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Yang F, Vincis Pereira Sanglard L, Lee CP, Ströher E, Singh S, Oh GGK, Millar AH, Small I, Colas des Francs-Small C. Mitochondrial atp1 mRNA knockdown by a custom-designed pentatricopeptide repeat protein alters ATP synthase. PLANT PHYSIOLOGY 2024; 194:2631-2647. [PMID: 38206203 PMCID: PMC10980415 DOI: 10.1093/plphys/kiae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024]
Abstract
Spontaneous mutations are rare in mitochondria and the lack of mitochondrial transformation methods has hindered genetic analyses. We show that a custom-designed RNA-binding pentatricopeptide repeat (PPR) protein binds and specifically induces cleavage of ATP synthase subunit1 (atp1) mRNA in mitochondria, significantly decreasing the abundance of the Atp1 protein and the assembled F1Fo ATP synthase in Arabidopsis (Arabidopsis thaliana). The transformed plants are characterized by delayed vegetative growth and reduced fertility. Five-fold depletion of Atp1 level was accompanied by a decrease in abundance of other ATP synthase subunits and lowered ATP synthesis rate of isolated mitochondria, but no change to mitochondrial electron transport chain complexes, adenylates, or energy charge in planta. Transcripts for amino acid transport and a variety of stress response processes were differentially expressed in lines containing the PPR protein, indicating changes to achieve cellular homeostasis when ATP synthase was highly depleted. Leaves of ATP synthase-depleted lines showed higher respiratory rates and elevated steady-state levels of numerous amino acids, most notably of the serine family. The results show the value of using custom-designed PPR proteins to influence the expression of specific mitochondrial transcripts to carry out reverse genetic studies on mitochondrial gene functions and the consequences of ATP synthase depletion on cellular functions in Arabidopsis.
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Affiliation(s)
- Fei Yang
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, P. R. China
| | - Lilian Vincis Pereira Sanglard
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Chun-Pong Lee
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Elke Ströher
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Swati Singh
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Glenda Guec Khim Oh
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - A Harvey Millar
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Catherine Colas des Francs-Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
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2
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Głodowicz P, Kuczyński K, Val R, Dietrich A, Rolle K. Mitochondrial transport of catalytic RNAs and targeting of the organellar transcriptome in human cells. J Mol Cell Biol 2024; 15:mjad051. [PMID: 37591617 PMCID: PMC11148835 DOI: 10.1093/jmcb/mjad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Mutations in the small genome present in mitochondria often result in severe pathologies. Different genetic strategies have been explored, aiming to rescue such mutations. A number of these strategies were based on the capacity of human mitochondria to import RNAs from the cytosol and designed to repress the replication of the mutated genomes or to provide the organelles with wild-type versions of mutant transcripts. However, the mutant RNAs present in mitochondria turned out to be an obstacle to therapy and little attention has been devoted so far to their elimination. Here, we present the development of a strategy to knockdown mitochondrial RNAs in human cells using the transfer RNA-like structure of Brome mosaic virus or Tobacco mosaic virus as a shuttle to drive trans-cleaving ribozymes into the organelles in human cell lines. We obtained a specific knockdown of the targeted mitochondrial ATP6 mRNA, followed by a deep drop in ATP6 protein and a functional impairment of the oxidative phosphorylation chain. Our strategy provides a powerful approach to eliminate mutant organellar transcripts and to analyse the control and communication of the human organellar genetic system.
