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Placido A, Sieber F, Gobert A, Gallerani R, Giegé P, Maréchal-Drouard L. Plant mitochondria use two pathways for the biogenesis of tRNA His. Nucleic Acids Res 2020; 48:8810-8811. [PMID: 32735659 PMCID: PMC7470966 DOI: 10.1093/nar/gkaa650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Antonio Placido
- Dipartimento di Biochimica e Biologia Molecolare ‘Ernesto Quagliariello’, Universita’ degli Studi di Bari ‘Aldo Moro’, Via Orabona 4, 70126 Bari, Italy
| | - François Sieber
- Institut de Biologie Moléculaire des Plantes, UPR 2357-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France
| | - Anthony Gobert
- Institut de Biologie Moléculaire des Plantes, UPR 2357-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France
| | - Raffaele Gallerani
- Dipartimento di Biochimica e Biologia Molecolare ‘Ernesto Quagliariello’, Universita’ degli Studi di Bari ‘Aldo Moro’, Via Orabona 4, 70126 Bari, Italy
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes, UPR 2357-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France
| | - Laurence Maréchal-Drouard
- 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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Doublet V, Ubrig E, Alioua A, Bouchon D, Marcadé I, Maréchal-Drouard L. Large gene overlaps and tRNA processing in the compact mitochondrial genome of the crustacean Armadillidium vulgare. RNA Biol 2015; 12:1159-68. [PMID: 26361137 DOI: 10.1080/15476286.2015.1090078] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
A faithful expression of the mitochondrial DNA is crucial for cell survival. Animal mitochondrial DNA (mtDNA) presents a highly compact gene organization. The typical 16.5 kbp animal mtDNA encodes 13 proteins, 2 rRNAs and 22 tRNAs. In the backyard pillbug Armadillidium vulgare, the rather small 13.9 kbp mtDNA encodes the same set of proteins and rRNAs as compared to animal kingdom mtDNA, but seems to harbor an incomplete set of tRNA genes. Here, we first confirm the expression of 13 tRNA genes in this mtDNA. Then we show the extensive repair of a truncated tRNA, the expression of tRNA involved in large gene overlaps and of tRNA genes partially or fully integrated within protein-coding genes in either direct or opposite orientation. Under selective pressure, overlaps between genes have been likely favored for strong genome size reduction. Our study underlines the existence of unknown biochemical mechanisms for the complete gene expression of A. vulgare mtDNA, and of co-evolutionary processes to keep overlapping genes functional in a compacted mitochondrial genome.
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Affiliation(s)
- Vincent Doublet
- a Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions , UMR CNRS 7267, Poitiers , France
| | - Elodie Ubrig
- b Institut de biologie moléculaire des plantes; associated with the University of Strasbourg , Strasbourg , France
| | - Abdelmalek Alioua
- b Institut de biologie moléculaire des plantes; associated with the University of Strasbourg , Strasbourg , France
| | - Didier Bouchon
- a Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions , UMR CNRS 7267, Poitiers , France
| | - Isabelle Marcadé
- a Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions , UMR CNRS 7267, Poitiers , France
| | - Laurence Maréchal-Drouard
- b Institut de biologie moléculaire des plantes; associated with the University of Strasbourg , Strasbourg , France
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Rao BS, Jackman JE. Life without post-transcriptional addition of G-1: two alternatives for tRNAHis identity in Eukarya. RNA (NEW YORK, N.Y.) 2015; 21:243-53. [PMID: 25505023 PMCID: PMC4338351 DOI: 10.1261/rna.048389.114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/06/2014] [Indexed: 05/23/2023]
Abstract
The identity of tRNA(His) is strongly associated with the presence of an additional 5'-guanosine residue (G-1) in all three domains of life. The critical nature of the G-1 residue is underscored by the fact that two entirely distinct mechanisms for its acquisition are observed, with cotranscriptional incorporation observed in Bacteria, while post-transcriptional addition of G-1 occurs in Eukarya. Here, through our investigation of eukaryotes that lack obvious homologs of the post-transcriptional G-1-addition enzyme Thg1, we identify alternative pathways to tRNA(His) identity that controvert these well-established rules. We demonstrate that Trypanosoma brucei, like Acanthamoeba castellanii, lacks the G-1 identity element on tRNA(His) and utilizes a noncanonical G-1-independent histidyl-tRNA synthetase (HisRS). Purified HisRS enzymes from A. castellanii and T. brucei exhibit a mechanism of tRNA(His) recognition that is distinct from canonical G-1-dependent synthetases. Moreover, noncanonical HisRS enzymes genetically complement the loss of THG1 in Saccharomyces cerevisiae, demonstrating the biological relevance of the G-1-independent aminoacylation activity. In contrast, in Caenorhabditis elegans, which is another Thg1-independent eukaryote, the G-1 residue is maintained, but here its acquisition is noncanonical. In this case, the G-1 is encoded and apparently retained after 5' end processing, which has so far only been observed in Bacteria and organelles. Collectively, these observations unearth a widespread and previously unappreciated diversity in eukaryotic tRNA(His) identity mechanisms.
