department of Molecular Biophysics and Biochemistry, and Department of Chemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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Kolesnikova OA, Entelis NS, Jacquin-Becker C, Goltzene F, Chrzanowska-Lightowlers ZM, Lightowlers RN, Martin RP, Tarassov I. Nuclear DNA-encoded tRNAs targeted into mitochondria can rescue a mitochondrial DNA mutation associated with the MERRF syndrome in cultured human cells. Hum Mol Genet 2004; 13:2519-34. [PMID: 15317755 DOI: 10.1093/hmg/ddh267] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations are an important cause of human disease for which there is no efficient treatment. Our aim was to determine whether the A8344G mitochondrial tRNA(Lys) mutation, which can cause the MERRF (myoclonic epilepsy with ragged-red fibers) syndrome, could be complemented by targeting tRNAs into mitochondria from the cytosol. Import of small RNAs into mitochondria has been demonstrated in many organisms, including protozoans, plants, fungi and animals. Although human mitochondria do not import tRNAs in vivo, we previously demonstrated that some yeast tRNA derivatives can be imported into isolated human mitochondria. We show here that yeast tRNALys derivatives expressed in immortalized human cells and in primary human fibroblasts are partially imported into mitochondria. Imported tRNAs are correctly aminoacylated and are able to participate in mitochondrial translation. In transmitochondrial cybrid cells and in patient-derived fibroblasts bearing the MERRF mutation, import of tRNALys is accompanied by a partial rescue of mitochondrial functions affected by the mutation such as mitochondrial translation, activity of respiratory complexes, electrochemical potential across the mitochondrial membrane and respiration rate. Import of a tRNALys with a mutation in the anticodon preventing recognition of the lysine codons does not lead to any rescue, whereas downregulation of the transgenic tRNAs by small interfering RNA (siRNA) transiently abolishes the functional rescue, showing that this rescue is due to the import. These findings prove for the first time the functionality of imported tRNAs in human mitochondria in vivo and highlight the potential for exploiting the RNA import pathway to treat patients with mtDNA diseases.
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Affiliation(s)
- Olga A Kolesnikova
- CNRS-FRE 2375, Institute of Physiology and Biological Chemistry, Université Louis Pasteur, 21 René Descartes, 67084 Strasbourg, France
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44
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Goswami S, Chatterjee S, Bhattacharyya SN, Basu S, Adhya S. Allosteric regulation of tRNA import: interactions between tRNA domains at the inner membrane of Leishmania mitochondria. Nucleic Acids Res 2003; 31:5552-9. [PMID: 14500817 PMCID: PMC206471 DOI: 10.1093/nar/gkg773] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Import of nucleus-encoded tRNAs into the mitochondria of the kinetoplastid protozoon Leishmania involves recognition of specific import signals by the membrane-bound import machinery. Multiple signals on different tRNA domains may be present, and further, importable RNAs interact positively (Type I) or negatively (Type II) with one another at the inner membrane in vitro. By co-transfection assays, it is shown here that tRNA(Tyr) (Type I) transiently stimulates the rate of entry of tRNA(Ile) (Type II) into Leishmania mitochondria in transfected cells, and conversely, is inhibited by tRNA(Ile). Truncation and mutagenesis experiments led to the co-localization of the effector and import activities of tRNA(Tyr) to the D domain, and those of tRNA(Ile) to the variable region-T domain (V-T region), indicating that both activities originate from a single RNA-receptor interaction. A third tRNA, human tRNA(Lys), is imported into Leishmania mitochondria in vitro as well as in vivo. This tRNA has Type I and Type II motifs in the D domain and the V-T region, respectively, and shows both Type I and Type II effector activities. Such dual-type tRNAs may interact simultaneously with the Type I and Type II binding sites of the inner membrane import machinery.
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MESH Headings
- Allosteric Regulation
- Animals
- Base Sequence
- Biological Transport
- Humans
- Intracellular Membranes/metabolism
- Leishmania/metabolism
- Mitochondria/metabolism
- Models, Biological
- Molecular Sequence Data
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Lys/metabolism
- RNA, Transfer, Tyr/chemistry
- Transfection
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Affiliation(s)
- Srikanta Goswami
- Genetic Engineering Laboratory, Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Calcutta 700032, India
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