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Affiliation(s)
- Paweł Głodowicz
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Konrad Kuczyński
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Romain Val
- Institute of Plant Molecular Biology, French National Center for Scientific Research (CNRS) and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - André Dietrich
- Institute of Plant Molecular Biology, French National Center for Scientific Research (CNRS) and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Katarzyna Rolle
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland
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3
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Forner J, Kleinschmidt D, Meyer EH, Fischer A, Morbitzer R, Lahaye T, Schöttler MA, Bock R. Targeted introduction of heritable point mutations into the plant mitochondrial genome. NATURE PLANTS 2022; 8:245-256. [PMID: 35301443 PMCID: PMC8940627 DOI: 10.1038/s41477-022-01108-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/10/2022] [Indexed: 05/05/2023]
Abstract
The development of technologies for the genetic manipulation of mitochondrial genomes remains a major challenge. Here we report a method for the targeted introduction of mutations into plant mitochondrial DNA (mtDNA) that we refer to as transcription activator-like effector nuclease (TALEN) gene-drive mutagenesis (GDM), or TALEN-GDM. The method combines TALEN-induced site-specific cleavage of the mtDNA with selection for mutations that confer resistance to the TALEN cut. Applying TALEN-GDM to the tobacco mitochondrial nad9 gene, we isolated a large set of mutants carrying single amino acid substitutions in the Nad9 protein. The mutants could be purified to homochondriomy and stably inherited their edited mtDNA in the expected maternal fashion. TALEN-GDM induces both transitions and transversions, and can access most nucleotide positions within the TALEN binding site. Our work provides an efficient method for targeted mitochondrial genome editing that produces genetically stable, homochondriomic and fertile plants with specific point mutations in their mtDNA.
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Affiliation(s)
- Joachim Forner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Dennis Kleinschmidt
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Etienne H Meyer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
- Institut für Pflanzenphysiologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Axel Fischer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Robert Morbitzer
- ZMBP, Allgemeine Genetik, Universität Tübingen, Tübingen, Germany
| | - Thomas Lahaye
- ZMBP, Allgemeine Genetik, Universität Tübingen, Tübingen, Germany
| | - Mark A Schöttler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.
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4
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Anand A, Pandi G. Noncoding RNA: An Insight into Chloroplast and Mitochondrial Gene Expressions. Life (Basel) 2021; 11:life11010049. [PMID: 33450961 PMCID: PMC7828403 DOI: 10.3390/life11010049] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 12/22/2022] Open
Abstract
Regulation of gene expression in any biological system is a complex process with many checkpoints at the transcriptional, post-transcriptional and translational levels. The control mechanism is mediated by various protein factors, secondary metabolites and a newly included regulatory member, i.e., noncoding RNAs (ncRNAs). It is known that ncRNAs modulate the mRNA or protein profiles of the cell depending on the degree of complementary and context of the microenvironment. In plants, ncRNAs are essential for growth and development in normal conditions by controlling various gene expressions and have emerged as a key player to guard plants during adverse conditions. In order to have smooth functioning of the plants under any environmental pressure, two very important DNA-harboring semi-autonomous organelles, namely, chloroplasts and mitochondria, are considered as main players. These organelles conduct the most crucial metabolic pathways that are required to maintain cell homeostasis. Thus, it is imperative to explore and envisage the molecular machineries responsible for gene regulation within the organelles and their coordination with nuclear transcripts. Therefore, the present review mainly focuses on ncRNAs origination and their gene regulation in chloroplasts and plant mitochondria.
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Affiliation(s)
- Asha Anand
- Correspondence: (A.A.); (G.P.); Tel.: +91-452-245-8230 (G.P.)
| | - Gopal Pandi
- Correspondence: (A.A.); (G.P.); Tel.: +91-452-245-8230 (G.P.)
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5
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Wang Y, Xu B, Sun R, Xu YJ, Ge JF. The application of nitrogen heterocycles in mitochondrial-targeting fluorescent markers with neutral skeletons. J Mater Chem B 2020; 8:7466-7474. [DOI: 10.1039/d0tb01377c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Neutral fluorescent markers containing nitrogen heterocycles as targeting groups were designed and prepared to screen out structural units for targeting mitochondria.