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Affiliation(s)
- Bhalchandra S Rao
- Molecular, Cellular and Developmental Biology Program, Center for RNA Biology and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jane E Jackman
- Molecular, Cellular and Developmental Biology Program, Center for RNA Biology and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Salinas T, El Farouk-Ameqrane S, Ubrig E, Sauter C, Duchêne AM, Maréchal-Drouard L. Molecular basis for the differential interaction of plant mitochondrial VDAC proteins with tRNAs. Nucleic Acids Res 2014; 42:9937-48. [PMID: 25114051 PMCID: PMC4150812 DOI: 10.1093/nar/gku728] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In plants, the voltage-dependent anion-selective channel (VDAC) is a major component of a pathway involved in transfer RNA (tRNA) translocation through the mitochondrial outer membrane. However, the way in which VDAC proteins interact with tRNAs is still unknown. Potato mitochondria contain two major mitochondrial VDAC proteins, VDAC34 and VDAC36. These two proteins, composed of a N-terminal α-helix and of 19 β-strands forming a β-barrel structure, share 75% sequence identity. Here, using both northwestern and gel shift experiments, we report that these two proteins interact differentially with nucleic acids. VDAC34 binds more efficiently with tRNAs or other nucleic acids than VDAC36. To further identify specific features and critical amino acids required for tRNA binding, 21 VDAC34 mutants were constructed and analyzed by northwestern. This allowed us to show that the β-barrel structure of VDAC34 and the first 50 amino acids that contain the α-helix are essential for RNA binding. Altogether the work shows that during evolution, plant mitochondrial VDAC proteins have diverged so as to interact differentially with nucleic acids, and this may reflect their involvement in various specialized biological functions.
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Affiliation(s)
- Thalia Salinas
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Samira El Farouk-Ameqrane
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Elodie Ubrig
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Claude Sauter
- Institut de Biologie Moléculaire et Cellulaire, UPR 9002 CNRS, associated with Strasbourg University, 15 rue René Descartes 67084 Strasbourg cedex, France
| | - Anne-Marie Duchêne
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Laurence Maréchal-Drouard
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
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Niazi AK, Mileshina D, Cosset A, Val R, Weber-Lotfi F, Dietrich A. Targeting nucleic acids into mitochondria: progress and prospects. Mitochondrion 2012; 13:548-58. [PMID: 22609422 DOI: 10.1016/j.mito.2012.05.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 05/14/2012] [Indexed: 12/18/2022]
Abstract
Given the essential functions of these organelles in cell homeostasis, their involvement in incurable diseases and their potential in biotechnological applications, genetic transformation of mitochondria has been a long pursued goal that has only been reached in a couple of unicellular organisms. The challenge led scientists to explore a wealth of different strategies for mitochondrial delivery of DNA or RNA in living cells. These are the subject of the present review. Targeting DNA into the organelles currently shows promise but remarkably a number of alternative approaches based on RNA trafficking were also established and will bring as well major contributions.