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Affiliation(s)
- Yue Wang
- College of Chemistry, Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Bing Xu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou 215123
- China
| | - Ru Sun
- College of Chemistry, Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Yu-Jie Xu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou 215123
- China
| | - Jian-Feng Ge
- College of Chemistry, Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
- Jiangsu Key Laboratory of Medical Optics
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6
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Zhang Y, Lu C. The Enigmatic Roles of PPR-SMR Proteins in Plants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900361. [PMID: 31380188 PMCID: PMC6662315 DOI: 10.1002/advs.201900361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/03/2019] [Indexed: 05/21/2023]
Abstract
The pentatricopeptide repeat (PPR) protein family, with more than 400 members, is one of the largest and most diverse protein families in land plants. A small subset of PPR proteins contain a C-terminal small MutS-related (SMR) domain. Although there are relatively few PPR-SMR proteins, they play essential roles in embryo development, chloroplast biogenesis and gene expression, and plastid-to-nucleus retrograde signaling. Here, recent advances in understanding the roles of PPR-SMR proteins and the SMR domain based on a combination of genetic, biochemical, and physiological analyses are described. In addition, the potential of the PPR-SMR protein SOT1 to serve as a tool for RNA manipulation is highlighted.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTaianShandong271018P. R. China
| | - Congming Lu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTaianShandong271018P. R. China
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7
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Kazama T, Okuno M, Watari Y, Yanase S, Koizuka C, Tsuruta Y, Sugaya H, Toyoda A, Itoh T, Tsutsumi N, Toriyama K, Koizuka N, Arimura SI. Curing cytoplasmic male sterility via TALEN-mediated mitochondrial genome editing. NATURE PLANTS 2019; 5:722-730. [PMID: 31285556 DOI: 10.1038/s41477-019-0459-z] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 05/23/2019] [Indexed: 05/22/2023]
Abstract
Sequence-specific nucleases are commonly used to modify the nuclear genome of plants. However, targeted modification of the mitochondrial genome of land plants has not yet been achieved. In plants, a type of male sterility called cytoplasmic male sterility (CMS) has been attributed to certain mitochondrial genes, but none of these genes has been validated by direct mitochondrial gene-targeted modification. Here, we knocked out CMS-associated genes (orf79 and orf125) of CMS varieties of rice and rapeseed, respectively, using transcription activator-like effector nucleases (TALENs) with mitochondria localization signals (mitoTALENs). We demonstrate that knocking out these genes cures male sterility, strongly suggesting that these genes are causes of CMS. Sequencing revealed that double-strand breaks induced by mitoTALENs were repaired by homologous recombination, and that during this process, the target genes and surrounding sequences were deleted. Our results show that mitoTALENs can be used to stably and heritably modify the mitochondrial genome in plants.
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Affiliation(s)
- Tomohiko Kazama
- Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.
| | - Miki Okuno
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Yuta Watari
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shungo Yanase
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Chie Koizuka
- College of Agriculture, Tamagawa University, Tokyo, Japan
| | - Yu Tsuruta
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hajime Sugaya
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Nobuhiro Tsutsumi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kinya Toriyama
- Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Nobuya Koizuka
- College of Agriculture, Tamagawa University, Tokyo, Japan.
| | - Shin-Ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
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8
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Niazi AK, Delannoy E, Iqbal RK, Mileshina D, Val R, Gabryelska M, Wyszko E, Soubigou-Taconnat L, Szymanski M, Barciszewski J, Weber-Lotfi F, Gualberto JM, Dietrich A. Mitochondrial Transcriptome Control and Intercompartment Cross-Talk During Plant Development. Cells 2019; 8:E583. [PMID: 31200566 PMCID: PMC6627697 DOI: 10.3390/cells8060583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 01/17/2023] Open
Abstract
We address here organellar genetic regulation and intercompartment genome coordination. We developed earlier a strategy relying on a tRNA-like shuttle to mediate import of nuclear transgene-encoded custom RNAs into mitochondria in plants. In the present work, we used this strategy to drive trans-cleaving hammerhead ribozymes into the organelles, to knock down specific mitochondrial RNAs and analyze the regulatory impact. In a similar approach, the tRNA mimic was used to import into mitochondria in Arabidopsis thaliana the orf77, an RNA associated with cytoplasmic male sterility in maize and possessing sequence identities with the atp9 mitochondrial RNA. In both cases, inducible expression of the transgenes allowed to characterise early regulation and signaling responses triggered by these respective manipulations of the organellar transcriptome. The results imply that the mitochondrial transcriptome is tightly controlled by a "buffering" mechanism at the early and intermediate stages of plant development, a control that is released at later stages. On the other hand, high throughput analyses showed that knocking down a specific mitochondrial mRNA triggered a retrograde signaling and an anterograde nuclear transcriptome response involving a series of transcription factor genes and small RNAs. Our results strongly support transcriptome coordination mechanisms within the organelles and between the organelles and the nucleus.
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Affiliation(s)
- Adnan Khan Niazi
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, Pakistan.
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France.
| | - Rana Khalid Iqbal
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Daria Mileshina
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Romain Val
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Marta Gabryelska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Eliza Wyszko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France.
| | - Maciej Szymanski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, A. Mickiewicz University Poznan, Ul. Umultowska 89, 61-614 Poznan, Poland.
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
- NanoBioMedical Centre of the Adam Mickiewicz University, Umultowska 85, 61614 Poznan, Poland.
| | - Frédérique Weber-Lotfi
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - José Manuel Gualberto
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - André Dietrich
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
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9
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Sultan LD, Mileshina D, Grewe F, Rolle K, Abudraham S, Głodowicz P, Niazi AK, Keren I, Shevtsov S, Klipcan L, Barciszewski J, Mower JP, Dietrich A, Ostersetzer-Biran O. The Reverse Transcriptase/RNA Maturase Protein MatR Is Required for the Splicing of Various Group II Introns in Brassicaceae Mitochondria. THE PLANT CELL 2016; 28:2805-2829. [PMID: 27760804 PMCID: PMC5155343 DOI: 10.1105/tpc.16.00398] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/26/2016] [Accepted: 10/19/2016] [Indexed: 05/18/2023]
Abstract
Group II introns are large catalytic RNAs that are ancestrally related to nuclear spliceosomal introns. Sequences corresponding to group II RNAs are found in many prokaryotes and are particularly prevalent within plants organellar genomes. Proteins encoded within the introns themselves (maturases) facilitate the splicing of their own host pre-RNAs. Mitochondrial introns in plants have diverged considerably in sequence and have lost their maturases. In angiosperms, only a single maturase has been retained in the mitochondrial DNA: the matR gene found within NADH dehydrogenase 1 (nad1) intron 4. Its conservation across land plants and RNA editing events, which restore conserved amino acids, indicates that matR encodes a functional protein. However, the biological role of MatR remains unclear. Here, we performed an in vivo investigation of the roles of MatR in Brassicaceae. Directed knockdown of matR expression via synthetically designed ribozymes altered the processing of various introns, including nad1 i4. Pull-down experiments further indicated that MatR is associated with nad1 i4 and several other intron-containing pre-mRNAs. MatR may thus represent an intermediate link in the gradual evolutionary transition from the intron-specific maturases in bacteria into their versatile spliceosomal descendants in the nucleus. The similarity between maturases and the core spliceosomal Prp8 protein further supports this intriguing theory.
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Affiliation(s)
- Laure D Sultan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Daria Mileshina
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 67084 Strasbourg, France
| | - Felix Grewe
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
| | - Katarzyna Rolle
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Sivan Abudraham
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Paweł Głodowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Adnan Khan Niazi
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 67084 Strasbourg, France
| | - Ido Keren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Sofia Shevtsov
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Liron Klipcan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
| | - André Dietrich
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 67084 Strasbourg, France
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
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10
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Dietrich A, Wallet C, Iqbal RK, Gualberto JM, Lotfi F. Organellar non-coding RNAs: Emerging regulation mechanisms. Biochimie 2015; 117:48-62. [DOI: 10.1016/j.biochi.2015.06.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/29/2015] [Indexed: 02/06/2023]
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11
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Mileshina D, Niazi AK, Wyszko E, Szymanski M, Val R, Valentin C, Barciszewski J, Dietrich A. Mitochondrial targeting of catalytic RNAs. Methods Mol Biol 2015; 1265:227-54. [PMID: 25634279 DOI: 10.1007/978-1-4939-2288-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Genetic transformation of mitochondria in multicellular eukaryotes has remained inaccessible, hindering fundamental investigations and applications to gene therapy or biotechnology. In this context, we have developed a strategy to target nuclear transgene-encoded RNAs into mitochondria in plants. We describe here mitochondrial targeting of trans-cleaving ribozymes destined to knockdown organelle RNAs for regulation studies and inverse genetics and biotechnological purposes. The design and functional assessment of chimeric RNAs combining the ribozyme and the mitochondrial shuttle are detailed, followed by all procedures to prepare constructs for in vivo expression, generate stable plant transformants, and establish target RNA knockdown in mitochondria.