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Affiliation(s)
- Adnan Khan Niazi
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
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Ibrahim N, Handa H, Cosset A, Koulintchenko M, Konstantinov Y, Lightowlers RN, Dietrich A, Weber-Lotfi F. DNA delivery to mitochondria: sequence specificity and energy enhancement. Pharm Res 2011; 28:2871-82. [PMID: 21748538 DOI: 10.1007/s11095-011-0516-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 06/15/2011] [Indexed: 12/15/2022]
Abstract
PURPOSE Mitochondria are competent for DNA uptake in vitro, a mechanism which may support delivery of therapeutic DNA to complement organelle DNA mutations. We document here key aspects of the DNA import process, so as to further lay the ground for mitochondrial transfection in intact cells. METHODS We developed DNA import assays with isolated mitochondria from different organisms, using DNA substrates of various sequences and sizes. Further import experiments investigated the possible role of ATP and protein phosphorylation in the uptake process. The fate of adenine nucleotides and the formation of phosphorylated proteins were analyzed. RESULTS We demonstrate that the efficiency of mitochondrial uptake depends on the sequence of the DNA to be translocated. The process becomes sequence-selective for large DNA substrates. Assays run with a natural mitochondrial plasmid identified sequence elements which promote organellar uptake. ATP enhances DNA import and allows tight integration of the exogenous DNA into mitochondrial nucleoids. ATP hydrolysis has to occur during the DNA uptake process and might trigger phosphorylation of co-factors. CONCLUSIONS Our data contribute critical information to optimize DNA delivery into mitochondria and open the prospect of targeting whole mitochondrial genomes or complex constructs into mammalian organelles in vitro and in vivo.
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Affiliation(s)
- Noha Ibrahim
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
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Mileshina D, Koulintchenko M, Konstantinov Y, Dietrich A. Transfection of plant mitochondria and in organello gene integration. Nucleic Acids Res 2011; 39:e115. [PMID: 21715377 PMCID: PMC3177224 DOI: 10.1093/nar/gkr517] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Investigation and manipulation of mitochondrial genetics in animal and plant cells remains restricted by the lack of an efficient in vivo transformation methodology. Mitochondrial transfection in whole cells and maintenance of the transfected DNA are main issues on this track. We showed earlier that isolated mitochondria from different organisms can import DNA. Exploiting this mechanism, we assessed the possibility to maintain exogenous DNA in plant organelles. Whereas homologous recombination is scarce in the higher plant nuclear compartment, recombination between large repeats generates the multipartite structure of the plant mitochondrial genome. These processes are under strict surveillance to avoid extensive genomic rearrangements. Nevertheless, following transfection of isolated organelles with constructs composed of a partial gfp gene flanked by fragments of mitochondrial DNA, we demonstrated in organello homologous recombination of the imported DNA with the resident DNA and integration of the reporter gene. Recombination yielded insertion of a continuous exogenous DNA fragment including the gfp sequence and at least 0.5 kb of flanking sequence on each side. According to our observations, transfection constructs carrying multiple sequences homologous to the mitochondrial DNA should be suitable and targeting of most regions in the organelle genome should be feasible, making the approach of general interest.
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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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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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Michaud M, Maréchal-Drouard L, Duchêne AM. RNA trafficking in plant cells: targeting of cytosolic mRNAs to the mitochondrial surface. PLANT MOLECULAR BIOLOGY 2010; 73:697-704. [PMID: 20506035 DOI: 10.1007/s11103-010-9650-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 05/07/2010] [Indexed: 05/06/2023]
Abstract
Subcellular localization of mRNA is a widespread and efficient way for targeting proteins to specific regions of a cell. Messenger RNA sorting appears as a key mechanism for posttranscriptional gene regulation, and its involvement in organelle biogenesis has been described in different organisms. Here we demonstrate that mRNA targeting to the surface of mitochondria occurs in higher plants. Cytosolic mRNAs corresponding to mitochondrial proteins, but also to some particular cytosolic proteins, were found associated to mitochondria, offering new perspectives for mitochondria biogenesis in plant cells.