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Affiliation(s)
- Daria Mileshina
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, France
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12
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Differential targeting of VDAC3 mRNA isoforms influences mitochondria morphology. Proc Natl Acad Sci U S A 2014; 111:8991-6. [PMID: 24889622 DOI: 10.1073/pnas.1402588111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Intracellular targeting of mRNAs has recently emerged as a prevalent mechanism to control protein localization. For mitochondria, a cotranslational model of protein import is now proposed in parallel to the conventional posttranslational model, and mitochondrial targeting of mRNAs has been demonstrated in various organisms. Voltage-dependent anion channels (VDACs) are the most abundant proteins in the outer mitochondrial membrane and the major transport pathway for numerous metabolites. Four nucleus-encoded VDACs have been identified in Arabidopsis thaliana. Alternative cleavage and polyadenylation generate two VDAC3 mRNA isoforms differing by their 3' UTR. By using quantitative RT-PCR and in vivo mRNA visualization approaches, the two mRNA variants were shown differentially associated with mitochondria. The longest mRNA presents a 3' extension named alternative UTR (aUTR) that is necessary and sufficient to target VDAC3 mRNA to the mitochondrial surface. Moreover, aUTR is sufficient for the mitochondrial targeting of a reporter transcript, and can be used as a tool to target an unrelated mRNA to the mitochondrial surface. Finally, VDAC3-aUTR mRNA variant impacts mitochondria morphology and size, demonstrating the role of mRNA targeting in mitochondria biogenesis.
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13
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Kazama T, Yagi Y, Toriyama K, Nakamura T. Heterogeneity of the 5'-end in plant mRNA may be involved in mitochondrial translation. FRONTIERS IN PLANT SCIENCE 2013; 4:517. [PMID: 24381580 PMCID: PMC3865367 DOI: 10.3389/fpls.2013.00517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 12/02/2013] [Indexed: 05/04/2023]
Affiliation(s)
- Tomohiko Kazama
- Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku UniversitySendai, Japan
| | - Yusuke Yagi
- Faculty of Agriculture, Kyushu UniversityFukuoka, Japan
| | - Kinya Toriyama
- Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku UniversitySendai, Japan
| | - Takahiro Nakamura
- Faculty of Agriculture, Kyushu UniversityFukuoka, Japan
- *Correspondence:
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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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Abstract
Mutations in the human mitochondrial genome are implicated in neuromuscular diseases, metabolic defects, and aging. An efficient and simple mechanism for neutralizing deleterious mitochondrial DNA (mtDNA) alterations has unfortunately remained elusive. Here, we report that a 20-ribonucleotide stem-loop sequence from the H1 RNA, the RNA component of the human RNase P enzyme, appended to a nonimported RNA directs the import of the resultant RNA fusion transcript into human mitochondria. The methodology is effective for both noncoding RNAs, such as tRNAs, and mRNAs. The RNA import component, polynucleotide phosphorylase (PNPASE), facilitates transfer of this hybrid RNA into the mitochondrial matrix. In addition, nucleus-encoded mRNAs for mitochondrial proteins, such as the mRNA of human mitochondrial ribosomal protein S12 (MRPS12), contain regulatory sequences in their 3'-untranslated region (UTR) that confers localization to the mitochondrial outer membrane, which is postulated to aid in protein translocation after translation. We show that for some mitochondrial-encoded transcripts, such as COX2, a 3'-UTR localization sequence is not required for mRNA import, whereas for corrective mitochondrial-encoded tRNAs, appending the 3'-UTR localization sequence was essential for efficient fusion-transcript translocation into mitochondria. In vivo, functional defects in mitochondrial RNA (mtRNA) translation and cell respiration were reversed in two human disease lines. Thus, this study indicates that a wide range of RNAs can be targeted to mitochondria by appending a targeting sequence that interacts with PNPASE, with or without a mitochondrial localization sequence, providing an exciting, general approach for overcoming mitochondrial genetic disorders.
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