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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
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Placido A, Sieber F, Gobert A, Gallerani R, Giegé P, Maréchal-Drouard L. Plant mitochondria use two pathways for the biogenesis of tRNAHis. Nucleic Acids Res 2010; 38:7711-7. [PMID: 20660484 PMCID: PMC2995067 DOI: 10.1093/nar/gkq646] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
All tRNAHis possess an essential extra G–1 guanosine residue at their 5′ end. In eukaryotes after standard processing by RNase P, G–1 is added by a tRNAHis guanylyl transferase. In prokaryotes, G–1 is genome-encoded and retained during maturation. In plant mitochondria, although trnH genes possess a G–1 we find here that both maturation pathways can be used. Indeed, tRNAHis with or without a G–1 are found in a plant mitochondrial tRNA fraction. Furthermore, a recombinant Arabidopsis mitochondrial RNase P can cleave tRNAHis precursors at both positions G+1 and G–1. The G–1 is essential for recognition by plant mitochondrial histidyl-tRNA synthetase. Whether, as shown in prokaryotes and eukaryotes, the presence of uncharged tRNAHis without G–1 has a function or not in plant mitochondrial gene regulation is an open question. We find that when a mutated version of a plant mitochondrial trnH gene containing no encoded extra G is introduced and expressed into isolated potato mitochondria, mature tRNAHis with a G–1 are recovered. This shows that a previously unreported tRNAHis guanylyltransferase activity is present in plant mitochondria.
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Affiliation(s)
- Antonio Placido
- Dipartimento di Biochimica e Biologia Molecolare Ernesto Quagliariello, Universita' degli Studi di Bari Aldo Moro, Via Orabona 4, 70126 Bari, Italy
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Placido A, Regina TM, Quagliariello C, Volpicella M, Gallerani R, Ceci LR. Mapping of 5′ and 3′-ends of sunflower mitochondrial nad6 mRNAs reveals a very complex transcription pattern which includes primary transcripts lacking 5′-UTR. Biochimie 2009; 91:924-32. [DOI: 10.1016/j.biochi.2009.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2008] [Accepted: 04/15/2009] [Indexed: 11/29/2022]
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Holec S, Lange H, Dietrich A, Gagliardi D. Polyadenylation-mediated RNA degradation in plant mitochondria. Methods Enzymol 2009; 447:439-61. [PMID: 19161855 DOI: 10.1016/s0076-6879(08)02221-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
In plant mitochondria, polyadenylation-mediated RNA degradation is involved in several key aspects of genome expression, including RNA maturation, RNA turnover, and RNA surveillance. We describe here a combination of in vivo, in vitro, and in organello methods that have been developed or optimized to characterize this RNA degradation pathway. These approaches include several PCR-based methods designed to identify polyadenylated RNA substrates, as well as in vitro and in organello systems, to study functional aspects of the RNA degradation processes. Taken together, identification of RNA substrates combined with information from degradation assays are invaluable tools to dissect the mechanisms and roles of RNA degradation in plant mitochondrial genome expression.
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Affiliation(s)
- Sarah Holec
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Conventionné avec l'Université Louis Pasteur, Strasbourg, France
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Choury D, Araya A. RNA editing site recognition in heterologous plant mitochondria. Curr Genet 2006; 50:405-16. [PMID: 17033819 DOI: 10.1007/s00294-006-0100-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Revised: 09/06/2006] [Accepted: 09/07/2006] [Indexed: 10/24/2022]
Abstract
RNA editing is a process that modifies the information content of mitochondrial messenger RNAs in flowering plants changing specific cytosine residues into uridine. To gain insight into editing site recognition, we used electroporation to introduce engineered wheat (Triticum aestivum) or potato (Solanum tuberosum) mitochondrial cox2 genes, and an atp9-containing chimeric gene, into non-cognate mitochondria, and observed the efficiency of editing in these contexts. Both wheat and potato mitochondria were able to express "foreign" constructs, and their products were properly spliced. Seventeen and twelve editing sites are present in the coding regions of wheat and potato cox2 transcripts, respectively. Eight are common to both plants, whereas nine are specific to wheat, and four to potato. An analogous situation is found for the atp9 mRNA coding regions from these species. We found that both mitochondria were able to recognize sites that are already present as T at the genomic level, making RNA editing unnecessary for that specific residue in the cognate organelle. Our results demonstrate that non-cognate mitochondria are able to edit residues that are not edited in their own transcripts, and support the hypothesis that the same trans-acting factor may recognize several editing sites.
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Affiliation(s)
- David Choury
- Laboratoire de Réplication et Expression des Génomes Eucaryotes et Rétroviraux, UMR 5097, Centre National de la Recherche Scientifique and Université Victor, Segalen Bordeaux II, 146, Bordeaux Cedex, France
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16
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Placido A, Damiano F, Sciancalepore M, De Benedetto C, Rainaldi G, Gallerani R. Comparison of promoters controlling on the sunflower mitochondrial genome the transcription of two copies of the same native trnK gene reveals some differences in their structure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:1207-16. [PMID: 16820139 DOI: 10.1016/j.bbabio.2006.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Revised: 04/18/2006] [Accepted: 05/09/2006] [Indexed: 10/24/2022]
Abstract
Two copies of native trnK (UUU) gene are encoded on the sunflower mitochondrial DNA. They lie within two 12-kb direct repeats, presumably generated by a duplication event. During an investigation aimed at detecting DNA regions activating the trnK1 and trnK2 genes, three distinct promoters have been identified. Their locations were deduced using standard procedures (RT-PCR, RNA capping and 5'RACE) usually employed for the detection of transcription initiation sites (TISs). Promoters P3 and P2 control two independent partially overlapping transcription units containing the trnK2 and ccb206 genes, respectively. Promoter P1 has been mapped about 5200 bp upstream of the trnK1 gene which is part of a transcription unit also containing exons c, d and e of the nad2 gene, 5' to the tRNA gene. Most probably this promoter is not alone in controlling this transcription unit because this DNA region could be cotranscribed, at least partially, starting from other two promoters located upstream of the trnC and trnN genes, respectively. These genes have been previously mapped in a 5' region adjacent to the cluster containing nad2 exons c, d and e and the trnK1 gene. The comparative analysis of promoters P3 and P1 suggests that the difference between them could be related to the duplication event generating the second copy of trnK gene. The availability of a high number of new promoters belonging to dicot mitochondrial genomes makes possible to note some of their specific features.
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Affiliation(s)
- Antonio Placido
- Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, via Orabona 4, 70126 Bari, Italy
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Koulintchenko M, Temperley RJ, Mason PA, Dietrich A, Lightowlers RN. Natural competence of mammalian mitochondria allows the molecular investigation of mitochondrial gene expression. Hum Mol Genet 2005; 15:143-54. [PMID: 16321989 DOI: 10.1093/hmg/ddi435] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Respiration, a fundamental process in mammalian cells, requires two genomes, those of the nucleus and the mitochondrion (mtDNA). Mutations of mtDNA are being increasingly recognized in disease and may play an important role in the ageing process. Accepting the vital role of mtDNA gene products, our limited knowledge concerning the details of mitochondrial gene expression is surprising. This is, in part, due to our inability to transfect mitochondria and to manipulate their genome. There have been claims of successful DNA import into isolated organelles, but most reports lacked evidence of expression and no method has furthered our understanding of gene expression. Here, we report that mammalian mitochondria possess a natural competence for DNA import. Using five functional assays, we show imported DNA can act as templates for DNA synthesis or promoter-driven transcription, with the resultant polycistronic RNA being processed (5' and 3') and excised mt-tRNA matured. Exploiting this natural competence will allow us to explore mitochondrial gene expression in organello and provides the potential for mitochondrial transfection in vivo.
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Affiliation(s)
- Milana Koulintchenko
- Mitochondrial Research Group, Institutes of Neuroscience, University of Newcastle upon Tyne, UK
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